|
| Status |
Public on May 07, 2013 |
| Title |
Treatment Rat 2 |
| Sample type |
SRA |
| |
|
| Source name |
Liver from ethanol-treated group
|
| Organism |
Rattus norvegicus |
| Characteristics |
strain: Inbred alcohol-preferring (iP10a)
Sex: Female
age at collection: 38 weeks
tissue: Liver
|
| Treatment protocol |
We took advantage of the fact iP10a rats will voluntarily consume pharmacologically relevant levels of alcohol daily. Ethanol exposure was achieved by ad libitum access to bottles containing 10, 20, and 30% ethanol (v/v) for 23 weeks.
|
| Growth protocol |
All rats had ad libitum access to food and tap water throughout the experiment (23 weeks).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Livers were snap frozen using a dry ice and isopentane bath. Total RNA was extracted using RNA Stat-60 (Amsbio) following manufacturer's directions.
We used the Illumina TruSeq RNA kit for library preparation with some modifications to the manufacturer’s directions (detailed below). Poly-A RNA was isolated by annealing biotinylated oligo-dT to total RNA and purifying using streptavidin-conjugated beads. RNA was fragmented for 4 minutes at 94°C to increase the population of 200-600 nt fragments. cDNA synthesis was accomplished using random hexamers. Fragment ends were repaired and 3’ ends were adenylated for adaptor ligation. Adaptor ligated fragments were enriched following 10 cycles of PCR. 320-600 bp molecules were size selected from the resulting amplicon pool using a PippinPrep (Sage Science). The final cDNA library was titrated by qRT-PCR and sequenced in 101 nt paired-end reads.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiScanSQ |
| |
|
| Data processing |
Reads were analyzed and mapped using CLCbio Genomics Workbench 4.9 software (Cambridge).
Reads were first normalized by reads per kilobase per million mapped reads (RPKM, Mortazavi et al. 2008 Nature Methods). Values were transformed by square root to stabilize variances, and then renormalized (a second time) by quantile normalization to adjust for among sample variation. A standard t-test with pooled error term was applied to determine p values, which were then corrected for a false discovery rate (FDR) of 5%.
Genome_build: RGSC_v3.4.63
|
| |
|
| Submission date |
May 06, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Amy Lossie |
| E-mail(s) |
alossie@purdue.edu
|
| Organization name |
Purdue University
|
| Street address |
125 S. Russell St.
|
| City |
West Lafayette |
| State/province |
IN |
| ZIP/Postal code |
47907 |
| Country |
USA |
| |
|
| Platform ID |
GPL17116 |
| Series (1) |
| GSE46669 |
A Snapshot of the Hepatic Transcriptome: Ad Libitum Alcohol Intake Suppresses Expression of Cholesterol Synthesis Genes in Alcohol-Preferring (P) Rats |
|
| Relations |
| BioSample |
SAMN02117590 |
| SRA |
SRX275472 |
