|
| Status |
Public on Jan 11, 2024 |
| Title |
two-month GTF2I-KO organoids, rep 2 |
| Sample type |
SRA |
| |
|
| Source name |
hiPSC-derived cortical organoids
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: hiPSC-derived cortical organoids
cell line: CVB
cell type: hiPSC-derived cortical organoids
genotype: GTF2I-KO
treatment: genetic modification
|
| Treatment protocol |
Cells were supplemented with growth factors including FGF, EGF, BDNF, GDNF, NT-3 as well as ascorbic acid and cAMP
|
| Growth protocol |
hiPSCs were cultured in mTeSR. Organoids were grown in neurobasal formulation supplemented with growth factors to promote proliferation and neuronal differentiation and maturation.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using a Qiagen Rneasy Mini kit
TruSeq RNA Sample Preparation Kit
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
JA08
|
| Data processing |
Data was analyzed by Rosalind (https://rosalind.onramp.bio)
reads were trimmed using cutadapt
quality scores were assessed using Fast QC
reads were aligned to Homo sapiens genome build hg19 using STAR
individual sample reads were quantified using HTseq and normalized via Relative Log Expression using DESeq2 R library
DESeq2 was used to calculate fold changes and p-values and perform optional covariate correction
Assembly: hg19
Supplementary files format and content: raw counts.csv
Supplementary files format and content: normalized counts.csv
|
| |
|
| Submission date |
Jan 08, 2024 |
| Last update date |
Jan 11, 2024 |
| Contact name |
Alysson R. Muotri |
| Organization name |
UNIVERSITY OF CALIFORNIA, SAN DIEGO
|
| Street address |
2880 Torrey Pines Scenic Road MC 0695
|
| City |
La Jolla |
| State/province |
CA |
| ZIP/Postal code |
92037-0695 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE252761 |
Loss of GTF2I promotes neuronal apoptosis and synaptic reduction in human cellular models of neurodevelopment |
|
| Relations |
| BioSample |
SAMN39299035 |
| SRA |
SRX23132905 |
