JasonLStein jason_stein@med.unc.edu Stein lab Genetics UNC Chapel Hill

Neuroscience Research Building 8109C, 115 Mason Farm Rd Chapel Hill NC 27599-7250 USA

Illumina Inc. expression@illumina.com, techsupport@illumina.com 1 800 809 4566 Illumina Inc.

9885 Towne Centre Drive San Diego CA 92121 USA

www.illumina.com Luisde la Torre-Ubieta YuanTian NeelroopNParikshak IsraelAHernandez MariaCMarchetto DylanKBaker DaningLu CassidyRHinman JenniferKLowe EricMWexler AlyssonRMuotri FredHGage KennethSKosik DanielHGeschwind Gene Expression Omnibus (GEO) GEO NCBI NLM NIH http://www.ncbi.nlm.nih.gov/geo geo@ncbi.nlm.nih.gov 2010-06-17 2010-06-17 2018-08-13 GPL10558 oligonucleotide beads commercial Homo sapiens Illumina Inc. see manufacturer's website The HumanHT-12 v4 Expression BeadChip provides high throughput processing of 12 samples per BeadChip without the need for expensive, specialized automation. The BeadChip is designed to support flexible usage across a wide-spectrum of experiments. The updated content on the HumanHT-12 v4 Expression BeadChips provides more biologically meaningful results through genome-wide transcriptional coverage of well-characterized genes, gene candidates, and splice variants. Each array on the HumanHT-12 v4 Expression BeadChip targets more than 31,000 annotated genes with more than 47,000 probes derived from the National Center for Biotechnology Information Reference Sequence (NCBI) RefSeq Release 38 (November 7, 2009) and other sources. Please use the GEO Data Submission Report Plug-in v1.0 for Gene Expression which may be downloaded from https://icom.illumina.com/icom/software.ilmn?id=234 to format the normalized and raw data. These should be submitted as part of a GEOarchive. Instructions for assembling a GEOarchive may be found at http://www.ncbi.nlm.nih.gov/projects/geo/info/spreadsheet.html October 11, 2012: annotation table updated with HumanHT-12_V4_0_R2_15002873_B.txt ftp://ftp.ncbi.nlm.nih.gov/geo/platforms/GPL10nnn/GPL10558/suppl/GPL10558_HumanHT-12_V4_0_R1_15002873_B.txt.gz ftp://ftp.ncbi.nlm.nih.gov/geo/platforms/GPL10nnn/GPL10558/suppl/GPL10558_HumanHT-12_V4_0_R2_15002873_B.txt.gz ID Unique identifier for the probe (across all products and species) Species Source Transcript sequence source name Search_Key Internal id useful for custom design array Transcript Internal transcript id ILMN_Gene Internal gene symbol Source_Reference_ID Id in the source database RefSeq_ID Refseq id Unigene_ID Unigene id Entrez_Gene_ID Entrez gene id GI Genbank id Accession Genbank accession number Symbol Gene symbol from the source database Protein_Product Genbank protein accession number Probe_Id Array_Address_Id Decoder id Probe_Type Information about what this probe is targeting Probe_Start Position of the probe relative to the 5' of the source transcript sequence SEQUENCE Probe sequence Chromosome Chromosome Probe_Chr_Orientation Orientation on the NCBI genome built Probe_Coordinates genomic position of the probe on the NCBI genome build 36 version 3 Cytoband Definition Gene description from the source Ontology_Component Cellular component annotations from Gene Ontology project Ontology_Process Biological process annotations from Gene Ontology project Ontology_Function Molecular function annotations from Gene Ontology project Synonyms Gene symbol synonyms from Refseq Obsolete_Probe_Id Identifier of probe id before bgx time GB_ACC GPL10558-tbl-1.txt 2014-05-12 2014-06-01 2014-06-01 GSM1385237 RNA 1 Human fetal tissue Homo sapiens 6 21 phNPC from Geschwind Lab 1 5 9.9 18 MEX M 1 phNPC: Neurobasal A (Invitrogen) supplemented with B27 (Gibco), GlutaMAX (Gibco), and Antibiotics and Antimycotics (Gibco)] as well as Retinoic Acid (500 ng/mL; Sigma), Forskolin (100 μM; Sigma), BDNF (10 ng/mL; Peprotech), NT-3 (10 ng/mL; Peprotech), and KCl (10mM); iPSC Kosik Lab: neurobasal media supplemented with N2, B27 and neurotrophic factor cocktail that included NT3, BDNF, and GDNF; iPSC Gage Lab: DMEM/F12, N2, BDNF/GDNF, and laminin. phNPC: Neurobasal A (Invitrogen) supplemented with 10% BIT (Stem Cell Technologies), Antibiotics and Antimycotics (Gibco), GlutaMAX (Gibco), and Heparin (1 μg/mL; Sigma)] with freshly added EGF, FGF2, PDGF (each at 20 ng/mL; Peprotech), and LIF (2 ng/mL; Millipore); iPSC Kosik Lab: N2 induction media with bFGF; iPSC Gage Lab: DMEM/F12; 1X N2; 1X B27 and FGF2 total RNA phNPCs: RNA was isolated using TRIzol reagent (Invitrogen) according to standard protocols; iPSC Kosik Lab: RNA was extracted using miRVANA kit, following the manufacturer’s protocol for total RNA; iPSC Gage Lab: Total cellular RNA was extracted using the RNeasy Protect Mini kit (QIAGEN, Valencia, CA). biotin Biotin Illumina protocol Illumina protocol phNPC from Geschwind Lab Donor: 6 Region: 21 DiffWk: 1 Replicate: 1 Passage: 5 Log2 normalization, quantile normalization, and ComBat batch correction NONE ID_REF VALUE Log2 normalization, quantile normalization, and ComBat batch correction Detection Pval GSM1385237-tbl-1.txt 2014-05-12 2014-06-01 2014-06-01 GSM1385238 RNA 1 Human fetal tissue Homo sapiens 8 46 phNPC from Geschwind Lab 1 6 10 18 ASW M 2 phNPC: Neurobasal A (Invitrogen) supplemented with B27 (Gibco), GlutaMAX (Gibco), and Antibiotics and Antimycotics (Gibco)] as well as Retinoic Acid (500 ng/mL; Sigma), Forskolin (100 μM; Sigma), BDNF (10 ng/mL; Peprotech), NT-3 (10 ng/mL; Peprotech), and KCl (10mM); iPSC Kosik Lab: neurobasal media supplemented with N2, B27 and neurotrophic factor cocktail that included NT3, BDNF, and GDNF; iPSC Gage Lab: DMEM/F12, N2, BDNF/GDNF, and laminin. phNPC: Neurobasal A (Invitrogen) supplemented with 10% BIT (Stem Cell Technologies), Antibiotics and Antimycotics (Gibco), GlutaMAX (Gibco), and Heparin (1 μg/mL; Sigma)] with freshly added EGF, FGF2, PDGF (each at 20 ng/mL; Peprotech), and LIF (2 ng/mL; Millipore); iPSC Kosik Lab: N2 induction media with bFGF; iPSC Gage Lab: DMEM/F12; 1X N2; 1X B27 and FGF2 total RNA phNPCs: RNA was isolated using TRIzol reagent (Invitrogen) according to standard protocols; iPSC Kosik Lab: RNA was extracted using miRVANA kit, following the manufacturer’s protocol for total RNA; iPSC Gage Lab: Total cellular RNA was extracted using the RNeasy Protect Mini kit (QIAGEN, Valencia, CA). biotin Biotin Illumina protocol Illumina protocol phNPC from Geschwind Lab Donor: 8 Region: 46 DiffWk: 1 Replicate: 1 Passage: 6 Log2 normalization, quantile normalization, and ComBat batch correction NONE ID_REF VALUE Log2 normalization, quantile normalization, and ComBat batch correction Detection Pval GSM1385238-tbl-1.txt 2014-05-12 2014-06-01 2014-06-01 GSM1385239 RNA 1 Human fetal tissue Homo sapiens 8 49 phNPC from Geschwind Lab 1 6 9.7 18 ASW M 2 phNPC: Neurobasal A (Invitrogen) supplemented with B27 (Gibco), GlutaMAX (Gibco), and Antibiotics and Antimycotics (Gibco)] as well as Retinoic Acid (500 ng/mL; Sigma), Forskolin (100 μM; Sigma), BDNF (10 ng/mL; Peprotech), NT-3 (10 ng/mL; Peprotech), and KCl (10mM); iPSC Kosik Lab: neurobasal media supplemented with N2, B27 and neurotrophic factor cocktail that included NT3, BDNF, and GDNF; iPSC Gage Lab: DMEM/F12, N2, BDNF/GDNF, and laminin. phNPC: Neurobasal A (Invitrogen) supplemented with 10% BIT (Stem Cell Technologies), Antibiotics and Antimycotics (Gibco), GlutaMAX (Gibco), and Heparin (1 μg/mL; Sigma)] with freshly added EGF, FGF2, PDGF (each at 20 ng/mL; Peprotech), and LIF (2 ng/mL; Millipore); iPSC Kosik Lab: N2 induction media with bFGF; iPSC Gage Lab: DMEM/F12; 1X N2; 1X B27 and FGF2 total RNA phNPCs: RNA was isolated using TRIzol reagent (Invitrogen) according to standard protocols; iPSC Kosik Lab: RNA was extracted using miRVANA kit, following the manufacturer’s protocol for total RNA; iPSC Gage Lab: Total cellular RNA was extracted using the RNeasy Protect Mini kit (QIAGEN, Valencia, CA). biotin Biotin Illumina protocol Illumina protocol phNPC from Geschwind Lab Donor: 8 Region: 49 DiffWk: 1 Replicate: 1 Passage: 6 Log2 normalization, quantile normalization, and ComBat batch correction NONE ID_REF VALUE Log2 normalization, quantile normalization, and ComBat batch correction Detection Pval GSM1385239-tbl-1.txt 2014-05-12 2014-06-01 2014-06-01 GSM1385240 RNA 1 Human fetal tissue Homo sapiens 8 43 phNPC from Geschwind Lab 12 6 8.8 18 ASW M 2 phNPC: Neurobasal A (Invitrogen) supplemented with B27 (Gibco), GlutaMAX (Gibco), and Antibiotics and Antimycotics (Gibco)] as well as Retinoic Acid (500 ng/mL; Sigma), Forskolin (100 μM; Sigma), BDNF (10 ng/mL; Peprotech), NT-3 (10 ng/mL; Peprotech), and KCl (10mM); iPSC Kosik Lab: neurobasal media supplemented with N2, B27 and neurotrophic factor cocktail that included NT3, BDNF, and GDNF; iPSC Gage Lab: DMEM/F12, N2, BDNF/GDNF, and laminin. phNPC: Neurobasal A (Invitrogen) supplemented with 10% BIT (Stem Cell Technologies), Antibiotics and Antimycotics (Gibco), GlutaMAX (Gibco), and Heparin (1 μg/mL; Sigma)] with freshly added EGF, FGF2, PDGF (each at 20 ng/mL; Peprotech), and LIF (2 ng/mL; Millipore); iPSC Kosik Lab: N2 induction media with bFGF; iPSC Gage Lab: DMEM/F12; 1X N2; 1X B27 and FGF2 total RNA phNPCs: RNA was isolated using TRIzol reagent (Invitrogen) according to standard protocols; iPSC Kosik Lab: RNA was extracted using miRVANA kit, following the manufacturer’s protocol for total RNA; iPSC Gage Lab: Total cellular RNA was extracted using the RNeasy Protect Mini kit (QIAGEN, Valencia, CA). biotin Biotin Illumina protocol Illumina protocol phNPC from Geschwind Lab Donor: 8 Region: 43 DiffWk: 12 Replicate: 1 Passage: 6 Log2 normalization, quantile normalization, and ComBat batch correction NONE ID_REF VALUE Log2 normalization, quantile normalization, and ComBat batch correction Detection Pval GSM1385240-tbl-1.txt 2014-05-12 2014-06-01 2014-06-01 GSM1385241 RNA 1 Human fetal tissue Homo sapiens 6 21 phNPC from Geschwind Lab 4 5 8.9 18 MEX M 2 phNPC: Neurobasal A (Invitrogen) supplemented with B27 (Gibco), GlutaMAX (Gibco), and Antibiotics and Antimycotics (Gibco)] as well as Retinoic Acid (500 ng/mL; Sigma), Forskolin (100 μM; Sigma), BDNF (10 ng/mL; Peprotech), NT-3 (10 ng/mL; Peprotech), and KCl (10mM); iPSC Kosik Lab: neurobasal media supplemented with N2, B27 and neurotrophic factor cocktail that included NT3, BDNF, and GDNF; iPSC Gage Lab: DMEM/F12, N2, BDNF/GDNF, and laminin. phNPC: Neurobasal A (Invitrogen) supplemented with 10% BIT (Stem Cell Technologies), Antibiotics and Antimycotics (Gibco), GlutaMAX (Gibco), and Heparin (1 μg/mL; Sigma)] with freshly added EGF, FGF2, PDGF (each at 20 ng/mL; Peprotech), and LIF (2 ng/mL; Millipore); iPSC Kosik Lab: N2 induction media with bFGF; iPSC Gage Lab: DMEM/F12; 1X N2; 1X B27 and FGF2 total RNA phNPCs: RNA was isolated using TRIzol reagent (Invitrogen) according to standard protocols; iPSC Kosik Lab: RNA was extracted using miRVANA kit, following the manufacturer’s protocol for total RNA; iPSC Gage Lab: Total cellular RNA was extracted using the RNeasy Protect Mini kit (QIAGEN, Valencia, CA). biotin Biotin Illumina protocol Illumina protocol phNPC from Geschwind Lab Donor: 6 Region: 21 DiffWk: 4 Replicate: 2 Passage: 5 Log2 normalization, quantile normalization, and ComBat batch correction NONE ID_REF VALUE Log2 normalization, quantile normalization, and ComBat batch correction Detection Pval GSM1385241-tbl-1.txt 2014-05-12 2014-06-01 2014-06-01 GSM1385242 RNA 1 Human fetal tissue Homo sapiens 8 49 phNPC from Geschwind Lab 1 5 10 18 ASW M 3 phNPC: Neurobasal A (Invitrogen) supplemented with B27 (Gibco), GlutaMAX (Gibco), and Antibiotics and Antimycotics (Gibco)] as well as Retinoic Acid (500 ng/mL; Sigma), Forskolin (100 μM; Sigma), BDNF (10 ng/mL; Peprotech), NT-3 (10 ng/mL; Peprotech), and KCl (10mM); iPSC Kosik Lab: neurobasal media supplemented with N2, B27 and neurotrophic factor cocktail that included NT3, BDNF, and GDNF; iPSC Gage Lab: DMEM/F12, N2, BDNF/GDNF, and laminin. phNPC: Neurobasal A (Invitrogen) supplemented with 10% BIT (Stem Cell Technologies), Antibiotics and Antimycotics (Gibco), GlutaMAX (Gibco), and Heparin (1 μg/mL; Sigma)] with freshly added EGF, FGF2, PDGF (each at 20 ng/mL; Peprotech), and LIF (2 ng/mL; Millipore); iPSC Kosik Lab: N2 induction media with bFGF; iPSC Gage Lab: DMEM/F12; 1X N2; 1X B27 and FGF2 total RNA phNPCs: RNA was isolated using TRIzol reagent (Invitrogen) according to standard protocols; iPSC Kosik Lab: RNA was extracted using miRVANA kit, following the manufacturer’s protocol for total RNA; iPSC Gage Lab: Total cellular RNA was extracted using the RNeasy Protect Mini kit (QIAGEN, Valencia, CA). biotin Biotin Illumina protocol Illumina protocol phNPC from Geschwind Lab Donor: 8 Region: 49 DiffWk: 1 Replicate: 1 Passage: 5 Log2 normalization, quantile normalization, and ComBat batch correction NONE ID_REF VALUE Log2 normalization, quantile normalization, and ComBat batch correction Detection Pval GSM1385242-tbl-1.txt 2014-05-12 2014-06-01 2014-06-01 GSM1385243 RNA 1 Human fetal tissue Homo sapiens 5 17 phNPC from Geschwind Lab 8 9 8.2 17 MEX F 3 phNPC: Neurobasal A (Invitrogen) supplemented with B27 (Gibco), GlutaMAX (Gibco), and Antibiotics and Antimycotics (Gibco)] as well as Retinoic Acid (500 ng/mL; Sigma), Forskolin (100 μM; Sigma), BDNF (10 ng/mL; Peprotech), NT-3 (10 ng/mL; Peprotech), and KCl (10mM); iPSC Kosik Lab: neurobasal media supplemented with N2, B27 and neurotrophic factor cocktail that included NT3, BDNF, and GDNF; iPSC Gage Lab: DMEM/F12, N2, BDNF/GDNF, and laminin. phNPC: Neurobasal A (Invitrogen) supplemented with 10% BIT (Stem Cell Technologies), Antibiotics and Antimycotics (Gibco), GlutaMAX (Gibco), and Heparin (1 μg/mL; Sigma)] with freshly added EGF, FGF2, PDGF (each at 20 ng/mL; Peprotech), and LIF (2 ng/mL; Millipore); iPSC Kosik Lab: N2 induction media with bFGF; iPSC Gage Lab: DMEM/F12; 1X N2; 1X B27 and FGF2 total RNA phNPCs: RNA was isolated using TRIzol reagent (Invitrogen) according to standard protocols; iPSC Kosik Lab: RNA was extracted using miRVANA kit, following the manufacturer’s protocol for total RNA; iPSC Gage Lab: Total cellular RNA was extracted using the RNeasy Protect Mini kit (QIAGEN, Valencia, CA). biotin Biotin Illumina protocol Illumina protocol phNPC from Geschwind Lab Donor: 5 Region: 17 DiffWk: 8 Replicate: 2 Passage: 9 Log2 normalization, quantile normalization, and ComBat batch correction NONE ID_REF VALUE Log2 normalization, quantile normalization, and ComBat batch correction Detection Pval GSM1385243-tbl-1.txt 2014-05-12 2014-06-01 2014-06-01 GSM1385244 RNA 1 Human fetal tissue Homo sapiens 8 43 phNPC from Geschwind Lab 4 7 9.8 18 ASW M 4 phNPC: Neurobasal A (Invitrogen) supplemented with B27 (Gibco), GlutaMAX (Gibco), and Antibiotics and Antimycotics (Gibco)] as well as Retinoic Acid (500 ng/mL; Sigma), Forskolin (100 μM; Sigma), BDNF (10 ng/mL; Peprotech), NT-3 (10 ng/mL; Peprotech), and KCl (10mM); iPSC Kosik Lab: neurobasal media supplemented with N2, B27 and neurotrophic factor cocktail that included NT3, BDNF, and GDNF; iPSC Gage Lab: DMEM/F12, N2, BDNF/GDNF, and laminin. phNPC: Neurobasal A (Invitrogen) supplemented with 10% BIT (Stem Cell Technologies), Antibiotics and Antimycotics (Gibco), GlutaMAX (Gibco), and Heparin (1 μg/mL; Sigma)] with freshly added EGF, FGF2, PDGF (each at 20 ng/mL; Peprotech), and LIF (2 ng/mL; Millipore); iPSC Kosik Lab: N2 induction media with bFGF; iPSC Gage Lab: DMEM/F12; 1X N2; 1X B27 and FGF2 total RNA phNPCs: RNA was isolated using TRIzol reagent (Invitrogen) according to standard protocols; iPSC Kosik Lab: RNA was extracted using miRVANA kit, following the manufacturer’s protocol for total RNA; iPSC Gage Lab: Total cellular RNA was extracted using the RNeasy Protect Mini kit (QIAGEN, Valencia, CA). biotin Biotin Illumina protocol Illumina protocol phNPC from Geschwind Lab Donor: 8 Region: 43 DiffWk: 4 Replicate: 1 Passage: 7 Log2 normalization, quantile normalization, and ComBat batch correction NONE ID_REF VALUE Log2 normalization, quantile normalization, and ComBat batch correction Detection Pval GSM1385244-tbl-1.txt 2014-05-12 2014-06-01 2014-06-01 GSM1385245 RNA 1 Human fetal tissue Homo sapiens 6 21 phNPC from Geschwind Lab 12 5 8.3 18 MEX M 4 phNPC: Neurobasal A (Invitrogen) supplemented with B27 (Gibco), GlutaMAX (Gibco), and Antibiotics and Antimycotics (Gibco)] as well as Retinoic Acid (500 ng/mL; Sigma), Forskolin (100 μM; Sigma), BDNF (10 ng/mL; Peprotech), NT-3 (10 ng/mL; Peprotech), and KCl (10mM); iPSC Kosik Lab: neurobasal media supplemented with N2, B27 and neurotrophic factor cocktail that included NT3, BDNF, and GDNF; iPSC Gage Lab: DMEM/F12, N2, BDNF/GDNF, and laminin. phNPC: Neurobasal A (Invitrogen) supplemented with 10% BIT (Stem Cell Technologies), Antibiotics and Antimycotics (Gibco), GlutaMAX (Gibco), and Heparin (1 μg/mL; Sigma)] with freshly added EGF, FGF2, PDGF (each at 20 ng/mL; Peprotech), and LIF (2 ng/mL; Millipore); iPSC Kosik Lab: N2 induction media with bFGF; iPSC Gage Lab: DMEM/F12; 1X N2; 1X B27 and FGF2 total RNA phNPCs: RNA was isolated using TRIzol reagent (Invitrogen) according to standard protocols; iPSC Kosik Lab: RNA was extracted using miRVANA kit, following the manufacturer’s protocol for total RNA; iPSC Gage Lab: Total cellular RNA was extracted using the RNeasy Protect Mini kit (QIAGEN, Valencia, CA). biotin Biotin Illumina protocol Illumina protocol phNPC from Geschwind Lab Donor: 6 Region: 21 DiffWk: 12 Replicate: 1 Passage: 5 Log2 normalization, quantile normalization, and ComBat batch correction NONE ID_REF VALUE Log2 normalization, quantile normalization, and ComBat batch correction Detection Pval GSM1385245-tbl-1.txt 2014-05-12 2014-06-01 2014-06-01 GSM1385246 RNA 1 Human fetal tissue Homo sapiens 8 43 phNPC from Geschwind Lab 1 7 9.7 18 ASW M 4 phNPC: Neurobasal A (Invitrogen) supplemented with B27 (Gibco), GlutaMAX (Gibco), and Antibiotics and Antimycotics (Gibco)] as well as Retinoic Acid (500 ng/mL; Sigma), Forskolin (100 μM; Sigma), BDNF (10 ng/mL; Peprotech), NT-3 (10 ng/mL; Peprotech), and KCl (10mM); iPSC Kosik Lab: neurobasal media supplemented with N2, B27 and neurotrophic factor cocktail that included NT3, BDNF, and GDNF; iPSC Gage Lab: DMEM/F12, N2, BDNF/GDNF, and laminin. phNPC: Neurobasal A (Invitrogen) supplemented with 10% BIT (Stem Cell Technologies), Antibiotics and Antimycotics (Gibco), GlutaMAX (Gibco), and Heparin (1 μg/mL; Sigma)] with freshly added EGF, FGF2, PDGF (each at 20 ng/mL; Peprotech), and LIF (2 ng/mL; Millipore); iPSC Kosik Lab: N2 induction media with bFGF; iPSC Gage Lab: DMEM/F12; 1X N2; 1X B27 and FGF2 total RNA phNPCs: RNA was isolated using TRIzol reagent (Invitrogen) according to standard protocols; iPSC Kosik Lab: RNA was extracted using miRVANA kit, following the manufacturer’s protocol for total RNA; iPSC Gage Lab: Total cellular RNA was extracted using the RNeasy Protect Mini kit (QIAGEN, Valencia, CA). biotin Biotin Illumina protocol Illumina protocol phNPC from Geschwind Lab Donor: 8 Region: 43 DiffWk: 1 Replicate: 2 Passage: 7 Log2 normalization, quantile normalization, and ComBat batch correction NONE ID_REF VALUE Log2 normalization, quantile normalization, and ComBat batch correction Detection Pval GSM1385246-tbl-1.txt 2014-05-12 2014-06-01 2014-06-01 GSM1385247 RNA 1 Human fetal tissue Homo sapiens 8 49 phNPC from Geschwind Lab 12 6 6.9 18 ASW M 4 phNPC: Neurobasal A (Invitrogen) supplemented with B27 (Gibco), GlutaMAX (Gibco), and Antibiotics and Antimycotics (Gibco)] as well as Retinoic Acid (500 ng/mL; Sigma), Forskolin (100 μM; Sigma), BDNF (10 ng/mL; Peprotech), NT-3 (10 ng/mL; Peprotech), and KCl (10mM); iPSC Kosik Lab: neurobasal media supplemented with N2, B27 and neurotrophic factor cocktail that included NT3, BDNF, and GDNF; iPSC Gage Lab: DMEM/F12, N2, BDNF/GDNF, and laminin. phNPC: Neurobasal A (Invitrogen) supplemented with 10% BIT (Stem Cell Technologies), Antibiotics and Antimycotics (Gibco), GlutaMAX (Gibco), and Heparin (1 μg/mL; Sigma)] with freshly added EGF, FGF2, PDGF (each at 20 ng/mL; Peprotech), and LIF (2 ng/mL; Millipore); iPSC Kosik Lab: N2 induction media with bFGF; iPSC Gage Lab: DMEM/F12; 1X N2; 1X B27 and FGF2 total RNA phNPCs: RNA was isolated using TRIzol reagent (Invitrogen) according to standard protocols; iPSC Kosik Lab: RNA was extracted using miRVANA kit, following the manufacturer’s protocol for total RNA; iPSC Gage Lab: Total cellular RNA was extracted using the RNeasy Protect Mini kit (QIAGEN, Valencia, CA). biotin Biotin Illumina protocol Illumina protocol phNPC from Geschwind Lab Donor: 8 Region: 49 DiffWk: 12 Replicate: 2 Passage: 6 Log2 normalization, quantile normalization, and ComBat batch correction NONE ID_REF VALUE Log2 normalization, quantile normalization, and ComBat batch correction Detection Pval GSM1385247-tbl-1.txt 2014-05-12 2014-06-01 2014-06-01 GSM1385248 RNA 1 Human fetal tissue Homo sapiens 8 49 phNPC from Geschwind Lab 4 5 9.5 18 ASW M 4 phNPC: Neurobasal A (Invitrogen) supplemented with B27 (Gibco), GlutaMAX (Gibco), and Antibiotics and Antimycotics (Gibco)] as well as Retinoic Acid (500 ng/mL; Sigma), Forskolin (100 μM; Sigma), BDNF (10 ng/mL; Peprotech), NT-3 (10 ng/mL; Peprotech), and KCl (10mM); iPSC Kosik Lab: neurobasal media supplemented with N2, B27 and neurotrophic factor cocktail that included NT3, BDNF, and GDNF; iPSC Gage Lab: DMEM/F12, N2, BDNF/GDNF, and laminin. phNPC: Neurobasal A (Invitrogen) supplemented with 10% BIT (Stem Cell Technologies), Antibiotics and Antimycotics (Gibco), GlutaMAX (Gibco), and Heparin (1 μg/mL; Sigma)] with freshly added