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Sample GSM1556310 Query DataSets for GSM1556310
Status Public on Apr 21, 2016
Title SZ3_5
Sample type SRA
 
Source name hiPSC forebrain Neurons
Organism Homo sapiens
Characteristics diagnosis: Schizophrenia
gender: female
repository source fibroblast id: GM01835 (Coriell)
Biomaterial provider Coriell Cell Repositories http://ccr.coriell.org/Sections/Search/Search.aspx?PgId=165&q=GM01835
Growth protocol hiPSC forebrain neurons were derived as described previously (Brennand et al., 2011). For neural differentiations, NPCs were dissociated with Accutase and plated in neural differentiation media (DMEM/F12-Glutamax, 1XN2, 1X B27-RA, 20 ng/ml BDNF, 20 ng/ml GDNF (Peprotech), 1 mm dibutyrl-cyclicAMP (Sigma), 200 nm ascorbic acid (Sigma) onto PORN/Laminin-coated plates. 200,000 cells/well of a 6-well plate. hiPSC derived-neurons were differentiated for 6 weeks.
Extracted molecule total RNA
Extraction protocol Cells were lysed in RNA BEE (Tel-test, Inc). RNA was chloroform extracted, pelleted with isopropanol, washed with 70% ethanol and resuspended in water. RNA was treated with RQ1 RNAse-free DNAse (Promega) for 30 minutes at 37C and then the reaction was inactivated by incubation with EGTA Stop buffer at 65C for 10 minutes.
RNA libraries were prepared for sequencing using standard Illumina protocols
Hi-Seq, 100nt, Paired-End Read, 4 samples per lane
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
 
Description 1835#1 5
Data processing The Illumina TruSeq RNA kit was used for 100nt/paired end reads, 4 samples were run per lane using the standard Truseq indices. Raw cDNA reads are aligned to the hg19 reference with the spliced gap aligner STAR, with count-based quantitation carried out via the Subread package featureCounts at both the geneic and exonic levels for UCSC and ensemble annotation builds.
Genome_build: hg19
Supplementary_files_format_and_content: txt format; the read count for each gene
 
Submission date Dec 01, 2014
Last update date May 15, 2019
Contact name Kristen Brennand
E-mail(s) kristen.brennand@mssm.edu
Organization name Icahn School of Medicine at Mount Sinai
Department Psychiatry
Street address 1425 Madison Ave, 9-20B
City New York
State/province NY
ZIP/Postal code 10029
Country USA
 
Platform ID GPL16791
Series (2)
GSE63734 Next Generation Sequencing Facilitates Comparisons of Control and Schizophrenia-Patient derived hiPSC-derived neurons
GSE80163 Dysregulation of miRNA-9 in a subset of schizophrenia patient-derived neural progenitor cells
Relations
BioSample SAMN03247029
SRA SRX791108

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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