|
| Status |
Public on Dec 20, 2023 |
| Title |
open_chor_00h_ck6Ml_s124 |
| Sample type |
SRA |
| |
|
| Source name |
choroid
|
| Organism |
Gallus gallus |
| Characteristics |
tissue: choroid
eye treatment: open
timept: 00h
chickid: ck6
eye: left
Sex: M
|
| Treatment protocol |
chick eyes were goggled (occl) or open
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted from choroid and retinal tissues using the QIAgen RNAeasy kit
Illumina TruSeq stranded kit using roughly equal amounts of RNA (between 100 and 300ng)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
104639_124
|
| Data processing |
raw data was processed by the standard Illumina pipeline to yeild trimmed fastq files
fastq data counted against transcripts (ensembl v105) with salmon
data summarized to gene-level with tximeta (bioconductor)
Assembly: GRCg6a (gene models – ensembl v105)
Supplementary files format and content: gzipped tab-delimited text – raw counts per ensembl gene ID per sample
|
| |
|
| Submission date |
Mar 20, 2023 |
| Last update date |
Dec 20, 2023 |
| Contact name |
Debora Nickla |
| Organization name |
New England College of Optometry
|
| Department |
Dept. of Biosciences and Disease
|
| Street address |
424 Beacon St
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02115 |
| Country |
USA |
| |
|
| Platform ID |
GPL26853 |
| Series (1) |
| GSE227724 |
Daily Patterns of Retinal and Choroidal Gene Expression and Circadian Biology in Myopia Pathogenesis |
|
| Relations |
| BioSample |
SAMN33831674 |
| SRA |
SRX19732386 |