EGF, FGF2, PDGF (each at 20 ng/mL; Peprotech), and LIF (2 ng/mL; Millipore); iPSC Kosik Lab: N2 induction media with bFGF; iPSC Gage Lab: DMEM/F12; 1X N2; 1X B27 and FGF2 total RNA phNPCs: RNA was isolated using TRIzol reagent (Invitrogen) according to standard protocols; iPSC Kosik Lab: RNA was extracted using miRVANA kit, following the manufacturer’s protocol for total RNA; iPSC Gage Lab: Total cellular RNA was extracted using the RNeasy Protect Mini kit (QIAGEN, Valencia, CA). biotin Biotin Illumina protocol Illumina protocol phNPC from Geschwind Lab Donor: 8 Region: 49 DiffWk: 4 Replicate: 1 Passage: 5 Log2 normalization, quantile normalization, and ComBat batch correction NONE ID_REF VALUE Log2 normalization, quantile normalization, and ComBat batch correction Detection Pval GSM1385248-tbl-1.txt 2014-05-12 2014-06-01 2014-06-01 GSM1385249 RNA 1 Human fetal tissue Homo sapiens 8 46 phNPC from Geschwind Lab 12 5 9.5 18 ASW M 4 phNPC: Neurobasal A (Invitrogen) supplemented with B27 (Gibco), GlutaMAX (Gibco), and Antibiotics and Antimycotics (Gibco)] as well as Retinoic Acid (500 ng/mL; Sigma), Forskolin (100 μM; Sigma), BDNF (10 ng/mL; Peprotech), NT-3 (10 ng/mL; Peprotech), and KCl (10mM); iPSC Kosik Lab: neurobasal media supplemented with N2, B27 and neurotrophic factor cocktail that included NT3, BDNF, and GDNF; iPSC Gage Lab: DMEM/F12, N2, BDNF/GDNF, and laminin. phNPC: Neurobasal A (Invitrogen) supplemented with 10% BIT (Stem Cell Technologies), Antibiotics and Antimycotics (Gibco), GlutaMAX (Gibco), and Heparin (1 μg/mL; Sigma)] with freshly added EGF, FGF2, PDGF (each at 20 ng/mL; Peprotech), and LIF (2 ng/mL; Millipore); iPSC Kosik Lab: N2 induction media with bFGF; iPSC Gage Lab: DMEM/F12; 1X N2; 1X B27 and FGF2 total RNA phNPCs: RNA was isolated using TRIzol reagent (Invitrogen) according to standard protocols; iPSC Kosik Lab: RNA was extracted using miRVANA kit, following the manufacturer’s protocol for total RNA; iPSC Gage Lab: Total cellular RNA was extracted using the RNeasy Protect Mini kit (QIAGEN, Valencia, CA). biotin Biotin Illumina protocol Illumina protocol phNPC from Geschwind Lab Donor: 8 Region: 46 DiffWk: 12 Replicate: 1 Passage: 5 Log2 normalization, quantile normalization, and ComBat batch correction NONE ID_REF VALUE Log2 normalization, quantile normalization, and ComBat batch correction Detection Pval GSM1385249-tbl-1.txt 2014-05-12 2014-06-01 2014-06-01 GSM1385250 RNA 1 Human fetal tissue Homo sapiens 6 21 phNPC from Geschwind Lab 4 6 9.5 18 MEX M 5 phNPC: Neurobasal A (Invitrogen) supplemented with B27 (Gibco), GlutaMAX (Gibco), and Antibiotics and Antimycotics (Gibco)] as well as Retinoic Acid (500 ng/mL; Sigma), Forskolin (100 μM; Sigma), BDNF (10 ng/mL; Peprotech), NT-3 (10 ng/mL; Peprotech), and KCl (10mM); iPSC Kosik Lab: neurobasal media supplemented with N2, B27 and neurotrophic factor cocktail that included NT3, BDNF, and GDNF; iPSC Gage Lab: DMEM/F12, N2, BDNF/GDNF, and laminin. phNPC: Neurobasal A (Invitrogen) supplemented with 10% BIT (Stem Cell Technologies), Antibiotics and Antimycotics (Gibco), GlutaMAX (Gibco), and Heparin (1 μg/mL; Sigma)] with freshly added EGF, FGF2, PDGF (each at 20 ng/mL; Peprotech), and LIF (2 ng/mL; Millipore); iPSC Kosik Lab: N2 induction media with bFGF; iPSC Gage Lab: DMEM/F12; 1X N2; 1X B27 and FGF2 total RNA phNPCs: RNA was isolated using TRIzol reagent (Invitrogen) according to standard protocols; iPSC Kosik Lab: RNA was extracted using miRVANA kit, following the manufacturer’s protocol for total RNA; iPSC Gage Lab: Total cellular RNA was extracted using the RNeasy Protect Mini kit (QIAGEN, Valencia, CA). biotin Biotin Illumina protocol Illumina protocol phNPC from Geschwind Lab Donor: 6 Region: 21 DiffWk: 4 Replicate: 2 Passage: 6 Log2 normalization, quantile normalization, and ComBat batch correction NONE ID_REF VALUE Log2 normalization, quantile normalization, and ComBat batch correction Detection Pval GSM1385250-tbl-1.txt 2014-05-12 2014-06-01 2014-06-01 GSM1385251 RNA 1 Human fetal tissue Homo sapiens 8 49 phNPC from Geschwind Lab 8 5 9.1 18 ASW M 5 phNPC: Neurobasal A (Invitrogen) supplemented with B27 (Gibco), GlutaMAX (Gibco), and Antibiotics and Antimycotics (Gibco)] as well as Retinoic Acid (500 ng/mL; Sigma), Forskolin (100 μM; Sigma), BDNF (10 ng/mL; Peprotech), NT-3 (10 ng/mL; Peprotech), and KCl (10mM); iPSC Kosik Lab: neurobasal media supplemented with N2, B27 and neurotrophic factor cocktail that included NT3, BDNF, and GDNF; iPSC Gage Lab: DMEM/F12, N2, BDNF/GDNF, and laminin. phNPC: Neurobasal A (Invitrogen) supplemented with 10% BIT (Stem Cell Technologies), Antibiotics and Antimycotics (Gibco), GlutaMAX (Gibco), and Heparin (1 μg/mL; Sigma)] with freshly added EGF, FGF2, PDGF (each at 20 ng/mL; Peprotech), and LIF (2 ng/mL; Millipore); iPSC Kosik Lab: N2 induction media with bFGF; iPSC Gage Lab: DMEM/F12; 1X N2; 1X B27 and FGF2 total RNA phNPCs: RNA was isolated using TRIzol reagent (Invitrogen) according to standard protocols; iPSC Kosik Lab: RNA was extracted using miRVANA kit, following the manufacturer’s protocol for total RNA; iPSC Gage Lab: Total cellular RNA was extracted using the RNeasy Protect Mini kit (QIAGEN, Valencia, CA). biotin Biotin Illumina protocol Illumina protocol phNPC from Geschwind Lab Donor: 8 Region: 49 DiffWk: 8 Replicate: 2 Passage: 5 Log2 normalization, quantile normalization, and ComBat batch correction NONE ID_REF VALUE Log2 normalization, quantile normalization, and ComBat batch correction Detection Pval GSM1385251-tbl-1.txt 2014-05-12 2014-06-01 2014-06-01 GSM1385252 RNA 1 Human fetal tissue Homo sapiens 8 46 phNPC from Geschwind Lab 8 6 9.6 18 ASW M 5 phNPC: Neurobasal A (Invitrogen) supplemented with B27 (Gibco), GlutaMAX (Gibco), and Antibiotics and Antimycotics (Gibco)] as well as Retinoic Acid (500 ng/mL; Sigma), Forskolin (100 μM; Sigma), BDNF (10 ng/mL; Peprotech), NT-3 (10 ng/mL; Peprotech), and KCl (10mM); iPSC Kosik Lab: neurobasal media supplemented with N2, B27 and neurotrophic factor cocktail that included NT3, BDNF, and GDNF; iPSC Gage Lab: DMEM/F12, N2, BDNF/GDNF, and laminin. phNPC: Neurobasal A (Invitrogen) supplemented with 10% BIT (Stem Cell Technologies), Antibiotics and Antimycotics (Gibco), GlutaMAX (Gibco), and Heparin (1 μg/mL; Sigma)] with freshly added EGF, FGF2, PDGF (each at 20 ng/mL; Peprotech), and LIF (2 ng/mL; Millipore); iPSC Kosik Lab: N2 induction media with bFGF; iPSC Gage Lab: DMEM/F12; 1X N2; 1X B27 and FGF2 total RNA phNPCs: RNA was isolated using TRIzol reagent (Invitrogen) according to standard protocols; iPSC Kosik Lab: RNA was extracted using miRVANA kit, following the manufacturer’s protocol for total RNA; iPSC Gage Lab: Total cellular RNA was extracted using the RNeasy Protect Mini kit (QIAGEN, Valencia, CA). biotin Biotin Illumina protocol Illumina protocol phNPC from Geschwind Lab Donor: 8 Region: 46 DiffWk: 8 Replicate: 2 Passage: 6 Log2 normalization, quantile normalization, and ComBat batch correction NONE ID_REF VALUE Log2 normalization, quantile normalization, and ComBat batch correction Detection Pval GSM1385252-tbl-1.txt 2014-05-12 2014-06-01 2014-06-01 GSM1385253 RNA 1 Human fetal tissue Homo sapiens 6 21 phNPC from Geschwind Lab 8 6 9.3 18 MEX M 6 phNPC: Neurobasal A (Invitrogen) supplemented with B27 (Gibco), GlutaMAX (Gibco), and Antibiotics and Antimycotics (Gibco)] as well as Retinoic Acid (500 ng/mL; Sigma), Forskolin (100 μM; Sigma), BDNF (10 ng/mL; Peprotech), NT-3 (10 ng/mL; Peprotech), and KCl (10mM); iPSC Kosik Lab: neurobasal media supplemented with N2, B27 and neurotrophic factor cocktail that included NT3, BDNF, and GDNF; iPSC Gage Lab: DMEM/F12, N2, BDNF/GDNF, and laminin. phNPC: Neurobasal A (Invitrogen) supplemented with 10% BIT (Stem Cell Technologies), Antibiotics and Antimycotics (Gibco), GlutaMAX (Gibco), and Heparin (1 μg/mL; Sigma)] with freshly added EGF, FGF2, PDGF (each at 20 ng/mL; Peprotech), and LIF (2 ng/mL; Millipore); iPSC Kosik Lab: N2 induction media with bFGF; iPSC Gage Lab: DMEM/F12; 1X N2; 1X B27 and FGF2 total RNA phNPCs: RNA was isolated using TRIzol reagent (Invitrogen) according to standard protocols; iPSC Kosik Lab: RNA was extracted using miRVANA kit, following the manufacturer’s protocol for total RNA; iPSC Gage Lab: Total cellular RNA was extracted using the RNeasy Protect Mini kit (QIAGEN, Valencia, CA). biotin Biotin Illumina protocol Illumina protocol phNPC from Geschwind Lab Donor: 6 Region: 21 DiffWk: 8 Replicate: 2 Passage: 6 Log2 normalization, quantile normalization, and ComBat batch correction NONE ID_REF VALUE Log2 normalization, quantile normalization, and ComBat batch correction Detection Pval GSM1385253-tbl-1.txt 2014-05-12 2014-06-01 2014-06-01 GSM1385254 RNA 1 Human fetal tissue Homo sapiens 8 46 phNPC from Geschwind Lab 8 6 9.5 18 ASW M 6 phNPC: Neurobasal A (Invitrogen) supplemented with B27 (Gibco), GlutaMAX (Gibco), and Antibiotics and Antimycotics (Gibco)] as well as Retinoic Acid (500 ng/mL; Sigma), Forskolin (100 μM; Sigma), BDNF (10 ng/mL; Peprotech), NT-3 (10 ng/mL; Peprotech), and KCl (10mM); iPSC Kosik Lab: neurobasal media supplemented with N2, B27 and neurotrophic factor cocktail that included NT3, BDNF, and GDNF; iPSC Gage Lab: DMEM/F12, N2, BDNF/GDNF, and laminin. phNPC: Neurobasal A (Invitrogen) supplemented with 10% BIT (Stem Cell Technologies), Antibiotics and Antimycotics (Gibco), GlutaMAX (Gibco), and Heparin (1 μg/mL; Sigma)] with freshly added EGF, FGF2, PDGF (each at 20 ng/mL; Peprotech), and LIF (2 ng/mL; Millipore); iPSC Kosik Lab: N2 induction media with bFGF; iPSC Gage Lab: DMEM/F12; 1X N2; 1X B27 and FGF2 total RNA phNPCs: RNA was isolated using TRIzol reagent (Invitrogen) according to standard protocols; iPSC Kosik Lab: RNA was extracted using miRVANA kit, following the manufacturer’s protocol for total RNA; iPSC Gage Lab: Total cellular RNA was extracted using the RNeasy Protect Mini kit (QIAGEN, Valencia, CA). biotin Biotin Illumina protocol Illumina protocol phNPC from Geschwind Lab Donor: 8 Region: 46 DiffWk: 8 Replicate: 1 Passage: 6 Log2 normalization, quantile normalization, and ComBat batch correction NONE ID_REF VALUE Log2 normalization, quantile normalization, and ComBat batch correction Detection Pval GSM1385254-tbl-1.txt 2014-05-12 2014-06-01 2014-06-01 GSM1385255 RNA 1 Human fetal tissue Homo sapiens 8 43 phNPC from Geschwind Lab 8 7 9.7 18 ASW M 6 phNPC: Neurobasal A (Invitrogen) supplemented with B27 (Gibco), GlutaMAX (Gibco), and Antibiotics and Antimycotics (Gibco)] as well as Retinoic Acid (500 ng/mL; Sigma), Forskolin (100 μM; Sigma), BDNF (10 ng/mL; Peprotech), NT-3 (10 ng/mL; Peprotech), and KCl (10mM); iPSC Kosik Lab: neurobasal media supplemented with N2, B27 and neurotrophic factor cocktail that included NT3, BDNF, and GDNF; iPSC Gage Lab: DMEM/F12, N2, BDNF/GDNF, and laminin. phNPC: Neurobasal A (Invitrogen) supplemented with 10% BIT (Stem Cell Technologies), Antibiotics and Antimycotics (Gibco), GlutaMAX (Gibco), and Heparin (1 μg/mL; Sigma)] with freshly added EGF, FGF2, PDGF (each at 20 ng/mL; Peprotech), and LIF (2 ng/mL; Millipore); iPSC Kosik Lab: N2 induction media with bFGF; iPSC Gage Lab: DMEM/F12; 1X N2; 1X B27 and FGF2 total RNA phNPCs: RNA was isolated using TRIzol reagent (Invitrogen) according to standard protocols; iPSC Kosik Lab: RNA was extracted using miRVANA kit, following the manufacturer’s protocol for total RNA; iPSC Gage Lab: Total cellular RNA was extracted using the RNeasy Protect Mini kit (QIAGEN, Valencia, CA). biotin Biotin Illumina protocol Illumina protocol phNPC from Geschwind Lab Donor: 8 Region: 43 DiffWk: 8 Replicate: 1 Passage: 7 Log2 normalization, quantile normalization, and ComBat batch correction NONE ID_REF VALUE Log2 normalization, quantile normalization, and ComBat batch correction Detection Pval GSM1385255-tbl-1.txt 2014-05-12 2014-06-01 2014-06-01 GSM1385256 RNA 1 Human fetal tissue Homo sapiens 8 43 phNPC from Geschwind Lab 8 6 9.3 18 ASW M 7 phNPC: Neurobasal A (Invitrogen) supplemented with B27 (Gibco), GlutaMAX (Gibco), and Antibiotics and Antimycotics (Gibco)] as well as Retinoic Acid (500 ng/mL; Sigma), Forskolin (100 μM; Sigma), BDNF (10 ng/mL; Peprotech), NT-3 (10 ng/mL; Peprotech), and KCl (10mM); iPSC Kosik Lab: neurobasal media supplemented with N2, B27 and neurotrophic factor cocktail that included NT3, BDNF, and GDNF; iPSC Gage Lab: DMEM/F12, N2, BDNF/GDNF, and laminin. phNPC: Neurobasal A (Invitrogen) supplemented with 10% BIT (Stem Cell Technologies), Antibiotics and Antimycotics (Gibco), GlutaMAX (Gibco), and Heparin (1 μg/mL; Sigma)] with freshly added EGF, FGF2, PDGF (each at 20 ng/mL; Peprotech), and LIF (2 ng/mL; Millipore); iPSC Kosik Lab: N2 induction media with bFGF; iPSC Gage Lab: DMEM/F12; 1X N2; 1X B27 and FGF2 total RNA phNPCs: RNA was isolated using TRIzol reagent (Invitrogen) according to standard protocols; iPSC Kosik Lab: RNA was extracted using miRVANA kit, following the manufacturer’s protocol for total RNA; iPSC Gage Lab: Total cellular RNA was extracted using the RNeasy Protect Mini kit (QIAGEN, Valencia, CA). biotin Biotin Illumina protocol Illumina protocol phNPC from Geschwind Lab Donor: 8 Region: 43 DiffWk: 8 Replicate: 2 Passage: 6 Log2 normalization, quantile normalization, and ComBat batch correction NONE ID_REF VALUE Log2 normalization, quantile normalization, and ComBat batch correction Detection Pval GSM1385256-tbl-1.txt 2014-05-12 2014-06-01 2014-06-01 GSM1385257 RNA 1 Human fetal tissue Homo sapiens 8 49 phNPC from Geschwind Lab 8 6 8.8 18 ASW M 7 phNPC: Neurobasal A (Invitrogen) supplemented with B27 (Gibco), GlutaMAX (Gibco), and Antibiotics and Antimycotics (Gibco)] as well as Retinoic Acid (500 ng/mL; Sigma), Forskolin (100 μM; Sigma), BDNF (10 ng/mL; Peprotech), NT-3 (10 ng/mL; Peprotech), and KCl (10mM); iPSC Kosik Lab: neurobasal media supplemented with N2, B27 and neurotrophic factor cocktail that included NT3, BDNF, and GDNF; iPSC Gage Lab: DMEM/F12, N2, BDNF/GDNF, and laminin. phNPC: Neurobasal A (Invitrogen) supplemented with 10% BIT (Stem Cell Technologies), Antibiotics and Antimycotics (Gibco), GlutaMAX (Gibco), and Heparin (1 μg/mL; Sigma)] with freshly added EGF, FGF2, PDGF (each at 20 ng/mL; Peprotech), and LIF (2 ng/mL; Millipore); iPSC Kosik Lab: N2 induction media with bFGF; iPSC Gage Lab: DMEM/F12; 1X N2; 1X B27 and FGF2 total RNA phNPCs: RNA was isolated using TRIzol reagent (Invitrogen) according to standard protocols; iPSC Kosik Lab: RNA was extracted using miRVANA kit, following the manufacturer’s protocol for total RNA; iPSC Gage Lab: Total cellular RNA was extracted using the RNeasy Protect Mini kit (QIAGEN, Valencia, CA). biotin Biotin Illumina protocol Illumina protocol phNPC from Geschwind Lab Donor: 8 Region: 49 DiffWk: 8 Replicate: 1 Passage: 6 Log2 normalization, quantile normalization, and ComBat batch correction NONE ID_REF VALUE Log2 normalization, quantile normalization, and ComBat batch correction Detection Pval GSM1385257-tbl-1.txt 2014-05-12 2014-06-01 2014-06-01 GSM1385258 RNA 1 Human fetal tissue Homo sapiens 6 21 phNPC from Geschwind Lab 12 5 8.1 18 MEX M 7 phNPC: Neurobasal A (Invitrogen) supplemented with B27 (Gibco), GlutaMAX (Gibco), and Antibiotics and Antimycotics (Gibco)] as well as Retinoic Acid (500 ng/mL; Sigma), Forskolin (100 μM; Sigma), BDNF (10 ng/mL; Peprotech), NT-3 (10 ng/mL; Peprotech), and KCl (10mM); iPSC Kosik Lab: neurobasal media supplemented with N2, B27 and neurotrophic factor cocktail that included NT3, BDNF, and GDNF; iPSC Gage Lab: DMEM/F12, N2, BDNF/GDNF, and laminin. phNPC: Neurobasal A (Invitrogen) supplemented with 10% BIT (Stem Cell Technologies), Antibiotics and Antimycotics (Gibco), GlutaMAX (Gibco), and Heparin (1 μg/mL; Sigma)] with freshly added EGF, FGF2, PDGF (each at 20 ng/mL; Peprotech), and LIF (2 ng/mL; Millipore); iPSC Kosik Lab: N2 induction media with bFGF; iPSC Gage Lab: DMEM/F12; 1X N2; 1X B27 and FGF2 total RNA phNPCs: RNA was isolated using TRIzol reagent (Invitrogen) according to standard protocols; iPSC Kosik Lab: RNA was extracted using miRVANA kit, following the manufacturer’s protocol for total RNA; iPSC Gage Lab: Total cellular RNA was extracted using the RNeasy Protect Mini kit (QIAGEN, Valencia, CA). biotin Biotin Illumina protocol Illumina protocol phNPC from Geschwind Lab Donor: 6 Region: 21 DiffWk: 12 Replicate: 2 Passage: 5 Log2 normalization, quantile normalization, and ComBat batch correction NONE ID_REF VALUE Log2 normalization, quantile normalization, and ComBat batch correction Detection Pval GSM1385258-tbl-1.txt 2014-05-12 2014-06-01 2014-06-01 GSM1385259 RNA 1 Human fetal tissue Homo sapiens 8 43 phNPC from Geschwind Lab 12 6 8.5 18 ASW M 7 phNPC: Neurobasal A (Invitrogen) supplemented with B27 (Gibco), GlutaMAX (Gibco), and Antibiotics and Antimycotics (Gibco)] as well as Retinoic Acid (500 ng/mL; Sigma), Forskolin (100 μM; Sigma), BDNF (10 ng/mL; Peprotech), NT-3 (10 ng/mL; Peprotech), and KCl (10mM); iPSC Kosik Lab: neurobasal media supplemented with N2, B27 and neurotrophic factor cocktail that included NT3, BDNF, and GDNF; iPSC Gage Lab: DMEM/F12, N2, BDNF/GDNF, and laminin. phNPC: Neurobasal A (Invitrogen) supplemented with 10% BIT (Stem Cell Technologies), Antibiotics and Antimycotics (Gibco), GlutaMAX (Gibco), and Heparin (1 μg/mL; Sigma)] with freshly added EGF, FGF2, PDGF (each at 20 ng/mL; Peprotech), and LIF (2 ng/mL; Millipore); iPSC Kosik Lab: N2 induction media with bFGF; iPSC Gage Lab: DMEM/F12; 1X N2; 1X B27 and FGF2 total RNA phNPCs: RNA was isolated using TRIzol reagent (Invitrogen) according to standard protocols; iPSC Kosik Lab: RNA was extracted using miRVANA kit, following the manufacturer’s protocol for total RNA; iPSC Gage Lab: Total cellular RNA was extracted using the RNeasy Protect Mini kit (QIAGEN, Valencia, CA). biotin Biotin Illumina protocol Illumina protocol phNPC from Geschwind Lab Donor: 8 Region: 43 DiffWk: 12 Replicate: 2 Passage: 6 Log2 normalization, quantile normalization, and ComBat batch correction NONE ID_REF VALUE Log2 normalization, quantile normalization, and ComBat batch correction Detection Pval GSM1385259-tbl-1.txt 2014-05-12 2014-06-01 2014-06-01 GSM1385260 RNA 1 Human fetal tissue Homo sapiens 5 17 phNPC from Geschwind Lab 1 10 9.8 17 MEX F 7 phNPC: Neurobasal A (Invitrogen) supplemented with B27 (Gibco), GlutaMAX (Gibco), and Antibiotics and Antimycotics (Gibco)] as well as Retinoic Acid (500 ng/mL; Sigma), Forskolin (100 μM; Sigma), BDNF (10 ng/mL; Peprotech), NT-3 (10 ng/mL; Peprotech), and KCl (10mM); iPSC Kosik Lab: neurobasal media supplemented with N2, B27 and neurotrophic factor cocktail that included NT3, BDNF, and GDNF; iPSC Gage Lab: DMEM/F12, N2, BDNF/GDNF, and laminin. phNPC: Neurobasal A (Invitrogen) supplemented with 10% BIT (Stem Cell Technologies), Antibiotics and Antimycotics (Gibco), GlutaMAX (Gibco), and Heparin (1 μg/mL; Sigma)] with freshly added EGF, FGF2, PDGF (each at 20 ng/mL; Peprotech), and LIF (2 ng/mL; Millipore); iPSC Kosik Lab: N2 induction media with bFGF; iPSC Gage Lab: DMEM/F12; 1X N2; 1X B27 and FGF2 total RNA phNPCs: RNA was isolated using TRIzol reagent (Invitrogen) according to standard protocols; iPSC Kosik Lab: RNA was extracted using miRVANA kit, following the manufacturer’s protocol for total RNA; iPSC Gage Lab: Total cellular RNA was extracted using the RNeasy Protect Mini kit (QIAGEN, Valencia, CA). biotin Biotin Illumina protocol Illumina protocol phNPC from Geschwind Lab Donor: 5 Region: 17 DiffWk: 1 Replicate: 1 Passage: 10 Log2 normalization, quantile normalization, and ComBat batch correction NONE ID_REF VALUE Log2 normalization, quantile normalization, and ComBat batch correction Detection Pval GSM1385260-tbl-1.txt 2014-05-12 2014-06-01 2014-06-01 GSM1385261 RNA 1 Human fetal tissue Homo sapiens 8 49 phNPC from Geschwind Lab 4 5 9.3 18 ASW M 8 phNPC: Neurobasal A (Invitrogen) supplemented with B27 (Gibco), GlutaMAX (Gibco), and Antibiotics and Antimycotics (Gibco)] as well as Retinoic Acid (500 ng/mL; Sigma), Forskolin (100 μM; Sigma), BDNF (10 ng/mL; Peprotech), NT-3 (10 ng/mL; Peprotech), and KCl (10mM); iPSC Kosik Lab: neurobasal media supplemented with N2, B27 and neurotrophic factor cocktail that included NT3, BDNF, and GDNF; iPSC Gage Lab: DMEM/F12, N2, BDNF/GDNF, and laminin. phNPC: Neurobasal A (Invitrogen) supplemented with 10% BIT (Stem Cell Technologies), Antibiotics and Antimycotics (Gibco), GlutaMAX (Gibco), and Heparin (1 μg/mL; Sigma)] with freshly added EGF, FGF2, PDGF (each at 20 ng/mL; Peprotech), and LIF (2 ng/mL; Millipore); iPSC Kosik Lab: N2 induction media with bFGF; iPSC Gage Lab: DMEM/F12; 1X N2; 1X B27 and FGF2 total RNA phNPCs: RNA was isolated using TRIzol reagent (Invitrogen) according to standard protocols; iPSC Kosik Lab: RNA was extracted using miRVANA kit, following the manufacturer’s protocol for total RNA; iPSC Gage Lab: Total cellular RNA was extracted using the RNeasy Protect Mini kit (QIAGEN, Valencia, CA). biotin Biotin Illumina protocol Illumina protocol phNPC from Geschwind Lab Donor: 8 Region: 49 DiffWk: 4 Replicate: 2 Passage: 5 Log2 normalization, quantile normalization, and ComBat batch correction NONE ID_REF VALUE Log2 normalization, quantile normalization, and ComBat batch correction Detection Pval GSM1385261-tbl-1.txt 2014-05-12 2014-06-01 2014-06-01 GSM1385262 RNA 1 Human fetal tissue Homo sapiens 5 17 phNPC from Geschwind Lab 4 10 9.4 17 MEX F 8 phNPC: Neurobasal A (Invitrogen) supplemented with B27 (Gibco), GlutaMAX (Gibco), and