|
| Status |
Public on Jan 14, 2023 |
| Title |
VPA, iPSC-derived neurons, biol rep 3 |
| Sample type |
SRA |
| |
|
| Source name |
iPSC line I-93-7
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: iPSC line I-93-7
cell type: iPSC-derived neurons
treatment: VPA
|
| Treatment protocol |
iPSC-derived neurons were treated with 200µg/ml VPA or DMSO at day 64 of neuronal induction and were harvested after 24 hours for RNA extraction.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using the mirVANA RNA isolation kit (ThermoFisher).
Libaries were generated using the Illumina Tru-Seq kit following manufactuer's protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Read quality was accessed using FastQC (version 0.11.9)
Raw reads were mapped to the Ensembl reference genome 104 (GRCh38) using Salmon (version 1.5.2).
Differentially expressed genes were detected using the DESeq2 R package (version 1.32.0).
Assembly: hg38
Supplementary files format and content: tab-delimited text files include gene counts for each Sample.
|
| |
|
| Submission date |
Jan 09, 2023 |
| Last update date |
Jan 15, 2023 |
| Contact name |
Calvin S Leung |
| Organization name |
Brown University
|
| Department |
MCB
|
| Lab |
Laboratories for Molecular Medicine, Room 322B
|
| Street address |
70 Ship Street
|
| City |
Providence |
| State/province |
RI |
| ZIP/Postal code |
02903 |
| Country |
USA |
| |
|
| Platform ID |
GPL16791 |
| Series (1) |
| GSE222509 |
Dysregulation of the chromatin environment leads to differential alternative splicing as a mechanism of disease in a human model of autism spectrum disorder |
|
| Relations |
| BioSample |
SAMN32648467 |
| SRA |
SRX18986631 |
