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Sample GSM6053286 Query DataSets for GSM6053286
Status Public on Apr 25, 2022
Title 00077E9C26
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
 
Description Original label before genotype mismatch fix: 00077E94A0
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 SAMN27723865
SRA SRX14954088

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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