Antibiotics and Antimycotics (Gibco)] as well as Retinoic Acid (500 ng/mL; Sigma), Forskolin (100 μM; Sigma), BDNF (10 ng/mL; Peprotech), NT-3 (10 ng/mL; Peprotech), and KCl (10mM); iPSC Kosik Lab: neurobasal media supplemented with N2, B27 and neurotrophic factor cocktail that included NT3, BDNF, and GDNF; iPSC Gage Lab: DMEM/F12, N2, BDNF/GDNF, and laminin. phNPC: Neurobasal A (Invitrogen) supplemented with 10% BIT (Stem Cell Technologies), Antibiotics and Antimycotics (Gibco), GlutaMAX (Gibco), and Heparin (1 μg/mL; Sigma)] with freshly added EGF, FGF2, PDGF (each at 20 ng/mL; Peprotech), and LIF (2 ng/mL; Millipore); iPSC Kosik Lab: N2 induction media with bFGF; iPSC Gage Lab: DMEM/F12; 1X N2; 1X B27 and FGF2 total RNA phNPCs: RNA was isolated using TRIzol reagent (Invitrogen) according to standard protocols; iPSC Kosik Lab: RNA was extracted using miRVANA kit, following the manufacturer’s protocol for total RNA; iPSC Gage Lab: Total cellular RNA was extracted using the RNeasy Protect Mini kit (QIAGEN, Valencia, CA). biotin Biotin Illumina protocol Illumina protocol phNPC from Geschwind Lab Donor: 5 Region: 17 DiffWk: 4 Replicate: 1 Passage: 10 Log2 normalization, quantile normalization, and ComBat batch correction NONE ID_REF VALUE Log2 normalization, quantile normalization, and ComBat batch correction Detection Pval GSM1385262-tbl-1.txt 2014-05-12 2014-06-01 2014-06-01 GSM1385263 RNA 1 Human fetal tissue Homo sapiens 6 21 phNPC from Geschwind Lab 1 6 9.6 18 MEX M 8 phNPC: Neurobasal A (Invitrogen) supplemented with B27 (Gibco), GlutaMAX (Gibco), and Antibiotics and Antimycotics (Gibco)] as well as Retinoic Acid (500 ng/mL; Sigma), Forskolin (100 μM; Sigma), BDNF (10 ng/mL; Peprotech), NT-3 (10 ng/mL; Peprotech), and KCl (10mM); iPSC Kosik Lab: neurobasal media supplemented with N2, B27 and neurotrophic factor cocktail that included NT3, BDNF, and GDNF; iPSC Gage Lab: DMEM/F12, N2, BDNF/GDNF, and laminin. phNPC: Neurobasal A (Invitrogen) supplemented with 10% BIT (Stem Cell Technologies), Antibiotics and Antimycotics (Gibco), GlutaMAX (Gibco), and Heparin (1 μg/mL; Sigma)] with freshly added EGF, FGF2, PDGF (each at 20 ng/mL; Peprotech), and LIF (2 ng/mL; Millipore); iPSC Kosik Lab: N2 induction media with bFGF; iPSC Gage Lab: DMEM/F12; 1X N2; 1X B27 and FGF2 total RNA phNPCs: RNA was isolated using TRIzol reagent (Invitrogen) according to standard protocols; iPSC Kosik Lab: RNA was extracted using miRVANA kit, following the manufacturer’s protocol for total RNA; iPSC Gage Lab: Total cellular RNA was extracted using the RNeasy Protect Mini kit (QIAGEN, Valencia, CA). biotin Biotin Illumina protocol Illumina protocol phNPC from Geschwind Lab Donor: 6 Region: 21 DiffWk: 1 Replicate: 1 Passage: 6 Log2 normalization, quantile normalization, and ComBat batch correction NONE ID_REF VALUE Log2 normalization, quantile normalization, and ComBat batch correction Detection Pval GSM1385263-tbl-1.txt 2014-05-12 2014-06-01 2014-06-01 GSM1385264 RNA 1 Human fetal tissue Homo sapiens 8 43 phNPC from Geschwind Lab 8 7 9.8 18 ASW M 9 phNPC: Neurobasal A (Invitrogen) supplemented with B27 (Gibco), GlutaMAX (Gibco), and Antibiotics and Antimycotics (Gibco)] as well as Retinoic Acid (500 ng/mL; Sigma), Forskolin (100 μM; Sigma), BDNF (10 ng/mL; Peprotech), NT-3 (10 ng/mL; Peprotech), and KCl (10mM); iPSC Kosik Lab: neurobasal media supplemented with N2, B27 and neurotrophic factor cocktail that included NT3, BDNF, and GDNF; iPSC Gage Lab: DMEM/F12, N2, BDNF/GDNF, and laminin. phNPC: Neurobasal A (Invitrogen) supplemented with 10% BIT (Stem Cell Technologies), Antibiotics and Antimycotics (Gibco), GlutaMAX (Gibco), and Heparin (1 μg/mL; Sigma)] with freshly added EGF, FGF2, PDGF (each at 20 ng/mL; Peprotech), and LIF (2 ng/mL; Millipore); iPSC Kosik Lab: N2 induction media with bFGF; iPSC Gage Lab: DMEM/F12; 1X N2; 1X B27 and FGF2 total RNA phNPCs: RNA was isolated using TRIzol reagent (Invitrogen) according to standard protocols; iPSC Kosik Lab: RNA was extracted using miRVANA kit, following the manufacturer’s protocol for total RNA; iPSC Gage Lab: Total cellular RNA was extracted using the RNeasy Protect Mini kit (QIAGEN, Valencia, CA). biotin Biotin Illumina protocol Illumina protocol phNPC from Geschwind Lab Donor: 8 Region: 43 DiffWk: 8 Replicate: 2 Passage: 7 Log2 normalization, quantile normalization, and ComBat batch correction NONE ID_REF VALUE Log2 normalization, quantile normalization, and ComBat batch correction Detection Pval GSM1385264-tbl-1.txt 2014-05-12 2014-06-01 2014-06-01 GSM1385265 RNA 1 Human fetal tissue Homo sapiens 8 49 phNPC from Geschwind Lab 8 6 8.6 18 ASW M 9 phNPC: Neurobasal A (Invitrogen) supplemented with B27 (Gibco), GlutaMAX (Gibco), and Antibiotics and Antimycotics (Gibco)] as well as Retinoic Acid (500 ng/mL; Sigma), Forskolin (100 μM; Sigma), BDNF (10 ng/mL; Peprotech), NT-3 (10 ng/mL; Peprotech), and KCl (10mM); iPSC Kosik Lab: neurobasal media supplemented with N2, B27 and neurotrophic factor cocktail that included NT3, BDNF, and GDNF; iPSC Gage Lab: DMEM/F12, N2, BDNF/GDNF, and laminin. phNPC: Neurobasal A (Invitrogen) supplemented with 10% BIT (Stem Cell Technologies), Antibiotics and Antimycotics (Gibco), GlutaMAX (Gibco), and Heparin (1 μg/mL; Sigma)] with freshly added EGF, FGF2, PDGF (each at 20 ng/mL; Peprotech), and LIF (2 ng/mL; Millipore); iPSC Kosik Lab: N2 induction media with bFGF; iPSC Gage Lab: DMEM/F12; 1X N2; 1X B27 and FGF2 total RNA phNPCs: RNA was isolated using TRIzol reagent (Invitrogen) according to standard protocols; iPSC Kosik Lab: RNA was extracted using miRVANA kit, following the manufacturer’s protocol for total RNA; iPSC Gage Lab: Total cellular RNA was extracted using the RNeasy Protect Mini kit (QIAGEN, Valencia, CA). biotin Biotin Illumina protocol Illumina protocol phNPC from Geschwind Lab Donor: 8 Region: 49 DiffWk: 8 Replicate: 2 Passage: 6 Log2 normalization, quantile normalization, and ComBat batch correction NONE ID_REF VALUE Log2 normalization, quantile normalization, and ComBat batch correction Detection Pval GSM1385265-tbl-1.txt 2014-05-12 2014-06-01 2014-06-01 GSM1385266 RNA 1 Human fetal tissue Homo sapiens 8 46 phNPC from Geschwind Lab 8 5 9.5 18 ASW M 9 phNPC: Neurobasal A (Invitrogen) supplemented with B27 (Gibco), GlutaMAX (Gibco), and Antibiotics and Antimycotics (Gibco)] as well as Retinoic Acid (500 ng/mL; Sigma), Forskolin (100 μM; Sigma), BDNF (10 ng/mL; Peprotech), NT-3 (10 ng/mL; Peprotech), and KCl (10mM); iPSC Kosik Lab: neurobasal media supplemented with N2, B27 and neurotrophic factor cocktail that included NT3, BDNF, and GDNF; iPSC Gage Lab: DMEM/F12, N2, BDNF/GDNF, and laminin. phNPC: Neurobasal A (Invitrogen) supplemented with 10% BIT (Stem Cell Technologies), Antibiotics and Antimycotics (Gibco), GlutaMAX (Gibco), and Heparin (1 μg/mL; Sigma)] with freshly added EGF, FGF2, PDGF (each at 20 ng/mL; Peprotech), and LIF (2 ng/mL; Millipore); iPSC Kosik Lab: N2 induction media with bFGF; iPSC Gage Lab: DMEM/F12; 1X N2; 1X B27 and FGF2 total RNA phNPCs: RNA was isolated using TRIzol reagent (Invitrogen) according to standard protocols; iPSC Kosik Lab: RNA was extracted using miRVANA kit, following the manufacturer’s protocol for total RNA; iPSC Gage Lab: Total cellular RNA was extracted using the RNeasy Protect Mini kit (QIAGEN, Valencia, CA). biotin Biotin Illumina protocol Illumina protocol phNPC from Geschwind Lab Donor: 8 Region: 46 DiffWk: 8 Replicate: 1 Passage: 5 Log2 normalization, quantile normalization, and ComBat batch correction NONE ID_REF VALUE Log2 normalization, quantile normalization, and ComBat batch correction Detection Pval GSM1385266-tbl-1.txt 2014-05-12 2014-06-01 2014-06-01 GSM1385267 RNA 1 Human fetal tissue Homo sapiens 5 17 phNPC from Geschwind Lab 8 10 9.2 17 MEX F 9 phNPC: Neurobasal A (Invitrogen) supplemented with B27 (Gibco), GlutaMAX (Gibco), and Antibiotics and Antimycotics (Gibco)] as well as Retinoic Acid (500 ng/mL; Sigma), Forskolin (100 μM; Sigma), BDNF (10 ng/mL; Peprotech), NT-3 (10 ng/mL; Peprotech), and KCl (10mM); iPSC Kosik Lab: neurobasal media supplemented with N2, B27 and neurotrophic factor cocktail that included NT3, BDNF, and GDNF; iPSC Gage Lab: DMEM/F12, N2, BDNF/GDNF, and laminin. phNPC: Neurobasal A (Invitrogen) supplemented with 10% BIT (Stem Cell Technologies), Antibiotics and Antimycotics (Gibco), GlutaMAX (Gibco), and Heparin (1 μg/mL; Sigma)] with freshly added EGF, FGF2, PDGF (each at 20 ng/mL; Peprotech), and LIF (2 ng/mL; Millipore); iPSC Kosik Lab: N2 induction media with bFGF; iPSC Gage Lab: DMEM/F12; 1X N2; 1X B27 and FGF2 total RNA phNPCs: RNA was isolated using TRIzol reagent (Invitrogen) according to standard protocols; iPSC Kosik Lab: RNA was extracted using miRVANA kit, following the manufacturer’s protocol for total RNA; iPSC Gage Lab: Total cellular RNA was extracted using the RNeasy Protect Mini kit (QIAGEN, Valencia, CA). biotin Biotin Illumina protocol Illumina protocol phNPC from Geschwind Lab Donor: 5 Region: 17 DiffWk: 8 Replicate: 2 Passage: 10 Log2 normalization, quantile normalization, and ComBat batch correction NONE ID_REF VALUE Log2 normalization, quantile normalization, and ComBat batch correction Detection Pval GSM1385267-tbl-1.txt 2014-05-12 2014-06-01 2014-06-01 GSM1385268 RNA 1 Human fetal tissue Homo sapiens 5 17 phNPC from Geschwind Lab 4 10 9.4 17 MEX F 10 phNPC: Neurobasal A (Invitrogen) supplemented with B27 (Gibco), GlutaMAX (Gibco), and Antibiotics and Antimycotics (Gibco)] as well as Retinoic Acid (500 ng/mL; Sigma), Forskolin (100 μM; Sigma), BDNF (10 ng/mL; Peprotech), NT-3 (10 ng/mL; Peprotech), and KCl (10mM); iPSC Kosik Lab: neurobasal media supplemented with N2, B27 and neurotrophic factor cocktail that included NT3, BDNF, and GDNF; iPSC Gage Lab: DMEM/F12, N2, BDNF/GDNF, and laminin. phNPC: Neurobasal A (Invitrogen) supplemented with 10% BIT (Stem Cell Technologies), Antibiotics and Antimycotics (Gibco), GlutaMAX (Gibco), and Heparin (1 μg/mL; Sigma)] with freshly added EGF, FGF2, PDGF (each at 20 ng/mL; Peprotech), and LIF (2 ng/mL; Millipore); iPSC Kosik Lab: N2 induction media with bFGF; iPSC Gage Lab: DMEM/F12; 1X N2; 1X B27 and FGF2 total RNA phNPCs: RNA was isolated using TRIzol reagent (Invitrogen) according to standard protocols; iPSC Kosik Lab: RNA was extracted using miRVANA kit, following the manufacturer’s protocol for total RNA; iPSC Gage Lab: Total cellular RNA was extracted using the RNeasy Protect Mini kit (QIAGEN, Valencia, CA). biotin Biotin Illumina protocol Illumina protocol phNPC from Geschwind Lab Donor: 5 Region: 17 DiffWk: 4 Replicate: 2 Passage: 10 Log2 normalization, quantile normalization, and ComBat batch correction NONE ID_REF VALUE Log2 normalization, quantile normalization, and ComBat batch correction Detection Pval GSM1385268-tbl-1.txt 2014-05-12 2014-06-01 2014-06-01 GSM1385269 RNA 1 Human fetal tissue Homo sapiens 5 17 phNPC from Geschwind Lab 8 10 9.3 17 MEX F 10 phNPC: Neurobasal A (Invitrogen) supplemented with B27 (Gibco), GlutaMAX (Gibco), and Antibiotics and Antimycotics (Gibco)] as well as Retinoic Acid (500 ng/mL; Sigma), Forskolin (100 μM; Sigma), BDNF (10 ng/mL; Peprotech), NT-3 (10 ng/mL; Peprotech), and KCl (10mM); iPSC Kosik Lab: neurobasal media supplemented with N2, B27 and neurotrophic factor cocktail that included NT3, BDNF, and GDNF; iPSC Gage Lab: DMEM/F12, N2, BDNF/GDNF, and laminin. phNPC: Neurobasal A (Invitrogen) supplemented with 10% BIT (Stem Cell Technologies), Antibiotics and Antimycotics (Gibco), GlutaMAX (Gibco), and Heparin (1 μg/mL; Sigma)] with freshly added EGF, FGF2, PDGF (each at 20 ng/mL; Peprotech), and LIF (2 ng/mL; Millipore); iPSC Kosik Lab: N2 induction media with bFGF; iPSC Gage Lab: DMEM/F12; 1X N2; 1X B27 and FGF2 total RNA phNPCs: RNA was isolated using TRIzol reagent (Invitrogen) according to standard protocols; iPSC Kosik Lab: RNA was extracted using miRVANA kit, following the manufacturer’s protocol for total RNA; iPSC Gage Lab: Total cellular RNA was extracted using the RNeasy Protect Mini kit (QIAGEN, Valencia, CA). biotin Biotin Illumina protocol Illumina protocol phNPC from Geschwind Lab Donor: 5 Region: 17 DiffWk: 8 Replicate: 1 Passage: 10 Log2 normalization, quantile normalization, and ComBat batch correction NONE ID_REF VALUE Log2 normalization, quantile normalization, and ComBat batch correction Detection Pval GSM1385269-tbl-1.txt 2014-05-12 2014-06-01 2014-06-01 GSM1385270 RNA 1 Human fetal tissue Homo sapiens 5 17 phNPC from Geschwind Lab 8 9 8.2 17 MEX F 11 phNPC: Neurobasal A (Invitrogen) supplemented with B27 (Gibco), GlutaMAX (Gibco), and Antibiotics and Antimycotics (Gibco)] as well as Retinoic Acid (500 ng/mL; Sigma), Forskolin (100 μM; Sigma), BDNF (10 ng/mL; Peprotech), NT-3 (10 ng/mL; Peprotech), and KCl (10mM); iPSC Kosik Lab: neurobasal media supplemented with N2, B27 and neurotrophic factor cocktail that included NT3, BDNF, and GDNF; iPSC Gage Lab: DMEM/F12, N2, BDNF/GDNF, and laminin. phNPC: Neurobasal A (Invitrogen) supplemented with 10% BIT (Stem Cell Technologies), Antibiotics and Antimycotics (Gibco), GlutaMAX (Gibco), and Heparin (1 μg/mL; Sigma)] with freshly added EGF, FGF2, PDGF (each at 20 ng/mL; Peprotech), and LIF (2 ng/mL; Millipore); iPSC Kosik Lab: N2 induction media with bFGF; iPSC Gage Lab: DMEM/F12; 1X N2; 1X B27 and FGF2 total RNA phNPCs: RNA was isolated using TRIzol reagent (Invitrogen) according to standard protocols; iPSC Kosik Lab: RNA was extracted using miRVANA kit, following the manufacturer’s protocol for total RNA; iPSC Gage Lab: Total cellular RNA was extracted using the RNeasy Protect Mini kit (QIAGEN, Valencia, CA). biotin Biotin Illumina protocol Illumina protocol phNPC from Geschwind Lab Donor: 5 Region: 17 DiffWk: 8 Replicate: 1 Passage: 9 Log2 normalization, quantile normalization, and ComBat batch correction NONE ID_REF VALUE Log2 normalization, quantile normalization, and ComBat batch correction Detection Pval GSM1385270-tbl-1.txt 2014-05-12 2014-06-01 2014-06-01 GSM1385271 RNA 1 Human fetal tissue Homo sapiens 8 46 phNPC from Geschwind Lab 4 5 10 18 ASW M 11 phNPC: Neurobasal A (Invitrogen) supplemented with B27 (Gibco), GlutaMAX (Gibco), and Antibiotics and Antimycotics (Gibco)] as well as Retinoic Acid (500 ng/mL; Sigma), Forskolin (100 μM; Sigma), BDNF (10 ng/mL; Peprotech), NT-3 (10 ng/mL; Peprotech), and KCl (10mM); iPSC Kosik Lab: neurobasal media supplemented with N2, B27 and neurotrophic factor cocktail that included NT3, BDNF, and GDNF; iPSC Gage Lab: DMEM/F12, N2, BDNF/GDNF, and laminin. phNPC: Neurobasal A (Invitrogen) supplemented with 10% BIT (Stem Cell Technologies), Antibiotics and Antimycotics (Gibco), GlutaMAX (Gibco), and Heparin (1 μg/mL; Sigma)] with freshly added EGF, FGF2, PDGF (each at 20 ng/mL; Peprotech), and LIF (2 ng/mL; Millipore); iPSC Kosik Lab: N2 induction media with bFGF; iPSC Gage Lab: DMEM/F12; 1X N2; 1X B27 and FGF2 total RNA phNPCs: RNA was isolated using TRIzol reagent (Invitrogen) according to standard protocols; iPSC Kosik Lab: RNA was extracted using miRVANA kit, following the manufacturer’s protocol for total RNA; iPSC Gage Lab: Total cellular RNA was extracted using the RNeasy Protect Mini kit (QIAGEN, Valencia, CA). biotin Biotin Illumina protocol Illumina protocol phNPC from Geschwind Lab Donor: 8 Region: 46 DiffWk: 4 Replicate: 2 Passage: 5 Log2 normalization, quantile normalization, and ComBat batch correction NONE ID_REF VALUE Log2 normalization, quantile normalization, and ComBat batch correction Detection Pval GSM1385271-tbl-1.txt 2014-05-12 2014-06-01 2014-06-01 GSM1385272 RNA 1 Human fetal tissue Homo sapiens 5 17 phNPC from Geschwind Lab 12 9 7.5 17 MEX F 11 phNPC: Neurobasal A (Invitrogen) supplemented with B27 (Gibco), GlutaMAX (Gibco), and Antibiotics and Antimycotics (Gibco)] as well as Retinoic Acid (500 ng/mL; Sigma), Forskolin (100 μM; Sigma), BDNF (10 ng/mL; Peprotech), NT-3 (10 ng/mL; Peprotech), and KCl (10mM); iPSC Kosik Lab: neurobasal media supplemented with N2, B27 and neurotrophic factor cocktail that included NT3, BDNF, and GDNF; iPSC Gage Lab: DMEM/F12, N2, BDNF/GDNF, and laminin. phNPC: Neurobasal A (Invitrogen) supplemented with 10% BIT (Stem Cell Technologies), Antibiotics and Antimycotics (Gibco), GlutaMAX (Gibco), and Heparin (1 μg/mL; Sigma)] with freshly added EGF, FGF2, PDGF (each at 20 ng/mL; Peprotech), and LIF (2 ng/mL; Millipore); iPSC Kosik Lab: N2 induction media with bFGF; iPSC Gage Lab: DMEM/F12; 1X N2; 1X B27 and FGF2 total RNA phNPCs: RNA was isolated using TRIzol reagent (Invitrogen) according to standard protocols; iPSC Kosik Lab: RNA was extracted using miRVANA kit, following the manufacturer’s protocol for total RNA; iPSC Gage Lab: Total cellular RNA was extracted using the RNeasy Protect Mini kit (QIAGEN, Valencia, CA). biotin Biotin Illumina protocol Illumina protocol phNPC from Geschwind Lab Donor: 5 Region: 17 DiffWk: 12 Replicate: 2 Passage: 9 Log2 normalization, quantile normalization, and ComBat batch correction NONE ID_REF VALUE Log2 normalization, quantile normalization, and ComBat batch correction Detection Pval GSM1385272-tbl-1.txt 2014-05-12 2014-06-01 2014-06-01 GSM1385273 RNA 1 Human fetal tissue Homo sapiens 8 46 phNPC from Geschwind Lab 1 5 9.7 18 ASW M 11 phNPC: Neurobasal A (Invitrogen) supplemented with B27 (Gibco), GlutaMAX (Gibco), and Antibiotics and Antimycotics (Gibco)] as well as Retinoic Acid (500 ng/mL; Sigma), Forskolin (100 μM; Sigma), BDNF (10 ng/mL; Peprotech), NT-3 (10 ng/mL; Peprotech), and KCl (10mM); iPSC Kosik Lab: neurobasal media supplemented with N2, B27 and neurotrophic factor cocktail that included NT3, BDNF, and GDNF; iPSC Gage Lab: DMEM/F12, N2, BDNF/GDNF, and laminin. phNPC: Neurobasal A (Invitrogen) supplemented with 10% BIT (Stem Cell Technologies), Antibiotics and Antimycotics (Gibco), GlutaMAX (Gibco), and Heparin (1 μg/mL; Sigma)] with freshly added EGF, FGF2, PDGF (each at 20 ng/mL; Peprotech), and LIF (2 ng/mL; Millipore); iPSC Kosik Lab: N2 induction media with bFGF; iPSC Gage Lab: DMEM/F12; 1X N2; 1X B27 and FGF2 total RNA phNPCs: RNA was isolated using TRIzol reagent (Invitrogen) according to standard protocols; iPSC Kosik Lab: RNA was extracted using miRVANA kit, following the manufacturer’s protocol for total RNA; iPSC Gage Lab: Total cellular RNA was extracted using the RNeasy Protect Mini kit (QIAGEN, Valencia, CA). biotin Biotin Illumina protocol Illumina protocol phNPC from Geschwind Lab Donor: 8 Region: 46 DiffWk: 1 Replicate: 1 Passage: 5 Log2 normalization, quantile normalization, and ComBat batch correction NONE ID_REF VALUE Log2 normalization, quantile normalization, and ComBat batch correction Detection Pval GSM1385273-tbl-1.txt 2014-05-12 2014-06-01 2014-06-01 GSM1385274 RNA 1 Human fetal tissue Homo sapiens 6 21 phNPC from Geschwind Lab 4 5 9 18 MEX M 11 phNPC: Neurobasal A (Invitrogen) supplemented with B27 (Gibco), GlutaMAX (Gibco), and Antibiotics and Antimycotics (Gibco)] as well as Retinoic Acid (500 ng/mL; Sigma), Forskolin (100 μM; Sigma), BDNF (10 ng/mL; Peprotech), NT-3 (10 ng/mL; Peprotech), and KCl (10mM); iPSC Kosik Lab: neurobasal media supplemented with N2, B27 and neurotrophic factor cocktail that included NT3, BDNF, and GDNF; iPSC Gage Lab: DMEM/F12, N2, BDNF/GDNF, and laminin. phNPC: Neurobasal A (Invitrogen) supplemented with 10% BIT (Stem Cell Technologies), Antibiotics and Antimycotics (Gibco), GlutaMAX (Gibco), and Heparin (1 μg/mL; Sigma)] with freshly added EGF, FGF2, PDGF (each at 20 ng/mL; Peprotech), and LIF (2 ng/mL; Millipore); iPSC Kosik Lab: N2 induction media with bFGF; iPSC Gage Lab: DMEM/F12; 1X N2; 1X B27 and FGF2 total RNA phNPCs: RNA was isolated using TRIzol reagent (Invitrogen) according to standard protocols; iPSC Kosik Lab: RNA was extracted using miRVANA kit, following the manufacturer’s protocol for total RNA; iPSC Gage Lab: Total cellular RNA was extracted using the RNeasy Protect Mini kit (QIAGEN, Valencia, CA). biotin Biotin Illumina protocol Illumina protocol phNPC from Geschwind Lab Donor: 6 Region: 21 DiffWk: 4 Replicate: 1 Passage: 5 Log2 normalization, quantile normalization, and ComBat batch correction NONE ID_REF VALUE Log2 normalization, quantile normalization, and ComBat batch correction Detection Pval GSM1385274-tbl-1.txt 2014-05-12 2014-06-01 2014-06-01 GSM1385275 RNA 1 Human fetal tissue Homo sapiens 6 21 phNPC from Geschwind Lab 1 6 10 18 MEX M 11 phNPC: Neurobasal A (Invitrogen) supplemented with B27 (Gibco), GlutaMAX (Gibco), and Antibiotics and Antimycotics (Gibco)] as well as Retinoic Acid (500 ng/mL; Sigma), Forskolin (100 μM; Sigma), BDNF (10 ng/mL; Peprotech), NT-3 (10 ng/mL; Peprotech), and KCl (10mM); iPSC Kosik Lab: neurobasal media supplemented with N2, B27 and neurotrophic factor cocktail that included NT3, BDNF, and GDNF; iPSC Gage Lab: DMEM/F12, N2, BDNF/GDNF, and laminin. phNPC: Neurobasal A (Invitrogen) supplemented with 10% BIT (Stem Cell Technologies), Antibiotics and Antimycotics (Gibco), GlutaMAX (Gibco), and Heparin (1 μg/mL; Sigma)] with freshly added EGF, FGF2, PDGF (each at 20 ng/mL; Peprotech), and LIF (2 ng/mL; Millipore); iPSC Kosik Lab: N2 induction media with bFGF; iPSC Gage Lab: DMEM/F12; 1X N2; 1X B27 and FGF2 total RNA phNPCs: RNA was isolated using TRIzol reagent (Invitrogen) according to standard protocols; iPSC Kosik Lab: RNA was extracted using miRVANA kit, following the manufacturer’s protocol for total RNA; iPSC Gage Lab: Total cellular RNA was extracted using the RNeasy Protect Mini kit (QIAGEN, Valencia, CA). biotin