|
| Status |
Public on Jun 07, 2023 |
| Title |
Wildtype_VAS_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
C57BL/6
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
genotype: WT
treatment: diet: Vitamin A sufficient diet
treatment: time_on_diet: 12 weeks
tissue type: RPE-choroid
|
| Treatment protocol |
After weaning, Stra6 knockout and WT mice were maintained on a diet deficient (0 IU/g) or sufficient (4 IU/g) in vitamin A for 12 weeks
|
| Growth protocol |
Before weaning (~28 days), the pups were kept with dams maintained on a standard rodent chow diet.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was harvested using TRIzol and Rneasy mini plus kit (Qiagen). At least 1 ug of total RNA was used for the construction of sequencing libraries (Novogene).
Library preparation and construction were performed by Novogene.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
Sample WS1
|
| Data processing |
The paired-end reads, provided by the fastq files, were aligned to to GRCm38/mm10 genome (UCSC genome source, 2011) using STAR (version 2.5.3a). An average of 87.4% of reads was uniquely mapped to the reference genome. The correlated annotation file (GTF) was applied and the gene expression level was determined by RSEM (version 1.2.30) quantification. Count normalization and differential gene expression was carried out using DESeq2 version 1.32.0. The Wald test was used for comparisons between treatment groups. To account for multiple testing, the FDR cutoff was set at 0.05. gProfiler was used for Gene Ontology and pathway analyses. An overrepresentation test was applied for significant changes in gene expression.
Assembly: mm10
Supplementary files format and content: comma separated values files include normalized counts produced by DESeq2
|
| |
|
| Submission date |
Dec 02, 2022 |
| Last update date |
Jun 07, 2023 |
| Contact name |
Johannes von Lintig |
| E-mail(s) |
jxv99@case.edu
|
| Phone |
2163683528
|
| Organization name |
Case Western Reserve University
|
| Department |
Pharmacology
|
| Street address |
2109 Adelbert Road
|
| City |
Cleveland |
| ZIP/Postal code |
44106 |
| Country |
USA |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE219252 |
Bulk RNA-seq of eyes isolated from wildtype and Stra6 knockout mice maintained on either a vitamin A sufficient or deficient diet |
|
| Relations |
| BioSample |
SAMN31997614 |
| SRA |
SRX18471298 |
