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Sample GSM2580014 Query DataSets for GSM2580014
Status Public on Aug 18, 2017
Title 3651_Astros
Sample type SRA
 
Source name GM03651 (Coriell)
Organism Homo sapiens
Characteristics cell type: hiPSC-astrocyte
gender: female
Biomaterial provider Coriell Cell Repositories https://catalog.coriell.org/0/Sections/Search/Sample_Detail.aspx?Ref=GM03651
Treatment protocol n/a
Growth protocol Forebrain NPCs were maintained at high density, grown on matrigel (BD Bioscience) in NPC medium (DMEM/F12 (Invitrogen: 10565), 1x N2 (Invitrogen: 17502-048), 1x B27-RA (Invitrogen: 12587-010)) and 20 ng/ml FGF2 (Invitrogen), resuspended in 1% BSA (Gibco) in PBS (Gibco)) and split approximately 1:3-1:4 every week with accutase (Millipore). NPCs could be expanded up to 14 passages. Forebrain NPCs were differentiated to astrocytes by seeding dissociated single cells at 15,000 cells/cm2 density on matrigel-coated plates in astrocyte medium (ScienCell: 1801, astrocyte medium (1801-b), 2% fetal bovine serum (0010), astrocyte growth supplement (1852) and 10U/ml penicillin/streptomycin solution (0503)). Initial NPC seeding density and single cell dissociation are critical, particularly during the first 30 days of differentiation, in order to efficiently generate a homogenous population of astrocytes.
Extracted molecule total RNA
Extraction protocol Cells were plated at 1,000,000 cells per well of a 6-well plate. Within 24-48 hrs, astrocyte cultures were washed with PBS and lysed with RLT buffer (Qiagen, # 74106) or Qiazol reagent (Qiagen). The total RNA was extracted from 30-day differentiated astrocytes with easy mini kit (Qiagen, # 74106) with on-column DNase Idigestion (Qiagen, #79254).
RNA libraries were prepared for sequencing using standard Illumina protocols
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
 
Description Sample 1
Data processing Paired-end RNA-seq data was generated with the Illumina HiSeq 2500 platform following the Illumina protocol. The raw sequencing reads were aligned to human hg19 genome using star aligner (version 2.5.0b).
Following read alignment, featureCounts (v1.5.0-p1) was used to quantify the gene expression at the gene level based on Ensembl gene model GRCh37.70.
Genes with at least 1 count per million (CPM) in more than 2 samples were considered expressed and hence retained for further analysis, otherwise removed.
The gene level read counts data was normalized using trimmed mean of M-values normalization (TMM) method to adjust for sequencing library size difference.
To control for potential sex differences in gene expression, sex effects were corrected by linear regression.
Genome_build: hg19
 
Submission date Apr 17, 2017
Last update date May 15, 2019
Contact name Kristen J. Brennand
Organization name Icahn School of Medicine at Mount Sinai
Department Department of Neuroscience & Friedman Brain Institute
Street address 1425 Madison Ave
City New York
State/province NY
ZIP/Postal code 10029
Country USA
 
Platform ID GPL16791
Series (1)
GSE97904 Functional astrocytes differentiated from hiPSCs
Relations
BioSample SAMN06760661
SRA SRX2742170

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

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