Biotin Illumina protocol Illumina protocol phNPC from Geschwind Lab Donor: 6 Region: 21 DiffWk: 1 Replicate: 2 Passage: 6 Log2 normalization, quantile normalization, and ComBat batch correction NONE ID_REF VALUE Log2 normalization, quantile normalization, and ComBat batch correction Detection Pval GSM1385275-tbl-1.txt 2014-05-12 2014-06-01 2014-06-01 GSM1385276 RNA 1 Human fetal tissue Homo sapiens 8 43 phNPC from Geschwind Lab 12 7 9.5 18 ASW M 11 phNPC: Neurobasal A (Invitrogen) supplemented with B27 (Gibco), GlutaMAX (Gibco), and Antibiotics and Antimycotics (Gibco)] as well as Retinoic Acid (500 ng/mL; Sigma), Forskolin (100 μM; Sigma), BDNF (10 ng/mL; Peprotech), NT-3 (10 ng/mL; Peprotech), and KCl (10mM); iPSC Kosik Lab: neurobasal media supplemented with N2, B27 and neurotrophic factor cocktail that included NT3, BDNF, and GDNF; iPSC Gage Lab: DMEM/F12, N2, BDNF/GDNF, and laminin. phNPC: Neurobasal A (Invitrogen) supplemented with 10% BIT (Stem Cell Technologies), Antibiotics and Antimycotics (Gibco), GlutaMAX (Gibco), and Heparin (1 μg/mL; Sigma)] with freshly added EGF, FGF2, PDGF (each at 20 ng/mL; Peprotech), and LIF (2 ng/mL; Millipore); iPSC Kosik Lab: N2 induction media with bFGF; iPSC Gage Lab: DMEM/F12; 1X N2; 1X B27 and FGF2 total RNA phNPCs: RNA was isolated using TRIzol reagent (Invitrogen) according to standard protocols; iPSC Kosik Lab: RNA was extracted using miRVANA kit, following the manufacturer’s protocol for total RNA; iPSC Gage Lab: Total cellular RNA was extracted using the RNeasy Protect Mini kit (QIAGEN, Valencia, CA). biotin Biotin Illumina protocol Illumina protocol phNPC from Geschwind Lab Donor: 8 Region: 43 DiffWk: 12 Replicate: 1 Passage: 7 Log2 normalization, quantile normalization, and ComBat batch correction NONE ID_REF VALUE Log2 normalization, quantile normalization, and ComBat batch correction Detection Pval GSM1385276-tbl-1.txt 2014-05-12 2014-06-01 2014-06-01 GSM1385277 RNA 1 Human fetal tissue Homo sapiens 8 43 phNPC from Geschwind Lab 12 7 9.1 18 ASW M 11 phNPC: Neurobasal A (Invitrogen) supplemented with B27 (Gibco), GlutaMAX (Gibco), and Antibiotics and Antimycotics (Gibco)] as well as Retinoic Acid (500 ng/mL; Sigma), Forskolin (100 μM; Sigma), BDNF (10 ng/mL; Peprotech), NT-3 (10 ng/mL; Peprotech), and KCl (10mM); iPSC Kosik Lab: neurobasal media supplemented with N2, B27 and neurotrophic factor cocktail that included NT3, BDNF, and GDNF; iPSC Gage Lab: DMEM/F12, N2, BDNF/GDNF, and laminin. phNPC: Neurobasal A (Invitrogen) supplemented with 10% BIT (Stem Cell Technologies), Antibiotics and Antimycotics (Gibco), GlutaMAX (Gibco), and Heparin (1 μg/mL; Sigma)] with freshly added EGF, FGF2, PDGF (each at 20 ng/mL; Peprotech), and LIF (2 ng/mL; Millipore); iPSC Kosik Lab: N2 induction media with bFGF; iPSC Gage Lab: DMEM/F12; 1X N2; 1X B27 and FGF2 total RNA phNPCs: RNA was isolated using TRIzol reagent (Invitrogen) according to standard protocols; iPSC Kosik Lab: RNA was extracted using miRVANA kit, following the manufacturer’s protocol for total RNA; iPSC Gage Lab: Total cellular RNA was extracted using the RNeasy Protect Mini kit (QIAGEN, Valencia, CA). biotin Biotin Illumina protocol Illumina protocol phNPC from Geschwind Lab Donor: 8 Region: 43 DiffWk: 12 Replicate: 2 Passage: 7 Log2 normalization, quantile normalization, and ComBat batch correction NONE ID_REF VALUE Log2 normalization, quantile normalization, and ComBat batch correction Detection Pval GSM1385277-tbl-1.txt 2014-05-12 2014-06-01 2014-06-01 GSM1385278 RNA 1 Human fetal tissue Homo sapiens 8 46 phNPC from Geschwind Lab 8 5 9.4 18 ASW M 11 phNPC: Neurobasal A (Invitrogen) supplemented with B27 (Gibco), GlutaMAX (Gibco), and Antibiotics and Antimycotics (Gibco)] as well as Retinoic Acid (500 ng/mL; Sigma), Forskolin (100 μM; Sigma), BDNF (10 ng/mL; Peprotech), NT-3 (10 ng/mL; Peprotech), and KCl (10mM); iPSC Kosik Lab: neurobasal media supplemented with N2, B27 and neurotrophic factor cocktail that included NT3, BDNF, and GDNF; iPSC Gage Lab: DMEM/F12, N2, BDNF/GDNF, and laminin. phNPC: Neurobasal A (Invitrogen) supplemented with 10% BIT (Stem Cell Technologies), Antibiotics and Antimycotics (Gibco), GlutaMAX (Gibco), and Heparin (1 μg/mL; Sigma)] with freshly added EGF, FGF2, PDGF (each at 20 ng/mL; Peprotech), and LIF (2 ng/mL; Millipore); iPSC Kosik Lab: N2 induction media with bFGF; iPSC Gage Lab: DMEM/F12; 1X N2; 1X B27 and FGF2 total RNA phNPCs: RNA was isolated using TRIzol reagent (Invitrogen) according to standard protocols; iPSC Kosik Lab: RNA was extracted using miRVANA kit, following the manufacturer’s protocol for total RNA; iPSC Gage Lab: Total cellular RNA was extracted using the RNeasy Protect Mini kit (QIAGEN, Valencia, CA). biotin Biotin Illumina protocol Illumina protocol phNPC from Geschwind Lab Donor: 8 Region: 46 DiffWk: 8 Replicate: 2 Passage: 5 Log2 normalization, quantile normalization, and ComBat batch correction NONE ID_REF VALUE Log2 normalization, quantile normalization, and ComBat batch correction Detection Pval GSM1385278-tbl-1.txt 2014-05-12 2014-06-01 2014-06-01 GSM1385279 RNA 1 Human fetal tissue Homo sapiens 8 46 phNPC from Geschwind Lab 12 6 8.5 18 ASW M 12 phNPC: Neurobasal A (Invitrogen) supplemented with B27 (Gibco), GlutaMAX (Gibco), and Antibiotics and Antimycotics (Gibco)] as well as Retinoic Acid (500 ng/mL; Sigma), Forskolin (100 μM; Sigma), BDNF (10 ng/mL; Peprotech), NT-3 (10 ng/mL; Peprotech), and KCl (10mM); iPSC Kosik Lab: neurobasal media supplemented with N2, B27 and neurotrophic factor cocktail that included NT3, BDNF, and GDNF; iPSC Gage Lab: DMEM/F12, N2, BDNF/GDNF, and laminin. phNPC: Neurobasal A (Invitrogen) supplemented with 10% BIT (Stem Cell Technologies), Antibiotics and Antimycotics (Gibco), GlutaMAX (Gibco), and Heparin (1 μg/mL; Sigma)] with freshly added EGF, FGF2, PDGF (each at 20 ng/mL; Peprotech), and LIF (2 ng/mL; Millipore); iPSC Kosik Lab: N2 induction media with bFGF; iPSC Gage Lab: DMEM/F12; 1X N2; 1X B27 and FGF2 total RNA phNPCs: RNA was isolated using TRIzol reagent (Invitrogen) according to standard protocols; iPSC Kosik Lab: RNA was extracted using miRVANA kit, following the manufacturer’s protocol for total RNA; iPSC Gage Lab: Total cellular RNA was extracted using the RNeasy Protect Mini kit (QIAGEN, Valencia, CA). biotin Biotin Illumina protocol Illumina protocol phNPC from Geschwind Lab Donor: 8 Region: 46 DiffWk: 12 Replicate: 1 Passage: 6 Log2 normalization, quantile normalization, and ComBat batch correction NONE ID_REF VALUE Log2 normalization, quantile normalization, and ComBat batch correction Detection Pval GSM1385279-tbl-1.txt 2014-05-12 2014-06-01 2014-06-01 GSM1385280 RNA 1 Human fetal tissue Homo sapiens 8 49 phNPC from Geschwind Lab 1 5 9.6 18 ASW M 12 phNPC: Neurobasal A (Invitrogen) supplemented with B27 (Gibco), GlutaMAX (Gibco), and Antibiotics and Antimycotics (Gibco)] as well as Retinoic Acid (500 ng/mL; Sigma), Forskolin (100 μM; Sigma), BDNF (10 ng/mL; Peprotech), NT-3 (10 ng/mL; Peprotech), and KCl (10mM); iPSC Kosik Lab: neurobasal media supplemented with N2, B27 and neurotrophic factor cocktail that included NT3, BDNF, and GDNF; iPSC Gage Lab: DMEM/F12, N2, BDNF/GDNF, and laminin. phNPC: Neurobasal A (Invitrogen) supplemented with 10% BIT (Stem Cell Technologies), Antibiotics and Antimycotics (Gibco), GlutaMAX (Gibco), and Heparin (1 μg/mL; Sigma)] with freshly added EGF, FGF2, PDGF (each at 20 ng/mL; Peprotech), and LIF (2 ng/mL; Millipore); iPSC Kosik Lab: N2 induction media with bFGF; iPSC Gage Lab: DMEM/F12; 1X N2; 1X B27 and FGF2 total RNA phNPCs: RNA was isolated using TRIzol reagent (Invitrogen) according to standard protocols; iPSC Kosik Lab: RNA was extracted using miRVANA kit, following the manufacturer’s protocol for total RNA; iPSC Gage Lab: Total cellular RNA was extracted using the RNeasy Protect Mini kit (QIAGEN, Valencia, CA). biotin Biotin Illumina protocol Illumina protocol phNPC from Geschwind Lab Donor: 8 Region: 49 DiffWk: 1 Replicate: 2 Passage: 5 Log2 normalization, quantile normalization, and ComBat batch correction NONE ID_REF VALUE Log2 normalization, quantile normalization, and ComBat batch correction Detection Pval GSM1385280-tbl-1.txt 2014-05-12 2014-06-01 2014-06-01 GSM1385281 RNA 1 Human fetal tissue Homo sapiens 8 43 phNPC from Geschwind Lab 1 6 8.4 18 ASW M 12 phNPC: Neurobasal A (Invitrogen) supplemented with B27 (Gibco), GlutaMAX (Gibco), and Antibiotics and Antimycotics (Gibco)] as well as Retinoic Acid (500 ng/mL; Sigma), Forskolin (100 μM; Sigma), BDNF (10 ng/mL; Peprotech), NT-3 (10 ng/mL; Peprotech), and KCl (10mM); iPSC Kosik Lab: neurobasal media supplemented with N2, B27 and neurotrophic factor cocktail that included NT3, BDNF, and GDNF; iPSC Gage Lab: DMEM/F12, N2, BDNF/GDNF, and laminin. phNPC: Neurobasal A (Invitrogen) supplemented with 10% BIT (Stem Cell Technologies), Antibiotics and Antimycotics (Gibco), GlutaMAX (Gibco), and Heparin (1 μg/mL; Sigma)] with freshly added EGF, FGF2, PDGF (each at 20 ng/mL; Peprotech), and LIF (2 ng/mL; Millipore); iPSC Kosik Lab: N2 induction media with bFGF; iPSC Gage Lab: DMEM/F12; 1X N2; 1X B27 and FGF2 total RNA phNPCs: RNA was isolated using TRIzol reagent (Invitrogen) according to standard protocols; iPSC Kosik Lab: RNA was extracted using miRVANA kit, following the manufacturer’s protocol for total RNA; iPSC Gage Lab: Total cellular RNA was extracted using the RNeasy Protect Mini kit (QIAGEN, Valencia, CA). biotin Biotin Illumina protocol Illumina protocol phNPC from Geschwind Lab Donor: 8 Region: 43 DiffWk: 1 Replicate: 2 Passage: 6 Log2 normalization, quantile normalization, and ComBat batch correction NONE ID_REF VALUE Log2 normalization, quantile normalization, and ComBat batch correction Detection Pval GSM1385281-tbl-1.txt 2014-05-12 2014-06-01 2014-06-01 GSM1385282 RNA 1 Human fetal tissue Homo sapiens 8 49 phNPC from Geschwind Lab 12 5 8.9 18 ASW M 13 phNPC: Neurobasal A (Invitrogen) supplemented with B27 (Gibco), GlutaMAX (Gibco), and Antibiotics and Antimycotics (Gibco)] as well as Retinoic Acid (500 ng/mL; Sigma), Forskolin (100 μM; Sigma), BDNF (10 ng/mL; Peprotech), NT-3 (10 ng/mL; Peprotech), and KCl (10mM); iPSC Kosik Lab: neurobasal media supplemented with N2, B27 and neurotrophic factor cocktail that included NT3, BDNF, and GDNF; iPSC Gage Lab: DMEM/F12, N2, BDNF/GDNF, and laminin. phNPC: Neurobasal A (Invitrogen) supplemented with 10% BIT (Stem Cell Technologies), Antibiotics and Antimycotics (Gibco), GlutaMAX (Gibco), and Heparin (1 μg/mL; Sigma)] with freshly added EGF, FGF2, PDGF (each at 20 ng/mL; Peprotech), and LIF (2 ng/mL; Millipore); iPSC Kosik Lab: N2 induction media with bFGF; iPSC Gage Lab: DMEM/F12; 1X N2; 1X B27 and FGF2 total RNA phNPCs: RNA was isolated using TRIzol reagent (Invitrogen) according to standard protocols; iPSC Kosik Lab: RNA was extracted using miRVANA kit, following the manufacturer’s protocol for total RNA; iPSC Gage Lab: Total cellular RNA was extracted using the RNeasy Protect Mini kit (QIAGEN, Valencia, CA). biotin Biotin Illumina protocol Illumina protocol phNPC from Geschwind Lab Donor: 8 Region: 49 DiffWk: 12 Replicate: 2 Passage: 5 Log2 normalization, quantile normalization, and ComBat batch correction NONE ID_REF VALUE Log2 normalization, quantile normalization, and ComBat batch correction Detection Pval GSM1385282-tbl-1.txt 2014-05-12 2014-06-01 2014-06-01 GSM1385283 RNA 1 Human fetal tissue Homo sapiens 8 49 phNPC from Geschwind Lab 4 6 9.5 18 ASW M 13 phNPC: Neurobasal A (Invitrogen) supplemented with B27 (Gibco), GlutaMAX (Gibco), and Antibiotics and Antimycotics (Gibco)] as well as Retinoic Acid (500 ng/mL; Sigma), Forskolin (100 μM; Sigma), BDNF (10 ng/mL; Peprotech), NT-3 (10 ng/mL; Peprotech), and KCl (10mM); iPSC Kosik Lab: neurobasal media supplemented with N2, B27 and neurotrophic factor cocktail that included NT3, BDNF, and GDNF; iPSC Gage Lab: DMEM/F12, N2, BDNF/GDNF, and laminin. phNPC: Neurobasal A (Invitrogen) supplemented with 10% BIT (Stem Cell Technologies), Antibiotics and Antimycotics (Gibco), GlutaMAX (Gibco), and Heparin (1 μg/mL; Sigma)] with freshly added EGF, FGF2, PDGF (each at 20 ng/mL; Peprotech), and LIF (2 ng/mL; Millipore); iPSC Kosik Lab: N2 induction media with bFGF; iPSC Gage Lab: DMEM/F12; 1X N2; 1X B27 and FGF2 total RNA phNPCs: RNA was isolated using TRIzol reagent (Invitrogen) according to standard protocols; iPSC Kosik Lab: RNA was extracted using miRVANA kit, following the manufacturer’s protocol for total RNA; iPSC Gage Lab: Total cellular RNA was extracted using the RNeasy Protect Mini kit (QIAGEN, Valencia, CA). biotin Biotin Illumina protocol Illumina protocol phNPC from Geschwind Lab Donor: 8 Region: 49 DiffWk: 4 Replicate: 1 Passage: 6 Log2 normalization, quantile normalization, and ComBat batch correction NONE ID_REF VALUE Log2 normalization, quantile normalization, and ComBat batch correction Detection Pval GSM1385283-tbl-1.txt 2014-05-12 2014-06-01 2014-06-01 GSM1385284 RNA 1 Human fetal tissue Homo sapiens 8 43 phNPC from Geschwind Lab 4 6 9.6 18 ASW M 13 phNPC: Neurobasal A (Invitrogen) supplemented with B27 (Gibco), GlutaMAX (Gibco), and Antibiotics and Antimycotics (Gibco)] as well as Retinoic Acid (500 ng/mL; Sigma), Forskolin (100 μM; Sigma), BDNF (10 ng/mL; Peprotech), NT-3 (10 ng/mL; Peprotech), and KCl (10mM); iPSC Kosik Lab: neurobasal media supplemented with N2, B27 and neurotrophic factor cocktail that included NT3, BDNF, and GDNF; iPSC Gage Lab: DMEM/F12, N2, BDNF/GDNF, and laminin. phNPC: Neurobasal A (Invitrogen) supplemented with 10% BIT (Stem Cell Technologies), Antibiotics and Antimycotics (Gibco), GlutaMAX (Gibco), and Heparin (1 μg/mL; Sigma)] with freshly added EGF, FGF2, PDGF (each at 20 ng/mL; Peprotech), and LIF (2 ng/mL; Millipore); iPSC Kosik Lab: N2 induction media with bFGF; iPSC Gage Lab: DMEM/F12; 1X N2; 1X B27 and FGF2 total RNA phNPCs: RNA was isolated using TRIzol reagent (Invitrogen) according to standard protocols; iPSC Kosik Lab: RNA was extracted using miRVANA kit, following the manufacturer’s protocol for total RNA; iPSC Gage Lab: Total cellular RNA was extracted using the RNeasy Protect Mini kit (QIAGEN, Valencia, CA). biotin Biotin Illumina protocol Illumina protocol phNPC from Geschwind Lab Donor: 8 Region: 43 DiffWk: 4 Replicate: 1 Passage: 6 Log2 normalization, quantile normalization, and ComBat batch correction NONE ID_REF VALUE Log2 normalization, quantile normalization, and ComBat batch correction Detection Pval GSM1385284-tbl-1.txt 2014-05-12 2014-06-01 2014-06-01 GSM1385285 RNA 1 Human fetal tissue Homo sapiens 8 46 phNPC from Geschwind Lab 4 6 9.6 18 ASW M 14 phNPC: Neurobasal A (Invitrogen) supplemented with B27 (Gibco), GlutaMAX (Gibco), and Antibiotics and Antimycotics (Gibco)] as well as Retinoic Acid (500 ng/mL; Sigma), Forskolin (100 μM; Sigma), BDNF (10 ng/mL; Peprotech), NT-3 (10 ng/mL; Peprotech), and KCl (10mM); iPSC Kosik Lab: neurobasal media supplemented with N2, B27 and neurotrophic factor cocktail that included NT3, BDNF, and GDNF; iPSC Gage Lab: DMEM/F12, N2, BDNF/GDNF, and laminin. phNPC: Neurobasal A (Invitrogen) supplemented with 10% BIT (Stem Cell Technologies), Antibiotics and Antimycotics (Gibco), GlutaMAX (Gibco), and Heparin (1 μg/mL; Sigma)] with freshly added EGF, FGF2, PDGF (each at 20 ng/mL; Peprotech), and LIF (2 ng/mL; Millipore); iPSC Kosik Lab: N2 induction media with bFGF; iPSC Gage Lab: DMEM/F12; 1X N2; 1X B27 and FGF2 total RNA phNPCs: RNA was isolated using TRIzol reagent (Invitrogen) according to standard protocols; iPSC Kosik Lab: RNA was extracted using miRVANA kit, following the manufacturer’s protocol for total RNA; iPSC Gage Lab: Total cellular RNA was extracted using the RNeasy Protect Mini kit (QIAGEN, Valencia, CA). biotin Biotin Illumina protocol Illumina protocol phNPC from Geschwind Lab Donor: 8 Region: 46 DiffWk: 4 Replicate: 2 Passage: 6 Log2 normalization, quantile normalization, and ComBat batch correction NONE ID_REF VALUE Log2 normalization, quantile normalization, and ComBat batch correction Detection Pval GSM1385285-tbl-1.txt 2014-05-12 2014-06-01 2014-06-01 GSM1385286 RNA 1 Human fetal tissue Homo sapiens 8 49 phNPC from Geschwind Lab 12 6 7.3 18 ASW M 14 phNPC: Neurobasal A (Invitrogen) supplemented with B27 (Gibco), GlutaMAX (Gibco), and Antibiotics and Antimycotics (Gibco)] as well as Retinoic Acid (500 ng/mL; Sigma), Forskolin (100 μM; Sigma), BDNF (10 ng/mL; Peprotech), NT-3 (10 ng/mL; Peprotech), and KCl (10mM); iPSC Kosik Lab: neurobasal media supplemented with N2, B27 and neurotrophic factor cocktail that included NT3, BDNF, and GDNF; iPSC Gage Lab: DMEM/F12, N2, BDNF/GDNF, and laminin. phNPC: Neurobasal A (Invitrogen) supplemented with 10% BIT (Stem Cell Technologies), Antibiotics and Antimycotics (Gibco), GlutaMAX (Gibco), and Heparin (1 μg/mL; Sigma)] with freshly added EGF, FGF2, PDGF (each at 20 ng/mL; Peprotech), and LIF (2 ng/mL; Millipore); iPSC Kosik Lab: N2 induction media with bFGF; iPSC Gage Lab: DMEM/F12; 1X N2; 1X B27 and FGF2 total RNA phNPCs: RNA was isolated using TRIzol reagent (Invitrogen) according to standard protocols; iPSC Kosik Lab: RNA was extracted using miRVANA kit, following the manufacturer’s protocol for total RNA; iPSC Gage Lab: Total cellular RNA was extracted using the RNeasy Protect Mini kit (QIAGEN, Valencia, CA). biotin Biotin Illumina protocol Illumina protocol phNPC from Geschwind Lab Donor: 8 Region: 49 DiffWk: 12 Replicate: 1 Passage: 6 Log2 normalization, quantile normalization, and ComBat batch correction NONE ID_REF VALUE Log2 normalization, quantile normalization, and ComBat batch correction Detection Pval GSM1385286-tbl-1.txt 2014-05-12 2014-06-01 2014-06-01 GSM1385287 RNA 1 Human fetal tissue Homo sapiens 6 21 phNPC from Geschwind Lab 12 6 8.6 18 MEX M 14 phNPC: Neurobasal A (Invitrogen) supplemented with B27 (Gibco), GlutaMAX (Gibco), and Antibiotics and Antimycotics (Gibco)] as well as Retinoic Acid (500 ng/mL; Sigma), Forskolin (100 μM; Sigma), BDNF (10 ng/mL; Peprotech), NT-3 (10 ng/mL; Peprotech), and KCl (10mM); iPSC Kosik Lab: neurobasal media supplemented with N2, B27 and neurotrophic factor cocktail that included NT3, BDNF, and GDNF; iPSC Gage Lab: DMEM/F12, N2, BDNF/GDNF, and laminin. phNPC: Neurobasal A (Invitrogen) supplemented with 10% BIT (Stem Cell Technologies), Antibiotics and Antimycotics (Gibco), GlutaMAX (Gibco), and Heparin (1 μg/mL; Sigma)] with freshly added EGF, FGF2, PDGF (each at 20 ng/mL; Peprotech), and LIF (2 ng/mL; Millipore); iPSC Kosik Lab: N2 induction media with bFGF; iPSC Gage Lab: DMEM/F12; 1X N2; 1X B27 and FGF2 total RNA phNPCs: RNA was isolated using TRIzol reagent (Invitrogen) according to standard protocols; iPSC Kosik Lab: RNA was extracted using miRVANA kit, following the manufacturer’s protocol for total RNA; iPSC Gage Lab: Total cellular RNA was extracted using the RNeasy Protect Mini kit (QIAGEN, Valencia, CA). biotin Biotin Illumina protocol Illumina protocol phNPC from Geschwind Lab Donor: 6 Region: 21 DiffWk: 12 Replicate: 1 Passage: 6 Log2 normalization, quantile normalization, and ComBat batch correction NONE ID_REF VALUE Log2 normalization, quantile normalization, and ComBat batch correction Detection Pval GSM1385287-tbl-1.txt 2014-05-12 2014-06-01 2014-06-01 GSM1385288 RNA 1 Human fetal tissue Homo sapiens 6 21 phNPC from Geschwind Lab 4 6 9.6 18 MEX M 14 phNPC: Neurobasal A (Invitrogen) supplemented with B27 (Gibco), GlutaMAX (Gibco), and Antibiotics and Antimycotics (Gibco)] as well as Retinoic Acid (500 ng/mL; Sigma), Forskolin (100 μM; Sigma), BDNF (10 ng/mL; Peprotech), NT-3 (10 ng/mL; Peprotech), and KCl (10mM); iPSC Kosik Lab: neurobasal media supplemented with N2, B27 and neurotrophic factor cocktail that included NT3, BDNF, and GDNF; iPSC Gage Lab: DMEM/F12, N2, BDNF/GDNF, and laminin. phNPC: Neurobasal A (Invitrogen) supplemented with 10% BIT (Stem Cell Technologies), Antibiotics and Antimycotics (Gibco), GlutaMAX (Gibco), and Heparin (1 μg/mL; Sigma)] with freshly added EGF, FGF2, PDGF (each at 20 ng/mL; Peprotech), and LIF (2 ng/mL; Millipore); iPSC Kosik Lab: N2 induction media with bFGF; iPSC Gage Lab: DMEM/F12; 1X N2; 1X B27 and FGF2 total RNA phNPCs: RNA was isolated using TRIzol reagent (Invitrogen) according to standard protocols; iPSC Kosik Lab: RNA was extracted using miRVANA kit, following the manufacturer’s protocol for total RNA; iPSC Gage Lab: Total cellular RNA was extracted using the RNeasy Protect Mini kit (QIAGEN, Valencia, CA). biotin Biotin Illumina protocol Illumina protocol phNPC from Geschwind Lab Donor: 6 Region: 21 DiffWk: 4 Replicate: 1 Passage: 6 Log2 normalization, quantile normalization, and ComBat batch correction NONE ID_REF VALUE Log2 normalization, quantile normalization, and ComBat batch correction Detection Pval GSM1385288-tbl-1.txt 2014-05-12 2014-06-01 2014-06-01 GSM1385289 RNA 1 Human fetal tissue Homo sapiens 8 43 phNPC from Geschwind Lab 1 7 9.8 18 ASW M 15 phNPC: Neurobasal A (Invitrogen) supplemented with B27 (Gibco), GlutaMAX (Gibco), and Antibiotics and Antimycotics (Gibco)] as well as Retinoic Acid (500 ng/mL; Sigma), Forskolin (100 μM; Sigma), BDNF (10 ng/mL; Peprotech), NT-3 (10 ng/mL; Peprotech), and KCl (10mM); iPSC Kosik Lab: neurobasal media supplemented with N2, B27 and neurotrophic factor cocktail that included NT3, BDNF, and GDNF; iPSC Gage Lab: DMEM/F12, N2, BDNF/GDNF, and laminin. phNPC: Neurobasal A (Invitrogen) supplemented with 10% BIT (Stem Cell Technologies), Antibiotics and Antimycotics (Gibco), GlutaMAX (Gibco), and Heparin (1 μg/mL; Sigma)] with freshly added EGF, FGF2, PDGF (each at 20 ng/mL; Peprotech), and LIF (2 ng/mL; Millipore); iPSC Kosik Lab: N2 induction media with bFGF; iPSC Gage Lab: DMEM/F12; 1X N2; 1X B27 and FGF2 total RNA phNPCs: RNA was isolated using TRIzol reagent (Invitrogen) according to standard protocols; iPSC Kosik Lab: RNA was extracted using miRVANA kit, following the manufacturer’s protocol for total RNA; iPSC Gage Lab: Total cellular RNA was extracted using the RNeasy Protect Mini kit (QIAGEN, Valencia, CA). biotin Biotin Illumina protocol Illumina protocol phNPC from Geschwind Lab Donor: 8 Region: 43 DiffWk: 1 Replicate: 1 Passage: 7 Log2 normalization, quantile normalization, and ComBat batch correction NONE ID_REF VALUE Log2 normalization, quantile normalization, and ComBat batch correction Detection Pval GSM1385289-tbl-1.txt 2014-05-12 2014-06-01 2014-06-01 GSM1385290 RNA 1 Human fetal tissue Homo sapiens 5 17 phNPC from Geschwind Lab 4 9 9.6 17 MEX F 15 phNPC: Neurobasal A (Invitrogen) supplemented with B27 (Gibco), GlutaMAX (Gibco), and Antibiotics and Antimycotics (Gibco)] as well as Retinoic Acid (500 ng/mL; Sigma), Forskolin (100 μM; Sigma), BDNF (10 ng/mL; Peprotech), NT-3 (10 ng/mL; Peprotech), and KCl (10mM); iPSC Kosik Lab: neurobasal media supplemented with N2, B27 and neurotrophic factor cocktail that included NT3, BDNF, and GDNF; iPSC Gage Lab: DMEM/F12, N2, BDNF/GDNF, and laminin. phNPC: Neurobasal A (Invitrogen) supplemented with 10% BIT (Stem Cell Technologies), Antibiotics and Antimycotics (Gibco), GlutaMAX (Gibco), and Heparin (1 μg/mL; Sigma)] with freshly added EGF, FGF2, PDGF (each at 20 ng/mL; Peprotech), and LIF (2 ng/mL; Millipore); iPSC Kosik Lab: N2 induction media with bFGF; iPSC Gage Lab: DMEM/F12; 1X N2; 1X B27 and FGF2 total RNA phNPCs: RNA was isolated using TRIzol reagent (Invitrogen) according to standard protocols; iPSC Kosik Lab: RNA was extracted using miRVANA kit, following the manufacturer’s protocol for total RNA; iPSC Gage Lab: Total cellular RNA was extracted using the RNeasy Protect Mini kit (QIAGEN, Valencia, CA). biotin Biotin Illumina protocol Illumina protocol phNPC from Geschwind Lab Donor: 5 Region: 17 DiffWk: 4 Replicate: 1 Passage: 9 Log2 normalization, quantile normalization, and ComBat batch correction NONE ID_REF VALUE Log2 normalization, quantile normalization, and ComBat batch correction Detection Pval GSM1385290-tbl-1.txt 2014-05-12 2014-06-01 2014-06-01 GSM1385291 RNA 1 Human fetal tissue Homo sapiens 8 49 phNPC from Geschwind Lab 12 5 9.2 18 ASW M 15 phNPC: Neurobasal A (Invitrogen) supplemented with B27 (Gibco), GlutaMAX (Gibco), and Antibiotics and Antimycotics (Gibco)] as well as Retinoic Acid (500 ng/mL; Sigma), Forskolin (100 μM; Sigma), BDNF (10 ng/mL; Peprotech), NT-3 (10 ng/mL; Peprotech), and KCl (10mM); iPSC Kosik Lab: neurobasal media supplemented with N2, B27 and neurotrophic factor cocktail that included NT3, BDNF, and GDNF; iPSC Gage Lab: DMEM/F12, N2, BDNF/GDNF, and laminin. phNPC: Neurobasal A (Invitrogen) supplemented with 10% BIT (Stem Cell Technologies), Antibiotics and Antimycotics (Gibco), GlutaMAX (Gibco), and Heparin (1 μg/mL; Sigma)] with freshly added EGF, FGF2, PDGF (each at 20 ng/mL; Peprotech), and LIF (2 ng/mL; Millipore); iPSC Kosik Lab: N2 induction media with bFGF; iPSC Gage Lab: DMEM/F12; 1X N2; 1X B27 and FGF2 total RNA phNPCs: RNA was isolated using TRIzol reagent (Invitrogen) according to standard protocols; iPSC Kosik Lab: RNA was extracted using miRVANA kit, following the manufacturer’s protocol for total RNA; iPSC Gage Lab: Total cellular RNA was extracted using the RNeasy Protect Mini kit (QIAGEN, Valencia, CA). biotin Biotin Illumina protocol Illumina protocol phNPC from Geschwind Lab Donor: 8 Region: 49 DiffWk: 12 Replicate: 1 Passage: 5 Log2 normalization, quantile normalization, and ComBat batch correction NONE ID_REF VALUE Log2 normalization, quantile normalization, and ComBat batch correction Detection Pval GSM1385291-tbl-1.txt 2014-05-12 2014-06-01 2014-06-01 GSM1385292 RNA 1 Human fetal tissue Homo sapiens 5 17 phNPC from Geschwind Lab 4 9 9.4 17 MEX F 16 phNPC: Neurobasal A (Invitrogen) supplemented with B27 (Gibco), GlutaMAX (Gibco), and Antibiotics and Antimycotics (Gibco)] as well as Retinoic Acid (500 ng/mL; Sigma), Forskolin (100 μM; Sigma), BDNF (10 ng/mL; Peprotech), NT-3 (10 ng/mL; Peprotech), and KCl (10mM); iPSC Kosik Lab: neurobasal media supplemented with N2, B27 and neurotrophic factor cocktail that included NT3, BDNF, and GDNF; iPSC Gage Lab: DMEM/F12, N2, BDNF/GDNF, and laminin. phNPC: Neurobasal A (Invitrogen) supplemented with 10% BIT (Stem Cell Technologies), Antibiotics and Antimycotics (Gibco), GlutaMAX (Gibco), and Heparin (1 μg/mL; Sigma)] with freshly added EGF, FGF2, PDGF (each at 20 ng/mL; Peprotech), and LIF (2 ng/mL; Millipore); iPSC Kosik Lab: N2 induction media with bFGF; iPSC Gage Lab: DMEM/F12; 1X N2; 1X B27 and FGF2 total RNA phNPCs: RNA was isolated using TRIzol reagent (Invitrogen) according to standard protocols; iPSC Kosik Lab: RNA was extracted using miRVANA kit, following the manufacturer’s protocol for total RNA; iPSC Gage Lab: Total cellular RNA was extracted using the RNeasy Protect Mini kit (QIAGEN, Valencia, CA). biotin Biotin Illumina protocol Illumina protocol phNPC from Geschwind Lab Donor: 5 Region: 17 DiffWk: 4 Replicate: 2 Passage: 9 Log2 normalization, quantile normalization, and ComBat batch correction NONE ID_REF VALUE Log2 normalization, quantile normalization, and ComBat batch correction Detection Pval GSM1385292-tbl-1.txt 2014-05-12 2014-06-01 2014-06-01 GSM1385293 RNA 1 Human fetal tissue Homo sapiens 8 49 phNPC from Geschwind Lab 8 5 9.2 18 ASW M 16 phNPC: Neurobasal A (Invitrogen) supplemented with B27 (Gibco), GlutaMAX (Gibco), and Antibiotics and Antimycotics (Gibco)] as well as Retinoic Acid (500 ng/mL; Sigma), Forskolin (100 μM; Sigma), BDNF (10 ng/mL; Peprotech), NT-3 (10 ng/mL; Peprotech), and KCl (10mM); iPSC Kosik Lab: neurobasal media supplemented with N2, B27 and neurotrophic factor cocktail that included NT3, BDNF, and GDNF; iPSC Gage Lab: DMEM/F12, N2, BDNF/GDNF, and laminin. phNPC: Neurobasal A (Invitrogen) supplemented with 10% BIT (Stem Cell Technologies), Antibiotics and Antimycotics (Gibco), GlutaMAX (Gibco), and Heparin (1 μg/mL; Sigma)] with freshly added EGF, FGF2, PDGF (each at 20 ng/mL; Peprotech), and LIF (2 ng/mL; Millipore); iPSC Kosik Lab: N2 induction media with bFGF; iPSC Gage Lab: DMEM/F12; 1X N2; 1X B27 and FGF2 total RNA phNPCs: RNA was isolated using TRIzol reagent (Invitrogen) according to standard protocols; iPSC Kosik Lab: RNA was extracted using miRVANA kit, following the manufacturer’s protocol for total RNA; iPSC Gage Lab: Total cellular RNA was extracted using the RNeasy Protect Mini kit (QIAGEN, Valencia, CA). biotin Biotin Illumina protocol Illumina protocol phNPC from Geschwind Lab Donor: 8 Region: 49 DiffWk: 8 Replicate: 1 Passage: 5 Log2 normalization, quantile normalization, and ComBat batch correction NONE ID_REF VALUE Log2 normalization, quantile normalization, and ComBat batch correction Detection Pval GSM1385293-tbl-1.txt 2014-05-12 2014-06-01 2014-06-01 GSM1385294 RNA 1 Human fetal tissue Homo sapiens 8 43 phNPC from Geschwind Lab 4 7 9.7 18 ASW M 16 phNPC: Neurobasal A (Invitrogen) supplemented with B27 (Gibco), GlutaMAX (Gibco), and Antibiotics and Antimycotics (Gibco)] as well as Retinoic Acid (500 ng/mL; Sigma), Forskolin (100 μM; Sigma), BDNF (10 ng/mL; Peprotech), NT-3 (10 ng/mL; Peprotech), and KCl (10mM); iPSC Kosik Lab: neurobasal media supplemented with N2, B27 and neurotrophic factor cocktail that included NT3, BDNF, and GDNF; iPSC Gage Lab: DMEM/F12, N2, BDNF/GDNF, and laminin. phNPC: Neurobasal A (Invitrogen) supplemented with 10% BIT (Stem Cell Technologies), Antibiotics and Antimycotics (Gibco), GlutaMAX (Gibco), and Heparin (1 μg/mL; Sigma)] with freshly added EGF, FGF2, PDGF (each at 20 ng/mL; Peprotech), and LIF (2 ng/mL; Millipore); iPSC Kosik Lab: N2 induction media with bFGF; iPSC Gage Lab: DMEM/F12; 1X N2; 1X B27 and FGF2 total RNA phNPCs: RNA was isolated using TRIzol reagent (Invitrogen) according to standard protocols; iPSC Kosik Lab: RNA was extracted using miRVANA kit, following the manufacturer’s protocol for total RNA; iPSC Gage Lab: Total cellular RNA was extracted using the RNeasy Protect Mini kit (QIAGEN, Valencia, CA). biotin Biotin Illumina protocol Illumina protocol phNPC from Geschwind Lab Donor: 8 Region: 43 DiffWk: 4 Replicate: 2 Passage: 7 Log2 normalization, quantile normalization, and ComBat batch correction NONE ID_REF VALUE Log2 normalization, quantile normalization, and ComBat batch correction Detection Pval GSM1385294-tbl-1.txt 2014-05-12 2014-06-01 2014-06-01 GSM1385295 RNA 1 Human fetal tissue Homo sapiens 8 43 phNPC from Geschwind Lab 4 6 9.6 18 ASW M 16 phNPC: Neurobasal A (Invitrogen) supplemented with B27 (Gibco), GlutaMAX (Gibco), and Antibiotics and Antimycotics (Gibco)] as well as Retinoic Acid (500 ng/mL; Sigma), Forskolin (100 μM; Sigma), BDNF (10 ng/mL; Peprotech), NT-3 (10 ng/mL; Peprotech), and KCl (10mM); iPSC Kosik Lab: neurobasal media supplemented with N2, B27 and neurotrophic factor cocktail that included NT3, BDNF, and GDNF; iPSC Gage Lab: DMEM/F12, N2, BDNF/GDNF, and laminin. phNPC: Neurobasal A (Invitrogen) supplemented with 10% BIT (Stem Cell Technologies), Antibiotics and Antimycotics (Gibco), GlutaMAX (Gibco), and Heparin (1 μg/mL; Sigma)] with freshly added EGF, FGF2, PDGF (each at 20 ng/mL; Peprotech), and LIF (2 ng/mL; Millipore); iPSC Kosik Lab: N2 induction media with bFGF; iPSC Gage Lab: DMEM/F12; 1X N2; 1X B27 and FGF2 total RNA phNPCs: RNA was isolated using TRIzol reagent (Invitrogen) according to standard protocols; iPSC Kosik Lab: RNA was extracted using miRVANA kit, following the manufacturer’s protocol for total RNA; iPSC Gage Lab: Total cellular RNA was extracted using the RNeasy Protect Mini kit (QIAGEN, Valencia, CA). biotin Biotin Illumina protocol Illumina protocol phNPC from Geschwind Lab Donor: 8 Region: 43 DiffWk: 4 Replicate: 2 Passage: 6 Log2 normalization, quantile normalization, and ComBat batch correction NONE ID_REF VALUE Log2 normalization, quantile normalization, and ComBat batch correction Detection Pval GSM1385295-tbl-1.txt 2014-05-12 2014-06-01 2014-06-01 GSM1385296 RNA 1 Human fetal tissue Homo sapiens 5 17 phNPC from Geschwind Lab 1 10 9.7 17 MEX F 16 phNPC: Neurobasal A (Invitrogen) supplemented with B27 (Gibco), GlutaMAX (Gibco), and Antibiotics and Antimycotics (Gibco)] as well as Retinoic Acid (500 ng/mL; Sigma), Forskolin (100 μM; Sigma), BDNF (10 ng/mL; Peprotech), NT-3 (10 ng/mL; Peprotech), and KCl (10mM); iPSC Kosik Lab: neurobasal media supplemented with N2, B27 and neurotrophic factor cocktail that included NT3, BDNF, and GDNF; iPSC Gage Lab: DMEM/F12, N2, BDNF/GDNF, and laminin. phNPC: Neurobasal A (Invitrogen) supplemented with 10% BIT (Stem Cell Technologies), Antibiotics and Antimycotics (Gibco), GlutaMAX (Gibco), and Heparin (1 μg/mL; Sigma)] with freshly added EGF, FGF2, PDGF (each at 20 ng/mL; Peprotech), and LIF (2 ng/mL; Millipore); iPSC Kosik Lab: N2 induction media with bFGF; iPSC Gage Lab: DMEM/F12; 1X N2; 1X B27 and FGF2 total RNA phNPCs: RNA was isolated using TRIzol reagent (Invitrogen) according to standard protocols; iPSC Kosik Lab: RNA was extracted using miRVANA kit, following the manufacturer’s protocol for total RNA; iPSC Gage Lab: Total cellular RNA was extracted using the RNeasy Protect Mini kit (QIAGEN, Valencia, CA). biotin Biotin Illumina protocol Illumina protocol phNPC from Geschwind Lab Donor: 5 Region: 17 DiffWk: 1 Replicate: 2 Passage: 10 Log2 normalization, quantile normalization, and ComBat batch correction NONE ID_REF VALUE Log2 normalization, quantile normalization, and ComBat batch correction Detection Pval GSM1385296-tbl-1.txt 2014-05-12 2014-06-01 2014-06-01 GSM1385297 RNA 1 Human fetal tissue Homo sapiens 8 46 phNPC from Geschwind Lab 1 6 10 18 ASW M 17 phNPC: Neurobasal A (Invitrogen) supplemented with B27 (Gibco), GlutaMAX (Gibco), and Antibiotics and Antimycotics (Gibco)] as well as Retinoic Acid (500 ng/mL; Sigma), Forskolin (100 μM; Sigma), BDNF (10 ng/mL; Peprotech), NT-3 (10 ng/mL; Peprotech), and KCl (10mM); iPSC Kosik Lab: neurobasal media supplemented with N2, B27 and neurotrophic factor cocktail that included NT3, BDNF, and GDNF; iPSC Gage Lab: DMEM/F12, N2, BDNF/GDNF, and laminin. phNPC: Neurobasal A (Invitrogen) supplemented with 10% BIT (Stem Cell Technologies), Antibiotics and Antimycotics (Gibco), GlutaMAX (Gibco), and Heparin (1 μg/mL; Sigma)] with freshly added EGF, FGF2, PDGF (each at 20 ng/mL; Peprotech), and LIF (2 ng/mL; Millipore); iPSC Kosik Lab: N2 induction media with bFGF; iPSC Gage Lab: DMEM/F12; 1X N2; 1X B27 and FGF2 total RNA phNPCs: RNA was isolated using TRIzol reagent (Invitrogen) according to standard protocols; iPSC Kosik Lab: RNA was extracted using miRVANA kit, following the manufacturer’s protocol for total RNA; iPSC Gage Lab: Total cellular RNA was extracted using the RNeasy Protect Mini kit (QIAGEN, Valencia, CA). biotin Biotin Illumina protocol Illumina protocol phNPC from Geschwind Lab Donor: 8 Region: 46 DiffWk: 1 Replicate: 2 Passage: 6 Log2 normalization, quantile normalization, and ComBat batch correction NONE ID_REF VALUE Log2 normalization, quantile normalization, and ComBat batch correction Detection Pval GSM1385297-tbl-1.txt 2014-05-12 2014-06-01 2014-06-01 GSM1385298 RNA 1 Human fetal tissue Homo sapiens 6 21 phNPC from Geschwind Lab 1 5 10 18 MEX M 17 phNPC: Neurobasal A (Invitrogen) supplemented with B27 (Gibco), GlutaMAX (Gibco), and Antibiotics and Antimycotics (Gibco)] as well as Retinoic Acid (500 ng/mL; Sigma), Forskolin (100 μM; Sigma), BDNF (10 ng/mL; Peprotech), NT-3 (10 ng/mL; Peprotech), and KCl (10mM); iPSC Kosik Lab: neurobasal media supplemented with N2, B27 and neurotrophic factor cocktail that included NT3, BDNF, and GDNF; iPSC Gage Lab: DMEM/F12, N2, BDNF/GDNF, and laminin. phNPC: Neurobasal A (Invitrogen) supplemented with 10% BIT (Stem Cell Technologies), Antibiotics and Antimycotics (Gibco), GlutaMAX (Gibco), and Heparin (1 μg/mL; Sigma)] with freshly added EGF, FGF2, PDGF (each at 20 ng/mL; Peprotech), and LIF (2 ng/mL; Millipore); iPSC Kosik Lab: N2 induction media with bFGF; iPSC Gage Lab: DMEM/F12; 1X N2; 1X B27 and FGF2 total RNA phNPCs: RNA was isolated using TRIzol reagent (Invitrogen) according to standard protocols; iPSC Kosik Lab: RNA was extracted using miRVANA kit, following the manufacturer’s protocol for total RNA; iPSC Gage Lab: Total cellular RNA was extracted using the RNeasy Protect Mini kit (QIAGEN, Valencia, CA). biotin Biotin Illumina protocol Illumina protocol phNPC from Geschwind Lab Donor: 6 Region: 21 DiffWk: 1 Replicate: 2 Passage: 5 Log2 normalization, quantile normalization, and ComBat batch correction NONE ID_REF VALUE Log2 normalization, quantile normalization, and ComBat batch correction Detection Pval GSM1385298-tbl-1.txt 2014-05-12 2014-06-01 2014-06-01 GSM1385299 RNA 1 Human fetal tissue Homo sapiens 8 46 phNPC from Geschwind Lab 4 6 9.7 18 ASW M 17 phNPC: Neurobasal A (Invitrogen) supplemented with B27 (Gibco), GlutaMAX (Gibco), and Antibiotics and Antimycotics (Gibco)] as well as Retinoic Acid (500 ng/mL; Sigma), Forskolin (100 μM; Sigma), BDNF (10 ng/mL; Peprotech), NT-3 (10 ng/mL; Peprotech), and KCl (10mM); iPSC Kosik Lab: neurobasal media supplemented with N2, B27 and neurotrophic factor cocktail that included NT3, BDNF, and GDNF; iPSC Gage Lab: DMEM/F12, N2, BDNF/GDNF, and laminin. phNPC: Neurobasal A (Invitrogen) supplemented with 10% BIT (Stem Cell Technologies), Antibiotics and Antimycotics (Gibco), GlutaMAX (Gibco), and Heparin (1 μg/mL; Sigma)] with freshly added EGF, FGF2, PDGF (each at 20 ng/mL; Peprotech), and LIF (2 ng/mL; Millipore); iPSC Kosik Lab: N2 induction media with bFGF; iPSC Gage Lab: DMEM/F12; 1X N2; 1X B27 and FGF2 total RNA phNPCs: RNA was isolated using TRIzol reagent (Invitrogen) according to standard protocols; iPSC Kosik Lab: RNA was extracted using miRVANA kit, following the manufacturer’s protocol for total RNA; iPSC Gage Lab: Total cellular RNA was extracted using the RNeasy Protect Mini kit (QIAGEN, Valencia, CA). biotin Biotin Illumina protocol Illumina protocol phNPC from Geschwind Lab Donor: 8 Region: 46 DiffWk: 4 Replicate: 1 Passage: 6 Log2 normalization, quantile normalization, and ComBat batch correction NONE ID_REF VALUE Log2 normalization, quantile normalization, and ComBat batch correction Detection Pval GSM1385299-tbl-1.txt 2014-05-12 2014-06-01 2014-06-01 GSM1385300 RNA 1 Human fetal tissue Homo sapiens 6 21 phNPC from Geschwind Lab 8 6 9.4 18 MEX M 17 phNPC: Neurobasal A (Invitrogen) supplemented with B27 (Gibco), GlutaMAX (Gibco), and Antibiotics and Antimycotics (Gibco)] as well as Retinoic Acid (500 ng/mL; Sigma), Forskolin (100 μM; Sigma), BDNF (10 ng/mL; Peprotech), NT-3 (10 ng/mL; Peprotech), and KCl (10mM); iPSC Kosik Lab: neurobasal media supplemented with N2, B27 and neurotrophic factor cocktail that included NT3, BDNF, and GDNF; iPSC Gage Lab: DMEM/F12, N2, BDNF/GDNF, and laminin. phNPC: Neurobasal A (Invitrogen) supplemented with 10% BIT (Stem Cell Technologies), Antibiotics and Antimycotics (Gibco), GlutaMAX (Gibco), and Heparin (1 μg/mL; Sigma)] with freshly added EGF, FGF2, PDGF (each at 20 ng/mL; Peprotech), and LIF (2 ng/mL; Millipore); iPSC Kosik Lab: N2 induction media with bFGF; iPSC Gage Lab: DMEM/F12; 1X N2; 1X B27 and FGF2 total RNA phNPCs: RNA was isolated using TRIzol reagent (Invitrogen) according to standard protocols; iPSC Kosik Lab: RNA was extracted using miRVANA kit, following the manufacturer’s protocol for total RNA; iPSC Gage Lab: Total cellular RNA was extracted using the RNeasy Protect Mini kit (QIAGEN, Valencia, CA). biotin Biotin Illumina protocol Illumina protocol phNPC from Geschwind Lab Donor: 6 Region: 21 DiffWk: 8 Replicate: 1 Passage: 6 Log2 normalization, quantile normalization, and ComBat batch correction NONE ID_REF VALUE Log2 normalization, quantile normalization, and ComBat batch correction Detection Pval GSM1385300-tbl-1.txt 2014-05-12 2014-06-01 2014-06-01 GSM1385301 RNA 1 Human fetal tissue Homo sapiens 6 21 phNPC from Geschwind Lab 12 6 7.2 18 MEX M 18 phNPC: Neurobasal A (Invitrogen) supplemented with B27 (Gibco), GlutaMAX (Gibco), and Antibiotics and Antimycotics (Gibco)] as well as Retinoic Acid (500 ng/mL; Sigma), Forskolin (100 μM; Sigma), BDNF (10 ng/mL; Peprotech), NT-3 (10 ng/mL; Peprotech), and KCl (10mM); iPSC Kosik Lab: neurobasal media supplemented with N2, B27 and neurotrophic factor cocktail that included NT3, BDNF, and GDNF; iPSC Gage Lab: DMEM/F12, N2, BDNF/GDNF, and laminin. phNPC: Neurobasal A (Invitrogen) supplemented with 10% BIT (Stem Cell Technologies), Antibiotics and Antimycotics (Gibco), GlutaMAX (Gibco), and Heparin (1 μg/mL; Sigma)] with freshly added EGF, FGF2, PDGF (each at 20 ng/mL; Peprotech), and LIF (2 ng/mL; Millipore); iPSC Kosik Lab: N2 induction media with bFGF; iPSC Gage Lab: DMEM/F12; 1X N2; 1X B27 and FGF2 total RNA phNPCs: RNA was isolated using TRIzol reagent (Invitrogen) according to standard protocols; iPSC Kosik Lab: RNA was extracted using miRVANA kit, following the manufacturer’s protocol for total RNA; iPSC Gage Lab: Total cellular RNA was extracted using the RNeasy Protect Mini kit (QIAGEN, Valencia, CA). biotin Biotin Illumina protocol Illumina protocol phNPC from Geschwind Lab Donor: 6 Region: 21 DiffWk: 12 Replicate: 2 Passage: 6 Log2 normalization, quantile normalization, and ComBat batch correction NONE ID_REF VALUE Log2 normalization, quantile normalization, and ComBat batch correction Detection Pval GSM1385301-tbl-1.txt 2014-05-12 2014-06-01 2014-06-01 GSM1385302 RNA 1 Human fetal tissue Homo sapiens 8 43 phNPC from Geschwind Lab 8 6 9.5 18 ASW M 18 phNPC: Neurobasal A (Invitrogen) supplemented with B27 (Gibco), GlutaMAX (Gibco), and Antibiotics and Antimycotics (Gibco)] as well as Retinoic Acid (500 ng/mL; Sigma), Forskolin (100 μM; Sigma), BDNF (10 ng/mL; Peprotech), NT-3 (10 ng/mL; Peprotech), and KCl (10mM); iPSC Kosik Lab: neurobasal media supplemented with N2, B27 and neurotrophic factor cocktail that included NT3, BDNF, and GDNF; iPSC Gage Lab: DMEM/F12, N2, BDNF/GDNF, and laminin. phNPC: Neurobasal A (Invitrogen) supplemented with 10% BIT (Stem Cell Technologies), Antibiotics and Antimycotics (Gibco), GlutaMAX (Gibco), and Heparin (1 μg/mL; Sigma)] with freshly added EGF, FGF2, PDGF (each at 20 ng/mL; Peprotech), and LIF (2 ng/mL; Millipore); iPSC Kosik Lab: N2 induction media with bFGF; iPSC Gage Lab: DMEM/F12; 1X N2; 1X B27 and FGF2 total RNA phNPCs: RNA was isolated using TRIzol reagent (Invitrogen) according to standard protocols; iPSC Kosik Lab: RNA was extracted using miRVANA kit, following the manufacturer’s protocol for total RNA; iPSC Gage Lab: Total cellular RNA was extracted using the RNeasy Protect Mini kit (QIAGEN, Valencia, CA). biotin Biotin Illumina protocol Illumina protocol phNPC from Geschwind Lab Donor: 8 Region: 43 DiffWk: 8 Replicate: 1 Passage: 6 Log2 normalization, quantile normalization, and ComBat batch correction NONE ID_REF VALUE Log2 normalization, quantile normalization, and ComBat batch correction Detection Pval GSM1385302-tbl-1.txt 2014-05-12 2014-06-01 2014-06-01 GSM1385303 RNA 1 Human fetal tissue Homo sapiens 8 46 phNPC from Geschwind Lab 12 6 8.9 18 