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Sample GSM5742176 Query DataSets for GSM5742176
Status Public on Dec 20, 2021
Title SZ10
Sample type SRA
 
Source name hiPSC-derived brain astrocytes
Organism Homo sapiens
Characteristics sample number: 6
cell type: hiPSC-derived brain astrocytes
hipsc source: skin fibroblasts
group status: Pair 4, unaffected twin
individual: Monozygotic twin without schizophrenia diagnosis
age: 69
patient gender: female
patient disease status: healthy
Treatment protocol Matured astrocytes were not treated
Growth protocol The primary cells were reprogrammed with Cytotune 2.0 iPS Sendai Reprogramming Kit for Oct4, Sox2, Klf4, and c-myc. The emerged colonies were individually subcloned. For differentiation, iPSCs were cultured in feeder-free conditions with Matrigel-coating and Essential 8 culture medium. Astroglial differentiation was carried out as described (Stem Cell Reports. 2017;9:1885-1897) by maintaining neural progenitor spheres in astrocyte differentiation medium in suspension for 5–7 months before dissociation and plating the cells on Matrigel-coated dishes for maturation 7 days prior to experiments.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted using RNeasy Mini Kit. The RNA quality was analyzed on the Agilent 2100 Bioanalyzer™ using an RNA6000 assay.
Sequencing libraries were prepared with Illumina NextSeq and SureSelect Strand Specific RNA Seq kits.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
 
Data processing Each sample was run mixed in all runs and lanes. RNA-sequencing reads for each sample were merged from three Illumina NextSeq 500 runs totalling 12 lanes. Reads were aligned to human genome hg38 using STAR aligner (Dobin et al. 2013) and annotated to genes using HTSeq (Anders et al. 2015).
Genome_build: hg38
Supplementary_files_format_and_content: Tab delimited text file containing unnormalized (raw) read counts per feature.
 
Submission date Dec 20, 2021
Last update date Dec 20, 2021
Contact name Iiris Hovatta
E-mail(s) iiris.hovatta@helsinki.fi
Organization name University of Helsinki
Department Department of Psychology and Logopedics
Lab Neurogenomics
Street address Haartmaninkatu 3
City Helsinki
ZIP/Postal code 00014
Country Finland
 
Platform ID GPL18573
Series (2)
GSE191248 Gene expression analysis of astrocytes differentiated from iPS cells generated from monozygotic twins discordant for schizophrenia
GSE191250 Contribution of astrocytes to familial risk and clinical manifestation of Schizophrenia
Relations
BioSample SAMN24244917
SRA SRX13453961

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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