|
| Status |
Public on Apr 25, 2022 |
| Title |
00077E9968 |
| Sample type |
SRA |
| |
|
| Source name |
eye
|
| Organism |
Rattus norvegicus |
| Characteristics |
tissue: eye
population: Heterogeneous Stock
|
| Treatment protocol |
As part of another study, some of the rats were exposed to a battery of behavioral tests and were allowed to self administer nicotine for 2.5 hours per day over the course of 12 days.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Whole eyes from 53 rats (one eye per rat) were frozen immediately after the rat was killed and stored at -80°C until RNA could be extracted. During RNA extraction, eyes were first thawed to room temperature and extraocular muscles were carefully removed. RNA was extracted using the Qiagen RNeasy Midi kit following the manufacturer's instructions.
Libraries were constructed for sequencing using Illumina NovaSeq instrument by Novogen, Inc using standard protocols for generating 150 bp paired-end reads.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Reads were aligned to the Rnor_6.0 genome using STAR in two-pass mode.
Samples were tested for mismatches with their genotypes by counting coding SNP alleles in the RNA sequences using GATK ASEReadCounter and comparing to the coding SNP genotypes of each rat.
Gene expression was quantified using RSEM.
Assembly: Rnor_6.0
Supplementary files format and content: Eye.expr.log2.bed is a table of log2(read count + 1) expression in BED format. The start and end columns refer only to the gene's TSS.
|
| |
|
| Submission date |
Apr 21, 2022 |
| Last update date |
Apr 25, 2022 |
| Contact name |
Daniel Munro |
| E-mail(s) |
dmunro@scripps.edu
|
| Organization name |
UC San Diego
|
| Department |
Psychiatry
|
| Lab |
Palmer Lab
|
| Street address |
9500 Gilman Drive
|
| City |
La Jolla |
| State/province |
CA |
| ZIP/Postal code |
92093 |
| Country |
USA |
| |
|
| Platform ID |
GPL25947 |
| Series (1) |
| GSE201236 |
Genome-wide association study finds multiple loci associated with intraocular pressure in HS rats |
|
| Relations |
| BioSample |
SAMN27723879 |
| SRA |
SRX14954058 |