ASW M 18 phNPC: Neurobasal A (Invitrogen) supplemented with B27 (Gibco), GlutaMAX (Gibco), and Antibiotics and Antimycotics (Gibco)] as well as Retinoic Acid (500 ng/mL; Sigma), Forskolin (100 μM; Sigma), BDNF (10 ng/mL; Peprotech), NT-3 (10 ng/mL; Peprotech), and KCl (10mM); iPSC Kosik Lab: neurobasal media supplemented with N2, B27 and neurotrophic factor cocktail that included NT3, BDNF, and GDNF; iPSC Gage Lab: DMEM/F12, N2, BDNF/GDNF, and laminin. phNPC: Neurobasal A (Invitrogen) supplemented with 10% BIT (Stem Cell Technologies), Antibiotics and Antimycotics (Gibco), GlutaMAX (Gibco), and Heparin (1 μg/mL; Sigma)] with freshly added EGF, FGF2, PDGF (each at 20 ng/mL; Peprotech), and LIF (2 ng/mL; Millipore); iPSC Kosik Lab: N2 induction media with bFGF; iPSC Gage Lab: DMEM/F12; 1X N2; 1X B27 and FGF2 total RNA phNPCs: RNA was isolated using TRIzol reagent (Invitrogen) according to standard protocols; iPSC Kosik Lab: RNA was extracted using miRVANA kit, following the manufacturer’s protocol for total RNA; iPSC Gage Lab: Total cellular RNA was extracted using the RNeasy Protect Mini kit (QIAGEN, Valencia, CA). biotin Biotin Illumina protocol Illumina protocol phNPC from Geschwind Lab Donor: 8 Region: 46 DiffWk: 12 Replicate: 2 Passage: 6 Log2 normalization, quantile normalization, and ComBat batch correction NONE ID_REF VALUE Log2 normalization, quantile normalization, and ComBat batch correction Detection Pval GSM1385303-tbl-1.txt 2014-05-12 2014-06-01 2014-06-01 GSM1385304 RNA 1 Human fetal tissue Homo sapiens 6 21 phNPC from Geschwind Lab 8 5 9 18 MEX M 19 phNPC: Neurobasal A (Invitrogen) supplemented with B27 (Gibco), GlutaMAX (Gibco), and Antibiotics and Antimycotics (Gibco)] as well as Retinoic Acid (500 ng/mL; Sigma), Forskolin (100 μM; Sigma), BDNF (10 ng/mL; Peprotech), NT-3 (10 ng/mL; Peprotech), and KCl (10mM); iPSC Kosik Lab: neurobasal media supplemented with N2, B27 and neurotrophic factor cocktail that included NT3, BDNF, and GDNF; iPSC Gage Lab: DMEM/F12, N2, BDNF/GDNF, and laminin. phNPC: Neurobasal A (Invitrogen) supplemented with 10% BIT (Stem Cell Technologies), Antibiotics and Antimycotics (Gibco), GlutaMAX (Gibco), and Heparin (1 μg/mL; Sigma)] with freshly added EGF, FGF2, PDGF (each at 20 ng/mL; Peprotech), and LIF (2 ng/mL; Millipore); iPSC Kosik Lab: N2 induction media with bFGF; iPSC Gage Lab: DMEM/F12; 1X N2; 1X B27 and FGF2 total RNA phNPCs: RNA was isolated using TRIzol reagent (Invitrogen) according to standard protocols; iPSC Kosik Lab: RNA was extracted using miRVANA kit, following the manufacturer’s protocol for total RNA; iPSC Gage Lab: Total cellular RNA was extracted using the RNeasy Protect Mini kit (QIAGEN, Valencia, CA). biotin Biotin Illumina protocol Illumina protocol phNPC from Geschwind Lab Donor: 6 Region: 21 DiffWk: 8 Replicate: 2 Passage: 5 Log2 normalization, quantile normalization, and ComBat batch correction NONE ID_REF VALUE Log2 normalization, quantile normalization, and ComBat batch correction Detection Pval GSM1385304-tbl-1.txt 2014-05-12 2014-06-01 2014-06-01 GSM1385305 RNA 1 Human fetal tissue Homo sapiens 8 49 phNPC from Geschwind Lab 1 6 9.7 18 ASW M 19 phNPC: Neurobasal A (Invitrogen) supplemented with B27 (Gibco), GlutaMAX (Gibco), and Antibiotics and Antimycotics (Gibco)] as well as Retinoic Acid (500 ng/mL; Sigma), Forskolin (100 μM; Sigma), BDNF (10 ng/mL; Peprotech), NT-3 (10 ng/mL; Peprotech), and KCl (10mM); iPSC Kosik Lab: neurobasal media supplemented with N2, B27 and neurotrophic factor cocktail that included NT3, BDNF, and GDNF; iPSC Gage Lab: DMEM/F12, N2, BDNF/GDNF, and laminin. phNPC: Neurobasal A (Invitrogen) supplemented with 10% BIT (Stem Cell Technologies), Antibiotics and Antimycotics (Gibco), GlutaMAX (Gibco), and Heparin (1 μg/mL; Sigma)] with freshly added EGF, FGF2, PDGF (each at 20 ng/mL; Peprotech), and LIF (2 ng/mL; Millipore); iPSC Kosik Lab: N2 induction media with bFGF; iPSC Gage Lab: DMEM/F12; 1X N2; 1X B27 and FGF2 total RNA phNPCs: RNA was isolated using TRIzol reagent (Invitrogen) according to standard protocols; iPSC Kosik Lab: RNA was extracted using miRVANA kit, following the manufacturer’s protocol for total RNA; iPSC Gage Lab: Total cellular RNA was extracted using the RNeasy Protect Mini kit (QIAGEN, Valencia, CA). biotin Biotin Illumina protocol Illumina protocol phNPC from Geschwind Lab Donor: 8 Region: 49 DiffWk: 1 Replicate: 2 Passage: 6 Log2 normalization, quantile normalization, and ComBat batch correction NONE ID_REF VALUE Log2 normalization, quantile normalization, and ComBat batch correction Detection Pval GSM1385305-tbl-1.txt 2014-05-12 2014-06-01 2014-06-01 GSM1385306 RNA 1 Human fetal tissue Homo sapiens 8 49 phNPC from Geschwind Lab 4 6 9.8 18 ASW M 19 phNPC: Neurobasal A (Invitrogen) supplemented with B27 (Gibco), GlutaMAX (Gibco), and Antibiotics and Antimycotics (Gibco)] as well as Retinoic Acid (500 ng/mL; Sigma), Forskolin (100 μM; Sigma), BDNF (10 ng/mL; Peprotech), NT-3 (10 ng/mL; Peprotech), and KCl (10mM); iPSC Kosik Lab: neurobasal media supplemented with N2, B27 and neurotrophic factor cocktail that included NT3, BDNF, and GDNF; iPSC Gage Lab: DMEM/F12, N2, BDNF/GDNF, and laminin. phNPC: Neurobasal A (Invitrogen) supplemented with 10% BIT (Stem Cell Technologies), Antibiotics and Antimycotics (Gibco), GlutaMAX (Gibco), and Heparin (1 μg/mL; Sigma)] with freshly added EGF, FGF2, PDGF (each at 20 ng/mL; Peprotech), and LIF (2 ng/mL; Millipore); iPSC Kosik Lab: N2 induction media with bFGF; iPSC Gage Lab: DMEM/F12; 1X N2; 1X B27 and FGF2 total RNA phNPCs: RNA was isolated using TRIzol reagent (Invitrogen) according to standard protocols; iPSC Kosik Lab: RNA was extracted using miRVANA kit, following the manufacturer’s protocol for total RNA; iPSC Gage Lab: Total cellular RNA was extracted using the RNeasy Protect Mini kit (QIAGEN, Valencia, CA). biotin Biotin Illumina protocol Illumina protocol phNPC from Geschwind Lab Donor: 8 Region: 49 DiffWk: 4 Replicate: 2 Passage: 6 Log2 normalization, quantile normalization, and ComBat batch correction NONE ID_REF VALUE Log2 normalization, quantile normalization, and ComBat batch correction Detection Pval GSM1385306-tbl-1.txt 2014-05-12 2014-06-01 2014-06-01 GSM1385307 RNA 1 Human fetal tissue Homo sapiens 6 21 phNPC from Geschwind Lab 8 5 9.1 18 MEX M 19 phNPC: Neurobasal A (Invitrogen) supplemented with B27 (Gibco), GlutaMAX (Gibco), and Antibiotics and Antimycotics (Gibco)] as well as Retinoic Acid (500 ng/mL; Sigma), Forskolin (100 μM; Sigma), BDNF (10 ng/mL; Peprotech), NT-3 (10 ng/mL; Peprotech), and KCl (10mM); iPSC Kosik Lab: neurobasal media supplemented with N2, B27 and neurotrophic factor cocktail that included NT3, BDNF, and GDNF; iPSC Gage Lab: DMEM/F12, N2, BDNF/GDNF, and laminin. phNPC: Neurobasal A (Invitrogen) supplemented with 10% BIT (Stem Cell Technologies), Antibiotics and Antimycotics (Gibco), GlutaMAX (Gibco), and Heparin (1 μg/mL; Sigma)] with freshly added EGF, FGF2, PDGF (each at 20 ng/mL; Peprotech), and LIF (2 ng/mL; Millipore); iPSC Kosik Lab: N2 induction media with bFGF; iPSC Gage Lab: DMEM/F12; 1X N2; 1X B27 and FGF2 total RNA phNPCs: RNA was isolated using TRIzol reagent (Invitrogen) according to standard protocols; iPSC Kosik Lab: RNA was extracted using miRVANA kit, following the manufacturer’s protocol for total RNA; iPSC Gage Lab: Total cellular RNA was extracted using the RNeasy Protect Mini kit (QIAGEN, Valencia, CA). biotin Biotin Illumina protocol Illumina protocol phNPC from Geschwind Lab Donor: 6 Region: 21 DiffWk: 8 Replicate: 1 Passage: 5 Log2 normalization, quantile normalization, and ComBat batch correction NONE ID_REF VALUE Log2 normalization, quantile normalization, and ComBat batch correction Detection Pval GSM1385307-tbl-1.txt 2014-05-12 2014-06-01 2014-06-01 GSM1385308 RNA 1 Human fetal tissue Homo sapiens 8 46 phNPC from Geschwind Lab 1 5 9.9 18 ASW M 20 phNPC: Neurobasal A (Invitrogen) supplemented with B27 (Gibco), GlutaMAX (Gibco), and Antibiotics and Antimycotics (Gibco)] as well as Retinoic Acid (500 ng/mL; Sigma), Forskolin (100 μM; Sigma), BDNF (10 ng/mL; Peprotech), NT-3 (10 ng/mL; Peprotech), and KCl (10mM); iPSC Kosik Lab: neurobasal media supplemented with N2, B27 and neurotrophic factor cocktail that included NT3, BDNF, and GDNF; iPSC Gage Lab: DMEM/F12, N2, BDNF/GDNF, and laminin. phNPC: Neurobasal A (Invitrogen) supplemented with 10% BIT (Stem Cell Technologies), Antibiotics and Antimycotics (Gibco), GlutaMAX (Gibco), and Heparin (1 μg/mL; Sigma)] with freshly added EGF, FGF2, PDGF (each at 20 ng/mL; Peprotech), and LIF (2 ng/mL; Millipore); iPSC Kosik Lab: N2 induction media with bFGF; iPSC Gage Lab: DMEM/F12; 1X N2; 1X B27 and FGF2 total RNA phNPCs: RNA was isolated using TRIzol reagent (Invitrogen) according to standard protocols; iPSC Kosik Lab: RNA was extracted using miRVANA kit, following the manufacturer’s protocol for total RNA; iPSC Gage Lab: Total cellular RNA was extracted using the RNeasy Protect Mini kit (QIAGEN, Valencia, CA). biotin Biotin Illumina protocol Illumina protocol phNPC from Geschwind Lab Donor: 8 Region: 46 DiffWk: 1 Replicate: 2 Passage: 5 Log2 normalization, quantile normalization, and ComBat batch correction NONE ID_REF VALUE Log2 normalization, quantile normalization, and ComBat batch correction Detection Pval GSM1385308-tbl-1.txt 2014-05-12 2014-06-01 2014-06-01 GSM1385309 RNA 1 Human fetal tissue Homo sapiens 8 46 phNPC from Geschwind Lab 4 5 10 18 ASW M 20 phNPC: Neurobasal A (Invitrogen) supplemented with B27 (Gibco), GlutaMAX (Gibco), and Antibiotics and Antimycotics (Gibco)] as well as Retinoic Acid (500 ng/mL; Sigma), Forskolin (100 μM; Sigma), BDNF (10 ng/mL; Peprotech), NT-3 (10 ng/mL; Peprotech), and KCl (10mM); iPSC Kosik Lab: neurobasal media supplemented with N2, B27 and neurotrophic factor cocktail that included NT3, BDNF, and GDNF; iPSC Gage Lab: DMEM/F12, N2, BDNF/GDNF, and laminin. phNPC: Neurobasal A (Invitrogen) supplemented with 10% BIT (Stem Cell Technologies), Antibiotics and Antimycotics (Gibco), GlutaMAX (Gibco), and Heparin (1 μg/mL; Sigma)] with freshly added EGF, FGF2, PDGF (each at 20 ng/mL; Peprotech), and LIF (2 ng/mL; Millipore); iPSC Kosik Lab: N2 induction media with bFGF; iPSC Gage Lab: DMEM/F12; 1X N2; 1X B27 and FGF2 total RNA phNPCs: RNA was isolated using TRIzol reagent (Invitrogen) according to standard protocols; iPSC Kosik Lab: RNA was extracted using miRVANA kit, following the manufacturer’s protocol for total RNA; iPSC Gage Lab: Total cellular RNA was extracted using the RNeasy Protect Mini kit (QIAGEN, Valencia, CA). biotin Biotin Illumina protocol Illumina protocol phNPC from Geschwind Lab Donor: 8 Region: 46 DiffWk: 4 Replicate: 1 Passage: 5 Log2 normalization, quantile normalization, and ComBat batch correction NONE ID_REF VALUE Log2 normalization, quantile normalization, and ComBat batch correction Detection Pval GSM1385309-tbl-1.txt 2014-05-12 2014-06-01 2014-06-01 GSM1385310 RNA 1 Human fetal tissue Homo sapiens 8 43 phNPC from Geschwind Lab 1 6 9.8 18 ASW M 20 phNPC: Neurobasal A (Invitrogen) supplemented with B27 (Gibco), GlutaMAX (Gibco), and Antibiotics and Antimycotics (Gibco)] as well as Retinoic Acid (500 ng/mL; Sigma), Forskolin (100 μM; Sigma), BDNF (10 ng/mL; Peprotech), NT-3 (10 ng/mL; Peprotech), and KCl (10mM); iPSC Kosik Lab: neurobasal media supplemented with N2, B27 and neurotrophic factor cocktail that included NT3, BDNF, and GDNF; iPSC Gage Lab: DMEM/F12, N2, BDNF/GDNF, and laminin. phNPC: Neurobasal A (Invitrogen) supplemented with 10% BIT (Stem Cell Technologies), Antibiotics and Antimycotics (Gibco), GlutaMAX (Gibco), and Heparin (1 μg/mL; Sigma)] with freshly added EGF, FGF2, PDGF (each at 20 ng/mL; Peprotech), and LIF (2 ng/mL; Millipore); iPSC Kosik Lab: N2 induction media with bFGF; iPSC Gage Lab: DMEM/F12; 1X N2; 1X B27 and FGF2 total RNA phNPCs: RNA was isolated using TRIzol reagent (Invitrogen) according to standard protocols; iPSC Kosik Lab: RNA was extracted using miRVANA kit, following the manufacturer’s protocol for total RNA; iPSC Gage Lab: Total cellular RNA was extracted using the RNeasy Protect Mini kit (QIAGEN, Valencia, CA). biotin Biotin Illumina protocol Illumina protocol phNPC from Geschwind Lab Donor: 8 Region: 43 DiffWk: 1 Replicate: 1 Passage: 6 Log2 normalization, quantile normalization, and ComBat batch correction NONE ID_REF VALUE Log2 normalization, quantile normalization, and ComBat batch correction Detection Pval GSM1385310-tbl-1.txt 2014-05-12 2014-06-01 2014-06-01 GSM1385311 RNA 1 Human fetal tissue Homo sapiens 5 17 phNPC from Geschwind Lab 1 9 9.6 17 MEX F 21 phNPC: Neurobasal A (Invitrogen) supplemented with B27 (Gibco), GlutaMAX (Gibco), and Antibiotics and Antimycotics (Gibco)] as well as Retinoic Acid (500 ng/mL; Sigma), Forskolin (100 μM; Sigma), BDNF (10 ng/mL; Peprotech), NT-3 (10 ng/mL; Peprotech), and KCl (10mM); iPSC Kosik Lab: neurobasal media supplemented with N2, B27 and neurotrophic factor cocktail that included NT3, BDNF, and GDNF; iPSC Gage Lab: DMEM/F12, N2, BDNF/GDNF, and laminin. phNPC: Neurobasal A (Invitrogen) supplemented with 10% BIT (Stem Cell Technologies), Antibiotics and Antimycotics (Gibco), GlutaMAX (Gibco), and Heparin (1 μg/mL; Sigma)] with freshly added EGF, FGF2, PDGF (each at 20 ng/mL; Peprotech), and LIF (2 ng/mL; Millipore); iPSC Kosik Lab: N2 induction media with bFGF; iPSC Gage Lab: DMEM/F12; 1X N2; 1X B27 and FGF2 total RNA phNPCs: RNA was isolated using TRIzol reagent (Invitrogen) according to standard protocols; iPSC Kosik Lab: RNA was extracted using miRVANA kit, following the manufacturer’s protocol for total RNA; iPSC Gage Lab: Total cellular RNA was extracted using the RNeasy Protect Mini kit (QIAGEN, Valencia, CA). biotin Biotin Illumina protocol Illumina protocol phNPC from Geschwind Lab Donor: 5 Region: 17 DiffWk: 1 Replicate: 2 Passage: 9 Log2 normalization, quantile normalization, and ComBat batch correction NONE ID_REF VALUE Log2 normalization, quantile normalization, and ComBat batch correction Detection Pval GSM1385311-tbl-1.txt 2014-05-12 2014-06-01 2014-06-01 GSM1385312 RNA 1 Human fetal tissue Homo sapiens 8 46 phNPC from Geschwind Lab 12 5 9.2 18 ASW M 21 phNPC: Neurobasal A (Invitrogen) supplemented with B27 (Gibco), GlutaMAX (Gibco), and Antibiotics and Antimycotics (Gibco)] as well as Retinoic Acid (500 ng/mL; Sigma), Forskolin (100 μM; Sigma), BDNF (10 ng/mL; Peprotech), NT-3 (10 ng/mL; Peprotech), and KCl (10mM); iPSC Kosik Lab: neurobasal media supplemented with N2, B27 and neurotrophic factor cocktail that included NT3, BDNF, and GDNF; iPSC Gage Lab: DMEM/F12, N2, BDNF/GDNF, and laminin. phNPC: Neurobasal A (Invitrogen) supplemented with 10% BIT (Stem Cell Technologies), Antibiotics and Antimycotics (Gibco), GlutaMAX (Gibco), and Heparin (1 μg/mL; Sigma)] with freshly added EGF, FGF2, PDGF (each at 20 ng/mL; Peprotech), and LIF (2 ng/mL; Millipore); iPSC Kosik Lab: N2 induction media with bFGF; iPSC Gage Lab: DMEM/F12; 1X N2; 1X B27 and FGF2 total RNA phNPCs: RNA was isolated using TRIzol reagent (Invitrogen) according to standard protocols; iPSC Kosik Lab: RNA was extracted using miRVANA kit, following the manufacturer’s protocol for total RNA; iPSC Gage Lab: Total cellular RNA was extracted using the RNeasy Protect Mini kit (QIAGEN, Valencia, CA). biotin Biotin Illumina protocol Illumina protocol phNPC from Geschwind Lab Donor: 8 Region: 46 DiffWk: 12 Replicate: 2 Passage: 5 Log2 normalization, quantile normalization, and ComBat batch correction NONE ID_REF VALUE Log2 normalization, quantile normalization, and ComBat batch correction Detection Pval GSM1385312-tbl-1.txt 2014-05-12 2014-06-01 2014-06-01 GSM1385313 RNA 1 Human fetal tissue Homo sapiens 5 17 phNPC from Geschwind Lab 1 9 9.9 17 MEX F 21 phNPC: Neurobasal A (Invitrogen) supplemented with B27 (Gibco), GlutaMAX (Gibco), and Antibiotics and Antimycotics (Gibco)] as well as Retinoic Acid (500 ng/mL; Sigma), Forskolin (100 μM; Sigma), BDNF (10 ng/mL; Peprotech), NT-3 (10 ng/mL; Peprotech), and KCl (10mM); iPSC Kosik Lab: neurobasal media supplemented with N2, B27 and neurotrophic factor cocktail that included NT3, BDNF, and GDNF; iPSC Gage Lab: DMEM/F12, N2, BDNF/GDNF, and laminin. phNPC: Neurobasal A (Invitrogen) supplemented with 10% BIT (Stem Cell Technologies), Antibiotics and Antimycotics (Gibco), GlutaMAX (Gibco), and Heparin (1 μg/mL; Sigma)] with freshly added EGF, FGF2, PDGF (each at 20 ng/mL; Peprotech), and LIF (2 ng/mL; Millipore); iPSC Kosik Lab: N2 induction media with bFGF; iPSC Gage Lab: DMEM/F12; 1X N2; 1X B27 and FGF2 total RNA phNPCs: RNA was isolated using TRIzol reagent (Invitrogen) according to standard protocols; iPSC Kosik Lab: RNA was extracted using miRVANA kit, following the manufacturer’s protocol for total RNA; iPSC Gage Lab: Total cellular RNA was extracted using the RNeasy Protect Mini kit (QIAGEN, Valencia, CA). biotin Biotin Illumina protocol Illumina protocol phNPC from Geschwind Lab Donor: 5 Region: 17 DiffWk: 1 Replicate: 1 Passage: 9 Log2 normalization, quantile normalization, and ComBat batch correction NONE ID_REF VALUE Log2 normalization, quantile normalization, and ComBat batch correction Detection Pval GSM1385313-tbl-1.txt 2014-05-12 2014-06-01 2014-06-01 GSM1385314 RNA 1 iPSC from fibroblast Homo sapiens Tau mutant Tau104 NA iPSC from Kosik Lab morphogens 4 days 8 NA 9.1 NA NA NA 22 phNPC: Neurobasal A (Invitrogen) supplemented with B27 (Gibco), GlutaMAX (Gibco), and Antibiotics and Antimycotics (Gibco)] as well as Retinoic Acid (500 ng/mL; Sigma), Forskolin (100 μM; Sigma), BDNF (10 ng/mL; Peprotech), NT-3 (10 ng/mL; Peprotech), and KCl (10mM); iPSC Kosik Lab: neurobasal media supplemented with N2, B27 and neurotrophic factor cocktail that included NT3, BDNF, and GDNF; iPSC Gage Lab: DMEM/F12, N2, BDNF/GDNF, and laminin. phNPC: Neurobasal A (Invitrogen) supplemented with 10% BIT (Stem Cell Technologies), Antibiotics and Antimycotics (Gibco), GlutaMAX (Gibco), and Heparin (1 μg/mL; Sigma)] with freshly added EGF, FGF2, PDGF (each at 20 ng/mL; Peprotech), and LIF (2 ng/mL; Millipore); iPSC Kosik Lab: N2 induction media with bFGF; iPSC Gage Lab: DMEM/F12; 1X N2; 1X B27 and FGF2 total RNA phNPCs: RNA was isolated using TRIzol reagent (Invitrogen) according to standard protocols; iPSC Kosik Lab: RNA was extracted using miRVANA kit, following the manufacturer’s protocol for total RNA; iPSC Gage Lab: Total cellular RNA was extracted using the RNeasy Protect Mini kit (QIAGEN, Valencia, CA). biotin Biotin Illumina protocol Illumina protocol iPSC from Kosik Lab morphogens 4 days Donor: Tau mutant Tau104 DiffWk: 8 Log2 normalization, quantile normalization, and ComBat batch correction NONE ID_REF VALUE Log2 normalization, quantile normalization, and ComBat batch correction Detection Pval GSM1385314-tbl-1.txt 2014-05-12 2014-06-01 2014-06-01 GSM1385315 RNA 1 iPSC from fibroblast Homo sapiens Control Tau6(IN2R) NA iPSC from Kosik Lab morphogens 8 days 4 NA 8.8 NA NA NA 22 phNPC: Neurobasal A (Invitrogen) supplemented with B27 (Gibco), GlutaMAX (Gibco), and Antibiotics and Antimycotics (Gibco)] as well as Retinoic Acid (500 ng/mL; Sigma), Forskolin (100 μM; Sigma), BDNF (10 ng/mL; Peprotech), NT-3 (10 ng/mL; Peprotech), and KCl (10mM); iPSC Kosik Lab: neurobasal media supplemented with N2, B27 and neurotrophic factor cocktail that included NT3, BDNF, and GDNF; iPSC Gage Lab: DMEM/F12, N2, BDNF/GDNF, and laminin. phNPC: Neurobasal A (Invitrogen) supplemented with 10% BIT (Stem Cell Technologies), Antibiotics and Antimycotics (Gibco), GlutaMAX (Gibco), and Heparin (1 μg/mL; Sigma)] with freshly added EGF, FGF2, PDGF (each at 20 ng/mL; Peprotech), and LIF (2 ng/mL; Millipore); iPSC Kosik Lab: N2 induction media with bFGF; iPSC Gage Lab: DMEM/F12; 1X N2; 1X B27 and FGF2 total RNA phNPCs: RNA was isolated using TRIzol reagent (Invitrogen) according to standard protocols; iPSC Kosik Lab: RNA was extracted using miRVANA kit, following the manufacturer’s protocol for total RNA; iPSC Gage Lab: Total cellular RNA was extracted using the RNeasy Protect Mini kit (QIAGEN, Valencia, CA). biotin Biotin Illumina protocol Illumina protocol iPSC from Kosik Lab morphogens 8 days Donor: Control Tau6(IN2R) DiffWk: 4 Log2 normalization, quantile normalization, and ComBat batch correction NONE ID_REF VALUE Log2 normalization, quantile normalization, and ComBat batch correction Detection Pval GSM1385315-tbl-1.txt 2014-05-12 2014-06-01 2014-06-01 GSM1385316 RNA 1 iPSC from fibroblast Homo sapiens Tau mutant Tau104 NA iPSC from Kosik Lab morphogens 4 days 1 NA 8.8 NA NA NA 22 phNPC: Neurobasal A (Invitrogen) supplemented with B27 (Gibco), GlutaMAX (Gibco), and Antibiotics and Antimycotics (Gibco)] as well as Retinoic Acid (500 ng/mL; Sigma), Forskolin (100 μM; Sigma), BDNF (10 ng/mL; Peprotech), NT-3 (10 ng/mL; Peprotech), and KCl (10mM); iPSC Kosik Lab: neurobasal media supplemented with N2, B27 and neurotrophic factor cocktail that included NT3, BDNF, and GDNF; iPSC Gage Lab: DMEM/F12, N2, BDNF/GDNF, and laminin. phNPC: Neurobasal A (Invitrogen) supplemented with 10% BIT (Stem Cell Technologies), Antibiotics and Antimycotics (Gibco), GlutaMAX (Gibco), and Heparin (1 μg/mL; Sigma)] with freshly added EGF, FGF2, PDGF (each at 20 ng/mL; Peprotech), and LIF (2 ng/mL; Millipore); iPSC Kosik Lab: N2 induction media with bFGF; iPSC Gage Lab: DMEM/F12; 1X N2; 1X B27 and FGF2 total RNA phNPCs: RNA was isolated using TRIzol reagent (Invitrogen) according to standard protocols; iPSC Kosik Lab: RNA