|
| Status |
Public on Dec 20, 2021 |
| Title |
SZ9 |
| Sample type |
SRA |
| |
|
| Source name |
hiPSC-derived brain astrocytes
|
| Organism |
Homo sapiens |
| Characteristics |
sample number: 5
cell type: hiPSC-derived brain astrocytes
hipsc source: skin fibroblasts
group status: Pair 4, affected twin
individual: Monozygotic twin with schizophrenia diagnosis and medication
age: 69
patient gender: female
patient disease status: schizophrenia
|
| 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 |
SAMN24244918 |
| SRA |
SRX13453960 |
