|
| Status |
Public on May 31, 2024 |
| Title |
Young Fischer344 rat retina-01 |
| Sample type |
SRA |
| |
|
| Source name |
neural retina
|
| Organism |
Rattus norvegicus |
| Characteristics |
tissue: neural retina
genotype: WT
treatment: untreated young-4 months
|
| Treatment protocol |
We used four months adult rats as young control and aged rats at 22-24 months of age with or without 8-AG treatment. The 22 months old rats were treated with 8-AG (5 mg/kg body weight per day) daily by supplementing 8-AG in drinking water or water only for the untreated old group. Animals were treated for 8 weeks until they were 24 months of age and they were euthanized and eyes were enucleated immediately.
|
| Growth protocol |
We obtained young and aged Fischer 344 rats from Char les River Laboratories and the National Institute on Aging [NIA]. All animals were housed under standard 12-h light/12-h dark conditions in the animal facility at University of Pittsburgh.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Each eye ball was opened by removing the cornea, iris and lens, and the neural retina was firstly isolated and put into RNAzol immediately and flash frozen in liquid nitrogen. After the neural retina being taken, RPE/choroids were isolated by washing the remaining eye cup with RNA zol and flash frozed in liquid nitrogen. Total RNA was isolated follwing manufacturer's instructions of RNAzol (Sigma-Aldrich, Saint-Louis, MO). Only samples with RNA integrity number (RIN) > 7 was selected for poly-A captured mRNA library preparation.
To compare old vs. young and 8-AG treated aged vs untreated aged neural retinae, mRNA libraries were prepared using poly-A capturation (N=3). For RNA from RPE/choroids, due to low RNA yield, mRNA lirbaries were genereated using polyA selection with enrichment for full-length transcripts.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
HiSeq X Ten |
| |
|
| Description |
SE6781_SA78654_S11_L002
|
| Data processing |
The reads were first mapped to the latest UCSC transcript set using Bowtie2 version 2.1.0
gene expression level was estimated using RSEM v1.2.15
Differentially expressed genes were identified using the edgeR program. Genes showing altered expression with p<0.05 and more than 1.5 fold changes were considered differentially expressed.
Goseq was used to perform GO enrichment analysis and Kobas was used to perform the pathway analysis.
Assembly: Rnor_6.0
Supplementary files format and content: txt and csv files include raw counts of each sample.
Supplementary files format and content: txt and csv files include RPKM values of each sample.
Supplementary files format and content: txt and csv files include fold change, p values, FDR and RPKM values of each sample in two groups
Supplementary files format and content: excel files include the DEGs upreguated and downregulated between two groups.
|
| |
|
| Submission date |
Jan 24, 2024 |
| Last update date |
May 31, 2024 |
| Contact name |
Yuanyuan Chen |
| E-mail(s) |
cheny1@pitt.edu
|
| Organization name |
University of Pittsburgh
|
| Department |
Ophthalmology
|
| Street address |
1622 Locust Street,
|
| City |
Pittsburgh |
| State/province |
PA |
| ZIP/Postal code |
15219 |
| Country |
USA |
| |
|
| Platform ID |
GPL24688 |
| Series (1) |
| GSE254123 |
Transcriptome comparison between Old vs young rat retinae |
|
| Relations |
| BioSample |
SAMN39599611 |
| SRA |
SRX23383598 |