was extracted using miRVANA kit, following the manufacturer’s protocol for total RNA; iPSC Gage Lab: Total cellular RNA was extracted using the RNeasy Protect Mini kit (QIAGEN, Valencia, CA). biotin Biotin Illumina protocol Illumina protocol iPSC from Kosik Lab morphogens 4 days Donor: Tau mutant Tau104 DiffWk: 1 Log2 normalization, quantile normalization, and ComBat batch correction NONE ID_REF VALUE Log2 normalization, quantile normalization, and ComBat batch correction Detection Pval GSM1385316-tbl-1.txt 2014-05-12 2014-06-01 2014-06-01 GSM1385317 RNA 1 iPSC from fibroblast Homo sapiens Control Tau6(IN2R) NA iPSC from Kosik Lab morphogens 8 days 0 NA 8.3 NA NA NA 22 phNPC: Neurobasal A (Invitrogen) supplemented with B27 (Gibco), GlutaMAX (Gibco), and Antibiotics and Antimycotics (Gibco)] as well as Retinoic Acid (500 ng/mL; Sigma), Forskolin (100 μM; Sigma), BDNF (10 ng/mL; Peprotech), NT-3 (10 ng/mL; Peprotech), and KCl (10mM); iPSC Kosik Lab: neurobasal media supplemented with N2, B27 and neurotrophic factor cocktail that included NT3, BDNF, and GDNF; iPSC Gage Lab: DMEM/F12, N2, BDNF/GDNF, and laminin. phNPC: Neurobasal A (Invitrogen) supplemented with 10% BIT (Stem Cell Technologies), Antibiotics and Antimycotics (Gibco), GlutaMAX (Gibco), and Heparin (1 μg/mL; Sigma)] with freshly added EGF, FGF2, PDGF (each at 20 ng/mL; Peprotech), and LIF (2 ng/mL; Millipore); iPSC Kosik Lab: N2 induction media with bFGF; iPSC Gage Lab: DMEM/F12; 1X N2; 1X B27 and FGF2 total RNA phNPCs: RNA was isolated using TRIzol reagent (Invitrogen) according to standard protocols; iPSC Kosik Lab: RNA was extracted using miRVANA kit, following the manufacturer’s protocol for total RNA; iPSC Gage Lab: Total cellular RNA was extracted using the RNeasy Protect Mini kit (QIAGEN, Valencia, CA). biotin Biotin Illumina protocol Illumina protocol iPSC from Kosik Lab morphogens 8 days Donor: Control Tau6(IN2R) DiffWk: 0 Log2 normalization, quantile normalization, and ComBat batch correction NONE ID_REF VALUE Log2 normalization, quantile normalization, and ComBat batch correction Detection Pval GSM1385317-tbl-1.txt 2014-05-12 2014-06-01 2014-06-01 GSM1385318 RNA 1 iPSC from fibroblast Homo sapiens Tau mutant Tau104 NA iPSC from Kosik Lab morphogens 8 days 8 NA 8.9 NA NA NA 23 phNPC: Neurobasal A (Invitrogen) supplemented with B27 (Gibco), GlutaMAX (Gibco), and Antibiotics and Antimycotics (Gibco)] as well as Retinoic Acid (500 ng/mL; Sigma), Forskolin (100 μM; Sigma), BDNF (10 ng/mL; Peprotech), NT-3 (10 ng/mL; Peprotech), and KCl (10mM); iPSC Kosik Lab: neurobasal media supplemented with N2, B27 and neurotrophic factor cocktail that included NT3, BDNF, and GDNF; iPSC Gage Lab: DMEM/F12, N2, BDNF/GDNF, and laminin. phNPC: Neurobasal A (Invitrogen) supplemented with 10% BIT (Stem Cell Technologies), Antibiotics and Antimycotics (Gibco), GlutaMAX (Gibco), and Heparin (1 μg/mL; Sigma)] with freshly added EGF, FGF2, PDGF (each at 20 ng/mL; Peprotech), and LIF (2 ng/mL; Millipore); iPSC Kosik Lab: N2 induction media with bFGF; iPSC Gage Lab: DMEM/F12; 1X N2; 1X B27 and FGF2 total RNA phNPCs: RNA was isolated using TRIzol reagent (Invitrogen) according to standard protocols; iPSC Kosik Lab: RNA was extracted using miRVANA kit, following the manufacturer’s protocol for total RNA; iPSC Gage Lab: Total cellular RNA was extracted using the RNeasy Protect Mini kit (QIAGEN, Valencia, CA). biotin Biotin Illumina protocol Illumina protocol iPSC from Kosik Lab morphogens 8 days Donor: Tau mutant Tau104 DiffWk: 8 Log2 normalization, quantile normalization, and ComBat batch correction NONE ID_REF VALUE Log2 normalization, quantile normalization, and ComBat batch correction Detection Pval GSM1385318-tbl-1.txt 2014-05-12 2014-06-01 2014-06-01 GSM1385319 RNA 1 iPSC from fibroblast Homo sapiens Control Tau6(IN2R) NA iPSC from Kosik Lab morphogens 4 days 4 NA 9.2 NA NA NA 23 phNPC: Neurobasal A (Invitrogen) supplemented with B27 (Gibco), GlutaMAX (Gibco), and Antibiotics and Antimycotics (Gibco)] as well as Retinoic Acid (500 ng/mL; Sigma), Forskolin (100 μM; Sigma), BDNF (10 ng/mL; Peprotech), NT-3 (10 ng/mL; Peprotech), and KCl (10mM); iPSC Kosik Lab: neurobasal media supplemented with N2, B27 and neurotrophic factor cocktail that included NT3, BDNF, and GDNF; iPSC Gage Lab: DMEM/F12, N2, BDNF/GDNF, and laminin. phNPC: Neurobasal A (Invitrogen) supplemented with 10% BIT (Stem Cell Technologies), Antibiotics and Antimycotics (Gibco), GlutaMAX (Gibco), and Heparin (1 μg/mL; Sigma)] with freshly added EGF, FGF2, PDGF (each at 20 ng/mL; Peprotech), and LIF (2 ng/mL; Millipore); iPSC Kosik Lab: N2 induction media with bFGF; iPSC Gage Lab: DMEM/F12; 1X N2; 1X B27 and FGF2 total RNA phNPCs: RNA was isolated using TRIzol reagent (Invitrogen) according to standard protocols; iPSC Kosik Lab: RNA was extracted using miRVANA kit, following the manufacturer’s protocol for total RNA; iPSC Gage Lab: Total cellular RNA was extracted using the RNeasy Protect Mini kit (QIAGEN, Valencia, CA). biotin Biotin Illumina protocol Illumina protocol iPSC from Kosik Lab morphogens 4 days Donor: Control Tau6(IN2R) DiffWk: 4 Log2 normalization, quantile normalization, and ComBat batch correction NONE ID_REF VALUE Log2 normalization, quantile normalization, and ComBat batch correction Detection Pval GSM1385319-tbl-1.txt 2014-05-12 2014-06-01 2014-06-01 GSM1385320 RNA 1 iPSC from fibroblast Homo sapiens Tau mutant Tau104 NA iPSC from Kosik Lab morphogens 8 days 1 NA 8.7 NA NA NA 23 phNPC: Neurobasal A (Invitrogen) supplemented with B27 (Gibco), GlutaMAX (Gibco), and Antibiotics and Antimycotics (Gibco)] as well as Retinoic Acid (500 ng/mL; Sigma), Forskolin (100 μM; Sigma), BDNF (10 ng/mL; Peprotech), NT-3 (10 ng/mL; Peprotech), and KCl (10mM); iPSC Kosik Lab: neurobasal media supplemented with N2, B27 and neurotrophic factor cocktail that included NT3, BDNF, and GDNF; iPSC Gage Lab: DMEM/F12, N2, BDNF/GDNF, and laminin. phNPC: Neurobasal A (Invitrogen) supplemented with 10% BIT (Stem Cell Technologies), Antibiotics and Antimycotics (Gibco), GlutaMAX (Gibco), and Heparin (1 μg/mL; Sigma)] with freshly added EGF, FGF2, PDGF (each at 20 ng/mL; Peprotech), and LIF (2 ng/mL; Millipore); iPSC Kosik Lab: N2 induction media with bFGF; iPSC Gage Lab: DMEM/F12; 1X N2; 1X B27 and FGF2 total RNA phNPCs: RNA was isolated using TRIzol reagent (Invitrogen) according to standard protocols; iPSC Kosik Lab: RNA was extracted using miRVANA kit, following the manufacturer’s protocol for total RNA; iPSC Gage Lab: Total cellular RNA was extracted using the RNeasy Protect Mini kit (QIAGEN, Valencia, CA). biotin Biotin Illumina protocol Illumina protocol iPSC from Kosik Lab morphogens 8 days Donor: Tau mutant Tau104 DiffWk: 1 Log2 normalization, quantile normalization, and ComBat batch correction NONE ID_REF VALUE Log2 normalization, quantile normalization, and ComBat batch correction Detection Pval GSM1385320-tbl-1.txt 2014-05-12 2014-06-01 2014-06-01 GSM1385321 RNA 1 iPSC from fibroblast Homo sapiens Control Tau6(IN2R) NA iPSC from Kosik Lab morphogens 4 days 0 NA 8.8 NA NA NA 23 phNPC: Neurobasal A (Invitrogen) supplemented with B27 (Gibco), GlutaMAX (Gibco), and Antibiotics and Antimycotics (Gibco)] as well as Retinoic Acid (500 ng/mL; Sigma), Forskolin (100 μM; Sigma), BDNF (10 ng/mL; Peprotech), NT-3 (10 ng/mL; Peprotech), and KCl (10mM); iPSC Kosik Lab: neurobasal media supplemented with N2, B27 and neurotrophic factor cocktail that included NT3, BDNF, and GDNF; iPSC Gage Lab: DMEM/F12, N2, BDNF/GDNF, and laminin. phNPC: Neurobasal A (Invitrogen) supplemented with 10% BIT (Stem Cell Technologies), Antibiotics and Antimycotics (Gibco), GlutaMAX (Gibco), and Heparin (1 μg/mL; Sigma)] with freshly added EGF, FGF2, PDGF (each at 20 ng/mL; Peprotech), and LIF (2 ng/mL; Millipore); iPSC Kosik Lab: N2 induction media with bFGF; iPSC Gage Lab: DMEM/F12; 1X N2; 1X B27 and FGF2 total RNA phNPCs: RNA was isolated using TRIzol reagent (Invitrogen) according to standard protocols; iPSC Kosik Lab: RNA was extracted using miRVANA kit, following the manufacturer’s protocol for total RNA; iPSC Gage Lab: Total cellular RNA was extracted using the RNeasy Protect Mini kit (QIAGEN, Valencia, CA). biotin Biotin Illumina protocol Illumina protocol iPSC from Kosik Lab morphogens 4 days Donor: Control Tau6(IN2R) DiffWk: 0 Log2 normalization, quantile normalization, and ComBat batch correction NONE ID_REF VALUE Log2 normalization, quantile normalization, and ComBat batch correction Detection Pval GSM1385321-tbl-1.txt 2014-05-12 2014-06-01 2014-06-01 GSM1385322 RNA 1 iPSC from fibroblast Homo sapiens Control Tau6(IN2R) NA iPSC from Kosik Lab morphogens 4 days 8 NA 8.8 NA NA NA 24 phNPC: Neurobasal A (Invitrogen) supplemented with B27 (Gibco), GlutaMAX (Gibco), and Antibiotics and Antimycotics (Gibco)] as well as Retinoic Acid (500 ng/mL; Sigma), Forskolin (100 μM; Sigma), BDNF (10 ng/mL; Peprotech), NT-3 (10 ng/mL; Peprotech), and KCl (10mM); iPSC Kosik Lab: neurobasal media supplemented with N2, B27 and neurotrophic factor cocktail that included NT3, BDNF, and GDNF; iPSC Gage Lab: DMEM/F12, N2, BDNF/GDNF, and laminin. phNPC: Neurobasal A (Invitrogen) supplemented with 10% BIT (Stem Cell Technologies), Antibiotics and Antimycotics (Gibco), GlutaMAX (Gibco), and Heparin (1 μg/mL; Sigma)] with freshly added EGF, FGF2, PDGF (each at 20 ng/mL; Peprotech), and LIF (2 ng/mL; Millipore); iPSC Kosik Lab: N2 induction media with bFGF; iPSC Gage Lab: DMEM/F12; 1X N2; 1X B27 and FGF2 total RNA phNPCs: RNA was isolated using TRIzol reagent (Invitrogen) according to standard protocols; iPSC Kosik Lab: RNA was extracted using miRVANA kit, following the manufacturer’s protocol for total RNA; iPSC Gage Lab: Total cellular RNA was extracted using the RNeasy Protect Mini kit (QIAGEN, Valencia, CA). biotin Biotin Illumina protocol Illumina protocol iPSC from Kosik Lab morphogens 4 days Donor: Control Tau6(IN2R) DiffWk: 8 Log2 normalization, quantile normalization, and ComBat batch correction NONE ID_REF VALUE Log2 normalization, quantile normalization, and ComBat batch correction Detection Pval GSM1385322-tbl-1.txt 2014-05-12 2014-06-01 2014-06-01 GSM1385323 RNA 1 iPSC from fibroblast Homo sapiens Tau mutant Tau104 NA iPSC from Kosik Lab morphogens 8 days 4 NA 8.9 NA NA NA 24 phNPC: Neurobasal A (Invitrogen) supplemented with B27 (Gibco), GlutaMAX (Gibco), and Antibiotics and Antimycotics (Gibco)] as well as Retinoic Acid (500 ng/mL; Sigma), Forskolin (100 μM; Sigma), BDNF (10 ng/mL; Peprotech), NT-3 (10 ng/mL; Peprotech), and KCl (10mM); iPSC Kosik Lab: neurobasal media supplemented with N2, B27 and neurotrophic factor cocktail that included NT3, BDNF, and GDNF; iPSC Gage Lab: DMEM/F12, N2, BDNF/GDNF, and laminin. phNPC: Neurobasal A (Invitrogen) supplemented with 10% BIT (Stem Cell Technologies), Antibiotics and Antimycotics (Gibco), GlutaMAX (Gibco), and Heparin (1 μg/mL; Sigma)] with freshly added EGF, FGF2, PDGF (each at 20 ng/mL; Peprotech), and LIF (2 ng/mL; Millipore); iPSC Kosik Lab: N2 induction media with bFGF; iPSC Gage Lab: DMEM/F12; 1X N2; 1X B27 and FGF2 total RNA phNPCs: RNA was isolated using TRIzol reagent (Invitrogen) according to standard protocols; iPSC Kosik Lab: RNA was extracted using miRVANA kit, following the manufacturer’s protocol for total RNA; iPSC Gage Lab: Total cellular RNA was extracted using the RNeasy Protect Mini kit (QIAGEN, Valencia, CA). biotin Biotin Illumina protocol Illumina protocol iPSC from Kosik Lab morphogens 8 days Donor: Tau mutant Tau104 DiffWk: 4 Log2 normalization, quantile normalization, and ComBat batch correction NONE ID_REF VALUE Log2 normalization, quantile normalization, and ComBat batch correction Detection Pval GSM1385323-tbl-1.txt 2014-05-12 2014-06-01 2014-06-01 GSM1385324 RNA 1 iPSC from fibroblast Homo sapiens Control Tau6(IN2R) NA iPSC from Kosik Lab morphogens 4 days 1 NA 9.3 NA NA NA 24 phNPC: Neurobasal A (Invitrogen) supplemented with B27 (Gibco), GlutaMAX (Gibco), and Antibiotics and Antimycotics (Gibco)] as well as Retinoic Acid (500 ng/mL; Sigma), Forskolin (100 μM; Sigma), BDNF (10 ng/mL; Peprotech), NT-3 (10 ng/mL; Peprotech), and KCl (10mM); iPSC Kosik Lab: neurobasal media supplemented with N2, B27 and neurotrophic factor cocktail that included NT3, BDNF, and GDNF; iPSC Gage Lab: DMEM/F12, N2, BDNF/GDNF, and laminin. phNPC: Neurobasal A (Invitrogen) supplemented with 10% BIT (Stem Cell Technologies), Antibiotics and Antimycotics (Gibco), GlutaMAX (Gibco), and Heparin (1 μg/mL; Sigma)] with freshly added EGF, FGF2, PDGF (each at 20 ng/mL; Peprotech), and LIF (2 ng/mL; Millipore); iPSC Kosik Lab: N2 induction media with bFGF; iPSC Gage Lab: DMEM/F12; 1X N2; 1X B27 and FGF2 total RNA phNPCs: RNA was isolated using TRIzol reagent (Invitrogen) according to standard protocols; iPSC Kosik Lab: RNA was extracted using miRVANA kit, following the manufacturer’s protocol for total RNA; iPSC Gage Lab: Total cellular RNA was extracted using the RNeasy Protect Mini kit (QIAGEN, Valencia, CA). biotin Biotin Illumina protocol Illumina protocol iPSC from Kosik Lab morphogens 4 days Donor: Control Tau6(IN2R) DiffWk: 1 Log2 normalization, quantile normalization, and ComBat batch correction NONE ID_REF VALUE Log2 normalization, quantile normalization, and ComBat batch correction Detection Pval GSM1385324-tbl-1.txt 2014-05-12 2014-06-01 2014-06-01 GSM1385325 RNA 1 iPSC from fibroblast Homo sapiens Tau mutant Tau104 NA iPSC from Kosik Lab morphogens 8 days 0 NA 9.3 NA NA NA 24 phNPC: Neurobasal A (Invitrogen) supplemented with B27 (Gibco), GlutaMAX (Gibco), and Antibiotics and Antimycotics (Gibco)] as well as Retinoic Acid (500 ng/mL; Sigma), Forskolin (100 μM; Sigma), BDNF (10 ng/mL; Peprotech), NT-3 (10 ng/mL; Peprotech), and KCl (10mM); iPSC Kosik Lab: neurobasal media supplemented with N2, B27 and neurotrophic factor cocktail that included NT3, BDNF, and GDNF; iPSC Gage Lab: DMEM/F12, N2, BDNF/GDNF, and laminin. phNPC: Neurobasal A (Invitrogen) supplemented with 10% BIT (Stem Cell Technologies), Antibiotics and Antimycotics (Gibco), GlutaMAX (Gibco), and Heparin (1 μg/mL; Sigma)] with freshly added EGF, FGF2, PDGF (each at 20 ng/mL; Peprotech), and LIF (2 ng/mL; Millipore); iPSC Kosik Lab: N2 induction media with bFGF; iPSC Gage Lab: DMEM/F12; 1X N2; 1X B27 and FGF2 total RNA phNPCs: RNA was isolated using TRIzol reagent (Invitrogen) according to standard protocols; iPSC Kosik Lab: RNA was extracted using miRVANA kit, following the manufacturer’s protocol for total RNA; iPSC Gage Lab: Total cellular RNA was extracted using the RNeasy Protect Mini kit (QIAGEN, Valencia, CA). biotin Biotin Illumina protocol Illumina protocol iPSC from Kosik Lab morphogens 8 days Donor: Tau mutant Tau104 DiffWk: 0 Log2 normalization, quantile normalization, and ComBat batch correction NONE ID_REF VALUE Log2 normalization, quantile normalization, and ComBat batch correction Detection Pval GSM1385325-tbl-1.txt 2014-05-12 2014-06-01 2014-06-01 GSM1385326 RNA 1 iPSC from fibroblast Homo sapiens Control Tau6(IN2R) NA iPSC from Kosik Lab morphogens 8 days 8 NA 8.9 NA NA NA 25 phNPC: Neurobasal A (Invitrogen) supplemented with B27 (Gibco), GlutaMAX (Gibco), and Antibiotics and Antimycotics (Gibco)] as well as Retinoic Acid (500 ng/mL; Sigma), Forskolin (100 μM; Sigma), BDNF (10 ng/mL; Peprotech), NT-3 (10 ng/mL; Peprotech), and KCl (10mM); iPSC Kosik Lab: neurobasal media supplemented with N2, B27 and neurotrophic factor cocktail that included NT3, BDNF, and GDNF; iPSC Gage Lab: DMEM/F12, N2, BDNF/GDNF, and laminin. phNPC: Neurobasal A (Invitrogen) supplemented with 10% BIT (Stem Cell Technologies), Antibiotics and Antimycotics (Gibco), GlutaMAX (Gibco), and Heparin (1 μg/mL; Sigma)] with freshly added EGF, FGF2, PDGF (each at 20 ng/mL; Peprotech), and LIF (2 ng/mL; Millipore); iPSC Kosik Lab: N2 induction media with bFGF; iPSC Gage Lab: DMEM/F12; 1X N2; 1X B27 and FGF2 total RNA phNPCs: RNA was isolated using TRIzol reagent (Invitrogen) according to standard protocols; iPSC Kosik Lab: RNA was extracted using miRVANA kit, following the manufacturer’s protocol for total RNA; iPSC Gage Lab: Total cellular RNA was extracted using the RNeasy Protect Mini kit (QIAGEN, Valencia, CA). biotin Biotin Illumina protocol Illumina protocol iPSC from Kosik Lab morphogens 8 days Donor: Control Tau6(IN2R) DiffWk: 8 Log2 normalization, quantile normalization, and ComBat batch correction NONE ID_REF VALUE Log2 normalization, quantile normalization, and ComBat batch correction Detection Pval GSM1385326-tbl-1.txt 2014-05-12 2014-06-01 2014-06-01 GSM1385327 RNA 1 iPSC from fibroblast Homo sapiens Tau mutant Tau104 NA iPSC from Kosik Lab morphogens 4 days 4 NA 9.3 NA NA NA 25 phNPC: Neurobasal A (Invitrogen) supplemented with B27 (Gibco), GlutaMAX (Gibco), and Antibiotics and Antimycotics (Gibco)] as well as Retinoic Acid (500 ng/mL; Sigma), Forskolin (100 μM; Sigma), BDNF (10 ng/mL; Peprotech), NT-3 (10 ng/mL; Peprotech), and KCl (10mM); iPSC Kosik Lab: neurobasal media supplemented with N2, B27 and neurotrophic factor cocktail that included NT3, BDNF, and GDNF; iPSC Gage Lab: DMEM/F12, N2, BDNF/GDNF, and laminin. phNPC: Neurobasal A (Invitrogen) supplemented with 10% BIT (Stem Cell Technologies), Antibiotics and Antimycotics (Gibco), GlutaMAX (Gibco), and Heparin (1 μg/mL; Sigma)] with freshly added EGF, FGF2, PDGF (each at 20 ng/mL; Peprotech), and LIF (2 ng/mL; Millipore); iPSC Kosik Lab: N2 induction media with bFGF; iPSC Gage Lab: DMEM/F12; 1X N2; 1X B27 and FGF2 total RNA phNPCs: RNA was isolated using TRIzol reagent (Invitrogen) according to standard protocols; iPSC Kosik Lab: RNA was extracted using miRVANA kit, following the manufacturer’s protocol for total RNA; iPSC Gage Lab: Total cellular RNA was extracted using the RNeasy Protect Mini kit (QIAGEN, Valencia, CA). biotin Biotin Illumina protocol Illumina protocol iPSC from Kosik Lab morphogens 4 days Donor: Tau mutant Tau104 DiffWk: 4 Log2 normalization, quantile normalization, and ComBat batch correction NONE ID_REF VALUE Log2 normalization, quantile normalization, and ComBat batch correction Detection Pval GSM1385327-tbl-1.txt 2014-05-12 2014-06-01 2014-06-01 GSM1385328 RNA 1 iPSC from fibroblast Homo sapiens Control Tau6(IN2R) NA iPSC from Kosik Lab morphogens 8 days 1 NA 8.6 NA NA NA 25 phNPC: Neurobasal A (Invitrogen) supplemented with B27 (Gibco), GlutaMAX (Gibco), and Antibiotics and Antimycotics (Gibco)] as well as Retinoic Acid (500 ng/mL; Sigma), Forskolin (100 μM; Sigma), BDNF (10 ng/mL; Peprotech), NT-3 (10 ng/mL; Peprotech), and KCl (10mM); iPSC Kosik Lab: neurobasal media supplemented with N2, B27 and neurotrophic factor cocktail that included NT3, BDNF, and GDNF; iPSC Gage Lab: DMEM/F12, N2, BDNF/GDNF, and laminin. phNPC: Neurobasal A (Invitrogen) supplemented with 10% BIT (Stem Cell Technologies), Antibiotics and Antimycotics (Gibco), GlutaMAX (Gibco), and Heparin (1 μg/mL; Sigma)] with freshly added EGF, FGF2, PDGF (each at 20 ng/mL; Peprotech), and LIF (2 ng/mL; Millipore); iPSC Kosik Lab: N2 induction media with bFGF; iPSC Gage Lab: DMEM/F12; 1X N2; 1X B27 and FGF2 total RNA phNPCs: RNA was isolated using TRIzol reagent (Invitrogen) according to standard protocols; iPSC Kosik Lab: RNA was extracted using miRVANA kit, following the manufacturer’s protocol for total RNA; iPSC Gage Lab: Total cellular RNA was extracted using the RNeasy Protect Mini kit (QIAGEN, Valencia, CA). biotin Biotin Illumina protocol Illumina protocol iPSC from Kosik Lab morphogens 8 days Donor: Control Tau6(IN2R) DiffWk: 1 Log2 normalization, quantile normalization, and ComBat batch correction NONE ID_REF VALUE Log2 normalization, quantile normalization, and ComBat batch correction Detection Pval GSM1385328-tbl-1.txt 2014-05-12 2014-06-01 2014-06-01 GSM1385329 RNA 1 iPSC from fibroblast Homo sapiens Tau mutant Tau104 NA iPSC from Kosik Lab morphogens 4 days 0 NA 9 NA NA NA 25 phNPC: Neurobasal A (Invitrogen) supplemented with B27 (Gibco), GlutaMAX (Gibco), and Antibiotics and Antimycotics (Gibco)] as well as Retinoic Acid (500 ng/mL; Sigma), Forskolin (100 μM; Sigma), BDNF (10 ng/mL; Peprotech), NT-3 (10 ng/mL; Peprotech), and KCl (10mM); iPSC Kosik Lab: neurobasal media supplemented with N2, B27 and neurotrophic factor cocktail that included NT3, BDNF, and GDNF; iPSC Gage Lab: DMEM/F12, N2, BDNF/GDNF, and laminin. phNPC: Neurobasal A (Invitrogen) supplemented with 10% BIT (Stem Cell Technologies), Antibiotics and Antimycotics (Gibco), GlutaMAX (Gibco), and Heparin (1 μg/mL; Sigma)] with freshly added EGF, FGF2, PDGF (each at 20 ng/mL; Peprotech), and LIF (2 ng/mL; Millipore); iPSC Kosik Lab: N2 induction media with bFGF; iPSC Gage Lab: DMEM/F12; 1X N2; 1X B27 and FGF2 total RNA phNPCs: RNA was isolated using TRIzol reagent (Invitrogen) according to standard protocols; iPSC Kosik Lab: RNA was extracted using miRVANA kit, following the manufacturer’s protocol for total RNA; iPSC Gage Lab: Total cellular RNA was extracted using the RNeasy Protect Mini kit (QIAGEN, Valencia, CA). biotin Biotin Illumina protocol Illumina protocol iPSC from Kosik Lab morphogens 4 days Donor: Tau mutant Tau104 DiffWk: 0 Log2 normalization, quantile normalization, and ComBat batch correction NONE ID_REF VALUE Log2 normalization, quantile normalization, and ComBat batch correction Detection Pval GSM1385329-tbl-1.txt 2014-05-12 2014-06-01 2014-06-01 GSM1385330 RNA 1 iPSC from fibroblast Homo sapiens control line cove cloneID: 3-7 iPSC from Gage Lab 0 NA 9.6 NA NA NA 22 phNPC: