NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM5742204 Query DataSets for GSM5742204
Status Public on Dec 20, 2021
Title 40_S6
Sample type SRA
 
Source name human iPSC-astrocyte progenitor transplanted RAG1 mouse cortical sample
Organisms Homo sapiens; Mus musculus
Characteristics sample number: 18
mouse strand: B6.12957-Rag1tm1Mom/J
cell type: human iPSC-astrocyte progenitor transplanted RAG1 mouse cortical sample
hipsc source: skin fibroblasts
group status: healthy control
mouse gender: female
patient gender: female
patient disease status: healthy
sample type: Mouse cortex transplanted human iPSC-astrocyte progenitors from healthy control person
Treatment protocol No treatment was applied.
Growth protocol iPSC-astrocyte progenitors: 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 6–7 months before dissociation. Transplantation: hiPSC-astrocyte progenitors (100,000 cells/µl in PBS) dissociated from sphere cultures were transplanted into newborn Rag1 knockout mouse (B6.12957-Rag1tm1Mom/J, The Jackson Laboratory) forebrain using the published protocol (Kim, et al., 2014). Cell transplantation was performed by injecting 300,000 cells into the brain at 5 locations: (0.8, 1.0, -1.5); (-0.8, 1.0, -1.5); (0.8, 2.0, -1.5); (-0.8, 2.0, -1.5); (0.0, -1.0, -1.5). The mice were killed when they were 11 months old and frontal cortex was separated.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted using Trizol and cleaned 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 mouse and human genomes using STAR aligner, version (Dobin et al. 2013) and annotated to genes using HTSeq (Anders et al. 2015).
Genome_build: mm10 and hg38
Supplementary_files_format_and_content: Tab delimeted 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 GPL19415
Series (2)
GSE191249 Gene expression analysis of transplanted hiPSC-astrocyte progenitors generated from monozygotic twin pair discordant for schizophrenia into mouse brain
GSE191250 Contribution of astrocytes to familial risk and clinical manifestation of Schizophrenia
Relations
BioSample SAMN24244932
SRA SRX13453952

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

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap