|
| Status |
Public on Oct 22, 2023 |
| Title |
RC1-C |
| Sample type |
SRA |
| |
|
| Source name |
RC-iPSC line
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: RC-iPSC line
cell type: retinal organoids
genotype: WT
treatment: Vehicle
time: Ctrl
|
| Treatment protocol |
On treatment day for PR3 studies, organoids were treated with PR3 (0.25uM) for 7 days prior to collection for RNA isolation.
|
| Growth protocol |
iPSC-derived retinal organoids were generated using our previously described protocol (Chirco et al Stem Cell Reports 2021)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was harvested using TriReagent and Chloroform-Ethanol extraction.
Library preparation and Illumina-based transcriptome sequencing was carried out at Novogene
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
HiSeq X Ten |
| |
|
| Data processing |
Following QC, alignments were using Salmon (V1.5.1) using GRCh37 - hg19 reference sequence
Differential expressions were determined through DESeq2 R package (v1.14.1 ).81 Genes with an adjusted p-value <0.05 (Benjamini and Hochberg’s approach) found by DESeq2 were assigned as differentially expressed.
Gene Ontology (GO) enrichment analysis of differentially expressed genes was implemented by the clusterProfiler R package, in which gene length bias was corrected.
Assembly: GRCH38
Supplementary files format and content: CSV file of readcounts from various conditions
|
| |
|
| Submission date |
Oct 17, 2023 |
| Last update date |
Oct 22, 2023 |
| Contact name |
Deepak A Lamba |
| E-mail(s) |
[email protected]
|
| Phone |
4153047743
|
| Organization name |
University of California, San Francisco
|
| Street address |
35 Medical Center Way, Rm1024
|
| City |
San Francisco |
| State/province |
CA |
| ZIP/Postal code |
94143 |
| Country |
USA |
| |
|
| Platform ID |
GPL20795 |
| Series (1) |
| GSE245545 |
Modeling and modulation of RHO signaling in human iPSC-derived retinal organoids from patients with RHO-CNV |
|
| Relations |
| BioSample |
SAMN37856810 |
| SRA |
SRX22115801 |