Neurobasal A (Invitrogen) supplemented with B27 (Gibco), GlutaMAX (Gibco), and Antibiotics and Antimycotics (Gibco)] as well as Retinoic Acid (500 ng/mL; Sigma), Forskolin (100 μM; Sigma), BDNF (10 ng/mL; Peprotech), NT-3 (10 ng/mL; Peprotech), and KCl (10mM); iPSC Kosik Lab: neurobasal media supplemented with N2, B27 and neurotrophic factor cocktail that included NT3, BDNF, and GDNF; iPSC Gage Lab: DMEM/F12, N2, BDNF/GDNF, and laminin. phNPC: Neurobasal A (Invitrogen) supplemented with 10% BIT (Stem Cell Technologies), Antibiotics and Antimycotics (Gibco), GlutaMAX (Gibco), and Heparin (1 μg/mL; Sigma)] with freshly added EGF, FGF2, PDGF (each at 20 ng/mL; Peprotech), and LIF (2 ng/mL; Millipore); iPSC Kosik Lab: N2 induction media with bFGF; iPSC Gage Lab: DMEM/F12; 1X N2; 1X B27 and FGF2 total RNA phNPCs: RNA was isolated using TRIzol reagent (Invitrogen) according to standard protocols; iPSC Kosik Lab: RNA was extracted using miRVANA kit, following the manufacturer’s protocol for total RNA; iPSC Gage Lab: Total cellular RNA was extracted using the RNeasy Protect Mini kit (QIAGEN, Valencia, CA). biotin Biotin Illumina protocol Illumina protocol iPSC from Gage Lab Donor: control line cove Region: cloneID: 3-7 DiffWk: 0 Log2 normalization, quantile normalization, and ComBat batch correction NONE ID_REF VALUE Log2 normalization, quantile normalization, and ComBat batch correction Detection Pval GSM1385330-tbl-1.txt 2014-05-12 2014-06-01 2014-06-01 GSM1385331 RNA 1 iPSC from fibroblast Homo sapiens control line chap cloneID: 1-2 iPSC from Gage Lab 4 NA 9.4 NA NA NA 22 phNPC: Neurobasal A (Invitrogen) supplemented with B27 (Gibco), GlutaMAX (Gibco), and Antibiotics and Antimycotics (Gibco)] as well as Retinoic Acid (500 ng/mL; Sigma), Forskolin (100 μM; Sigma), BDNF (10 ng/mL; Peprotech), NT-3 (10 ng/mL; Peprotech), and KCl (10mM); iPSC Kosik Lab: neurobasal media supplemented with N2, B27 and neurotrophic factor cocktail that included NT3, BDNF, and GDNF; iPSC Gage Lab: DMEM/F12, N2, BDNF/GDNF, and laminin. phNPC: Neurobasal A (Invitrogen) supplemented with 10% BIT (Stem Cell Technologies), Antibiotics and Antimycotics (Gibco), GlutaMAX (Gibco), and Heparin (1 μg/mL; Sigma)] with freshly added EGF, FGF2, PDGF (each at 20 ng/mL; Peprotech), and LIF (2 ng/mL; Millipore); iPSC Kosik Lab: N2 induction media with bFGF; iPSC Gage Lab: DMEM/F12; 1X N2; 1X B27 and FGF2 total RNA phNPCs: RNA was isolated using TRIzol reagent (Invitrogen) according to standard protocols; iPSC Kosik Lab: RNA was extracted using miRVANA kit, following the manufacturer’s protocol for total RNA; iPSC Gage Lab: Total cellular RNA was extracted using the RNeasy Protect Mini kit (QIAGEN, Valencia, CA). biotin Biotin Illumina protocol Illumina protocol iPSC from Gage Lab Donor: control line chap Region: cloneID: 1-2 DiffWk: 4 Log2 normalization, quantile normalization, and ComBat batch correction NONE ID_REF VALUE Log2 normalization, quantile normalization, and ComBat batch correction Detection Pval GSM1385331-tbl-1.txt 2014-05-12 2014-06-01 2014-06-01 GSM1385332 RNA 1 iPSC from fibroblast Homo sapiens control line cent cloneID: 3-3 iPSC from Gage Lab 4 NA 8.4 NA NA NA 22 phNPC: Neurobasal A (Invitrogen) supplemented with B27 (Gibco), GlutaMAX (Gibco), and Antibiotics and Antimycotics (Gibco)] as well as Retinoic Acid (500 ng/mL; Sigma), Forskolin (100 μM; Sigma), BDNF (10 ng/mL; Peprotech), NT-3 (10 ng/mL; Peprotech), and KCl (10mM); iPSC Kosik Lab: neurobasal media supplemented with N2, B27 and neurotrophic factor cocktail that included NT3, BDNF, and GDNF; iPSC Gage Lab: DMEM/F12, N2, BDNF/GDNF, and laminin. phNPC: Neurobasal A (Invitrogen) supplemented with 10% BIT (Stem Cell Technologies), Antibiotics and Antimycotics (Gibco), GlutaMAX (Gibco), and Heparin (1 μg/mL; Sigma)] with freshly added EGF, FGF2, PDGF (each at 20 ng/mL; Peprotech), and LIF (2 ng/mL; Millipore); iPSC Kosik Lab: N2 induction media with bFGF; iPSC Gage Lab: DMEM/F12; 1X N2; 1X B27 and FGF2 total RNA phNPCs: RNA was isolated using TRIzol reagent (Invitrogen) according to standard protocols; iPSC Kosik Lab: RNA was extracted using miRVANA kit, following the manufacturer’s protocol for total RNA; iPSC Gage Lab: Total cellular RNA was extracted using the RNeasy Protect Mini kit (QIAGEN, Valencia, CA). biotin Biotin Illumina protocol Illumina protocol iPSC from Gage Lab Donor: control line cent Region: cloneID: 3-3 DiffWk: 4 Log2 normalization, quantile normalization, and ComBat batch correction NONE ID_REF VALUE Log2 normalization, quantile normalization, and ComBat batch correction Detection Pval GSM1385332-tbl-1.txt 2014-05-12 2014-06-01 2014-06-01 GSM1385333 RNA 1 iPSC from fibroblast Homo sapiens control line cove cloneID: 3-1 iPSC from Gage Lab 4 NA 9.3 NA NA NA 23 phNPC: Neurobasal A (Invitrogen) supplemented with B27 (Gibco), GlutaMAX (Gibco), and Antibiotics and Antimycotics (Gibco)] as well as Retinoic Acid (500 ng/mL; Sigma), Forskolin (100 μM; Sigma), BDNF (10 ng/mL; Peprotech), NT-3 (10 ng/mL; Peprotech), and KCl (10mM); iPSC Kosik Lab: neurobasal media supplemented with N2, B27 and neurotrophic factor cocktail that included NT3, BDNF, and GDNF; iPSC Gage Lab: DMEM/F12, N2, BDNF/GDNF, and laminin. phNPC: Neurobasal A (Invitrogen) supplemented with 10% BIT (Stem Cell Technologies), Antibiotics and Antimycotics (Gibco), GlutaMAX (Gibco), and Heparin (1 μg/mL; Sigma)] with freshly added EGF, FGF2, PDGF (each at 20 ng/mL; Peprotech), and LIF (2 ng/mL; Millipore); iPSC Kosik Lab: N2 induction media with bFGF; iPSC Gage Lab: DMEM/F12; 1X N2; 1X B27 and FGF2 total RNA phNPCs: RNA was isolated using TRIzol reagent (Invitrogen) according to standard protocols; iPSC Kosik Lab: RNA was extracted using miRVANA kit, following the manufacturer’s protocol for total RNA; iPSC Gage Lab: Total cellular RNA was extracted using the RNeasy Protect Mini kit (QIAGEN, Valencia, CA). biotin Biotin Illumina protocol Illumina protocol iPSC from Gage Lab Donor: control line cove Region: cloneID: 3-1 DiffWk: 4 Log2 normalization, quantile normalization, and ComBat batch correction NONE ID_REF VALUE Log2 normalization, quantile normalization, and ComBat batch correction Detection Pval GSM1385333-tbl-1.txt 2014-05-12 2014-06-01 2014-06-01 GSM1385334 RNA 1 iPSC from fibroblast Homo sapiens control line chap cloneID: 1-5 iPSC from Gage Lab 0 NA 10 NA NA NA 23 phNPC: Neurobasal A (Invitrogen) supplemented with B27 (Gibco), GlutaMAX (Gibco), and Antibiotics and Antimycotics (Gibco)] as well as Retinoic Acid (500 ng/mL; Sigma), Forskolin (100 μM; Sigma), BDNF (10 ng/mL; Peprotech), NT-3 (10 ng/mL; Peprotech), and KCl (10mM); iPSC Kosik Lab: neurobasal media supplemented with N2, B27 and neurotrophic factor cocktail that included NT3, BDNF, and GDNF; iPSC Gage Lab: DMEM/F12, N2, BDNF/GDNF, and laminin. phNPC: Neurobasal A (Invitrogen) supplemented with 10% BIT (Stem Cell Technologies), Antibiotics and Antimycotics (Gibco), GlutaMAX (Gibco), and Heparin (1 μg/mL; Sigma)] with freshly added EGF, FGF2, PDGF (each at 20 ng/mL; Peprotech), and LIF (2 ng/mL; Millipore); iPSC Kosik Lab: N2 induction media with bFGF; iPSC Gage Lab: DMEM/F12; 1X N2; 1X B27 and FGF2 total RNA phNPCs: RNA was isolated using TRIzol reagent (Invitrogen) according to standard protocols; iPSC Kosik Lab: RNA was extracted using miRVANA kit, following the manufacturer’s protocol for total RNA; iPSC Gage Lab: Total cellular RNA was extracted using the RNeasy Protect Mini kit (QIAGEN, Valencia, CA). biotin Biotin Illumina protocol Illumina protocol iPSC from Gage Lab Donor: control line chap Region: cloneID: 1-5 DiffWk: 0 Log2 normalization, quantile normalization, and ComBat batch correction NONE ID_REF VALUE Log2 normalization, quantile normalization, and ComBat batch correction Detection Pval GSM1385334-tbl-1.txt 2014-05-12 2014-06-01 2014-06-01 GSM1385335 RNA 1 iPSC from fibroblast Homo sapiens control line cent cloneID: 3-6 iPSC from Gage Lab 0 NA 9.7 NA NA NA 23 phNPC: Neurobasal A (Invitrogen) supplemented with B27 (Gibco), GlutaMAX (Gibco), and Antibiotics and Antimycotics (Gibco)] as well as Retinoic Acid (500 ng/mL; Sigma), Forskolin (100 μM; Sigma), BDNF (10 ng/mL; Peprotech), NT-3 (10 ng/mL; Peprotech), and KCl (10mM); iPSC Kosik Lab: neurobasal media supplemented with N2, B27 and neurotrophic factor cocktail that included NT3, BDNF, and GDNF; iPSC Gage Lab: DMEM/F12, N2, BDNF/GDNF, and laminin. phNPC: Neurobasal A (Invitrogen) supplemented with 10% BIT (Stem Cell Technologies), Antibiotics and Antimycotics (Gibco), GlutaMAX (Gibco), and Heparin (1 μg/mL; Sigma)] with freshly added EGF, FGF2, PDGF (each at 20 ng/mL; Peprotech), and LIF (2 ng/mL; Millipore); iPSC Kosik Lab: N2 induction media with bFGF; iPSC Gage Lab: DMEM/F12; 1X N2; 1X B27 and FGF2 total RNA phNPCs: RNA was isolated using TRIzol reagent (Invitrogen) according to standard protocols; iPSC Kosik Lab: RNA was extracted using miRVANA kit, following the manufacturer’s protocol for total RNA; iPSC Gage Lab: Total cellular RNA was extracted using the RNeasy Protect Mini kit (QIAGEN, Valencia, CA). biotin Biotin Illumina protocol Illumina protocol iPSC from Gage Lab Donor: control line cent Region: cloneID: 3-6 DiffWk: 0 Log2 normalization, quantile normalization, and ComBat batch correction NONE ID_REF VALUE Log2 normalization, quantile normalization, and ComBat batch correction Detection Pval GSM1385335-tbl-1.txt 2014-05-12 2014-06-01 2014-06-01 GSM1385336 RNA 1 iPSC from fibroblast Homo sapiens control line cove cloneID: 3-7 iPSC from Gage Lab 4 NA 9 NA NA NA 24 phNPC: Neurobasal A (Invitrogen) supplemented with B27 (Gibco), GlutaMAX (Gibco), and Antibiotics and Antimycotics (Gibco)] as well as Retinoic Acid (500 ng/mL; Sigma), Forskolin (100 μM; Sigma), BDNF (10 ng/mL; Peprotech), NT-3 (10 ng/mL; Peprotech), and KCl (10mM); iPSC Kosik Lab: neurobasal media supplemented with N2, B27 and neurotrophic factor cocktail that included NT3, BDNF, and GDNF; iPSC Gage Lab: DMEM/F12, N2, BDNF/GDNF, and laminin. phNPC: Neurobasal A (Invitrogen) supplemented with 10% BIT (Stem Cell Technologies), Antibiotics and Antimycotics (Gibco), GlutaMAX (Gibco), and Heparin (1 μg/mL; Sigma)] with freshly added EGF, FGF2, PDGF (each at 20 ng/mL; Peprotech), and LIF (2 ng/mL; Millipore); iPSC Kosik Lab: N2 induction media with bFGF; iPSC Gage Lab: DMEM/F12; 1X N2; 1X B27 and FGF2 total RNA phNPCs: RNA was isolated using TRIzol reagent (Invitrogen) according to standard protocols; iPSC Kosik Lab: RNA was extracted using miRVANA kit, following the manufacturer’s protocol for total RNA; iPSC Gage Lab: Total cellular RNA was extracted using the RNeasy Protect Mini kit (QIAGEN, Valencia, CA). biotin Biotin Illumina protocol Illumina protocol iPSC from Gage Lab Donor: control line cove Region: cloneID: 3-7 DiffWk: 4 Log2 normalization, quantile normalization, and ComBat batch correction NONE ID_REF VALUE Log2 normalization, quantile normalization, and ComBat batch correction Detection Pval GSM1385336-tbl-1.txt 2014-05-12 2014-06-01 2014-06-01 GSM1385337 RNA 1 iPSC from fibroblast Homo sapiens control line chap cloneID: 1-2 iPSC from Gage Lab 0 NA 9.8 NA NA NA 24 phNPC: Neurobasal A (Invitrogen) supplemented with B27 (Gibco), GlutaMAX (Gibco), and Antibiotics and Antimycotics (Gibco)] as well as Retinoic Acid (500 ng/mL; Sigma), Forskolin (100 μM; Sigma), BDNF (10 ng/mL; Peprotech), NT-3 (10 ng/mL; Peprotech), and KCl (10mM); iPSC Kosik Lab: neurobasal media supplemented with N2, B27 and neurotrophic factor cocktail that included NT3, BDNF, and GDNF; iPSC Gage Lab: DMEM/F12, N2, BDNF/GDNF, and laminin. phNPC: Neurobasal A (Invitrogen) supplemented with 10% BIT (Stem Cell Technologies), Antibiotics and Antimycotics (Gibco), GlutaMAX (Gibco), and Heparin (1 μg/mL; Sigma)] with freshly added EGF, FGF2, PDGF (each at 20 ng/mL; Peprotech), and LIF (2 ng/mL; Millipore); iPSC Kosik Lab: N2 induction media with bFGF; iPSC Gage Lab: DMEM/F12; 1X N2; 1X B27 and FGF2 total RNA phNPCs: RNA was isolated using TRIzol reagent (Invitrogen) according to standard protocols; iPSC Kosik Lab: RNA was extracted using miRVANA kit, following the manufacturer’s protocol for total RNA; iPSC Gage Lab: Total cellular RNA was extracted using the RNeasy Protect Mini kit (QIAGEN, Valencia, CA). biotin Biotin Illumina protocol Illumina protocol iPSC from Gage Lab Donor: control line chap Region: cloneID: 1-2 DiffWk: 0 Log2 normalization, quantile normalization, and ComBat batch correction NONE ID_REF VALUE Log2 normalization, quantile normalization, and ComBat batch correction Detection Pval GSM1385337-tbl-1.txt 2014-05-12 2014-06-01 2014-06-01 GSM1385338 RNA 1 iPSC from fibroblast Homo sapiens control line cent cloneID: 3-3 iPSC from Gage Lab 0 NA 9.3 NA NA NA 24 phNPC: Neurobasal A (Invitrogen) supplemented with B27 (Gibco), GlutaMAX (Gibco), and Antibiotics and Antimycotics (Gibco)] as well as Retinoic Acid (500 ng/mL; Sigma), Forskolin (100 μM; Sigma), BDNF (10 ng/mL; Peprotech), NT-3 (10 ng/mL; Peprotech), and KCl (10mM); iPSC Kosik Lab: neurobasal media supplemented with N2, B27 and neurotrophic factor cocktail that included NT3, BDNF, and GDNF; iPSC Gage Lab: DMEM/F12, N2, BDNF/GDNF, and laminin. phNPC: Neurobasal A (Invitrogen) supplemented with 10% BIT (Stem Cell Technologies), Antibiotics and Antimycotics (Gibco), GlutaMAX (Gibco), and Heparin (1 μg/mL; Sigma)] with freshly added EGF, FGF2, PDGF (each at 20 ng/mL; Peprotech), and LIF (2 ng/mL; Millipore); iPSC Kosik Lab: N2 induction media with bFGF; iPSC Gage Lab: DMEM/F12; 1X N2; 1X B27 and FGF2 total RNA phNPCs: RNA was isolated using TRIzol reagent (Invitrogen) according to standard protocols; iPSC Kosik Lab: RNA was extracted using miRVANA kit, following the manufacturer’s protocol for total RNA; iPSC Gage Lab: Total cellular RNA was extracted using the RNeasy Protect Mini kit (QIAGEN, Valencia, CA). biotin Biotin Illumina protocol Illumina protocol iPSC from Gage Lab Donor: control line cent Region: cloneID: 3-3 DiffWk: 0 Log2 normalization, quantile normalization, and ComBat batch correction NONE ID_REF VALUE Log2 normalization, quantile normalization, and ComBat batch correction Detection Pval GSM1385338-tbl-1.txt 2014-05-12 2014-06-01 2014-06-01 GSM1385339 RNA 1 iPSC from fibroblast Homo sapiens control line cove cloneID: 3-1 iPSC from Gage Lab 0 NA 9.6 NA NA NA 25 phNPC: Neurobasal A (Invitrogen) supplemented with B27 (Gibco), GlutaMAX (Gibco), and Antibiotics and Antimycotics (Gibco)] as well as Retinoic Acid (500 ng/mL; Sigma), Forskolin (100 μM; Sigma), BDNF (10 ng/mL; Peprotech), NT-3 (10 ng/mL; Peprotech), and KCl (10mM); iPSC Kosik Lab: neurobasal media supplemented with N2, B27 and neurotrophic factor cocktail that included NT3, BDNF, and GDNF; iPSC Gage Lab: DMEM/F12, N2, BDNF/GDNF, and laminin. phNPC: Neurobasal A (Invitrogen) supplemented with 10% BIT (Stem Cell Technologies), Antibiotics and Antimycotics (Gibco), GlutaMAX (Gibco), and Heparin (1 μg/mL; Sigma)] with freshly added EGF, FGF2, PDGF (each at 20 ng/mL; Peprotech), and LIF (2 ng/mL; Millipore); iPSC Kosik Lab: N2 induction media with bFGF; iPSC Gage Lab: DMEM/F12; 1X N2; 1X B27 and FGF2 total RNA phNPCs: RNA was isolated using TRIzol reagent (Invitrogen) according to standard protocols; iPSC Kosik Lab: RNA was extracted using miRVANA kit, following the manufacturer’s protocol for total RNA; iPSC Gage Lab: Total cellular RNA was extracted using the RNeasy Protect Mini kit (QIAGEN, Valencia, CA). biotin Biotin Illumina protocol Illumina protocol iPSC from Gage Lab Donor: control line cove Region: cloneID: 3-1 DiffWk: 0 Log2 normalization, quantile normalization, and ComBat batch correction NONE ID_REF VALUE Log2 normalization, quantile normalization, and ComBat batch correction Detection Pval GSM1385339-tbl-1.txt 2014-05-12 2014-06-01 2014-06-01 GSM1385340 RNA 1 iPSC from fibroblast Homo sapiens control line chap cloneID: 1-5 iPSC from Gage Lab 4 NA 9.5 NA NA NA 25 phNPC: Neurobasal A (Invitrogen) supplemented with B27 (Gibco), GlutaMAX (Gibco), and Antibiotics and Antimycotics (Gibco)] as well as Retinoic Acid (500 ng/mL; Sigma), Forskolin (100 μM; Sigma), BDNF (10 ng/mL; Peprotech), NT-3 (10 ng/mL; Peprotech), and KCl (10mM); iPSC Kosik Lab: neurobasal media supplemented with N2, B27 and neurotrophic factor cocktail that included NT3, BDNF, and GDNF; iPSC Gage Lab: DMEM/F12, N2, BDNF/GDNF, and laminin. phNPC: Neurobasal A (Invitrogen) supplemented with 10% BIT (Stem Cell Technologies), Antibiotics and Antimycotics (Gibco), GlutaMAX (Gibco), and Heparin (1 μg/mL; Sigma)] with freshly added EGF, FGF2, PDGF (each at 20 ng/mL; Peprotech), and LIF (2 ng/mL; Millipore); iPSC Kosik Lab: N2 induction media with bFGF; iPSC Gage Lab: DMEM/F12; 1X N2; 1X B27 and FGF2 total RNA phNPCs: RNA was isolated using TRIzol reagent (Invitrogen) according to standard protocols; iPSC Kosik Lab: RNA was extracted using miRVANA kit, following the manufacturer’s protocol for total RNA; iPSC Gage Lab: Total cellular RNA was extracted using the RNeasy Protect Mini kit (QIAGEN, Valencia, CA). biotin Biotin Illumina protocol Illumina protocol iPSC from Gage Lab Donor: control line chap Region: cloneID: 1-5 DiffWk: 4 Log2 normalization, quantile normalization, and ComBat batch correction NONE ID_REF VALUE Log2 normalization, quantile normalization, and ComBat batch correction Detection Pval GSM1385340-tbl-1.txt 2014-05-12 2014-06-01 2014-06-01 GSM1385341 RNA 1 iPSC from fibroblast Homo sapiens control line cent cloneID: 3-6 iPSC from Gage Lab 4 NA 8.8 NA NA NA 25 phNPC: Neurobasal A (Invitrogen) supplemented with B27 (Gibco), GlutaMAX (Gibco), and Antibiotics and Antimycotics (Gibco)] as well as Retinoic Acid (500 ng/mL; Sigma), Forskolin (100 μM; Sigma), BDNF (10 ng/mL; Peprotech), NT-3 (10 ng/mL; Peprotech), and KCl (10mM); iPSC Kosik Lab: neurobasal media supplemented with N2, B27 and neurotrophic factor cocktail that included NT3, BDNF, and GDNF; iPSC Gage Lab: DMEM/F12, N2, BDNF/GDNF, and laminin. phNPC: Neurobasal A (Invitrogen) supplemented with 10% BIT (Stem Cell Technologies), Antibiotics and Antimycotics (Gibco), GlutaMAX (Gibco), and Heparin (1 μg/mL; Sigma)] with freshly added EGF, FGF2, PDGF (each at 20 ng/mL; Peprotech), and LIF (2 ng/mL; Millipore); iPSC Kosik Lab: N2 induction media with bFGF; iPSC Gage Lab: DMEM/F12; 1X N2; 1X B27 and FGF2 total RNA phNPCs: RNA was isolated using TRIzol reagent (Invitrogen) according to standard protocols; iPSC Kosik Lab: RNA was extracted using miRVANA kit, following the manufacturer’s protocol for total RNA; iPSC Gage Lab: Total cellular RNA was extracted using the RNeasy Protect Mini kit (QIAGEN, Valencia, CA). biotin Biotin Illumina protocol Illumina protocol iPSC from Gage Lab Donor: control line cent Region: cloneID: 3-6 DiffWk: 4 Log2 normalization, quantile normalization, and ComBat batch correction NONE ID_REF VALUE Log2 normalization, quantile normalization, and ComBat batch correction Detection Pval GSM1385341-tbl-1.txt 2014-05-12 2014-06-01 2018-08-13 GSE57595 24991955

In vitro neural stem cell models are widely used to model a wide range of neuropsychiatric conditions. However, how well such models correspond to in vivo brain has not been evaluated in an unbiased, comprehensive manner. We used transcriptomic analyses to compare in vitro systems to developing human fetal brain and observed strong conservation of in vivo gene expression and network architecture in differentiating primary human neural progenitor cells (phNPCs). Conserved modules are enriched in genes associated with ASD, supporting the utility of phNPCs for studying neuropsychiatric disease. We also developed and validated a machine learning approach called CoNTExT that identifies the developmental maturity and regional identity of in vitro models. We observed strong differences between in vitro models, including hiPSC-derived neural progenitors from multiple laboratories. This work provides a framework for evaluating in vitro systems and supports their value in studying the molecular mechanisms of human neurodevelopmental disease. In this GEO submission, we upload data from 5 lines of phNPCs as well as hiPSCs cultured in two different laboratories all at multiple differentiation time points.

phNPCs: For each of 5 lines generated from 3 donors (15-16 PCW), two independent differentiation experiments each containing two replicates were performed and harvested at four time points (1, 4, 8, 12 wks PD; ~16 samples per line; 77 total samples). We confirmed RNA integrity by RIN score with the Agilent 2100 Bioanalyzer (mean +/- sd: 9.16 +/- 0.78). iPSC: Two hiPSC datasets were RNA profiled as part of this study. hiPSCs grown in the Kosik lab was derived from two independent, non-isogenic IPS lines: one derived from a patient carrying a mutant Tau variant G55R and one reference control. For each of these lines, two samples were harvested at each of 0, 1, 4, and 8 weeks PD (total n=16 samples). hiPSCs grown in the Gage lab were from six samples derived from 3 control lines at each of two time points (0 and 4 wk PD, total n=12 samples). Samples were randomized to microarray chip by all biological variables of interest (donor, line, passage, replicate number, differentiation week, plate date, and RIN) to control for potential batch effects. Expression profiling by array ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE57nnn/GSE57595/suppl/GSE57595_RAW.tar ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE57nnn/GSE57595/suppl/GSE57595_non-normalized.txt.gz