|
| Status |
Public on Oct 31, 2014 |
| Title |
F2 ind29 |
| Sample type |
SRA |
| |
|
| Source name |
Liver
|
| Organism |
Rattus norvegicus |
| Characteristics |
Sex: Male
tissue: liver
genotype/variation: F2
|
| Growth protocol |
The rats were bred and maintained in an approved animal facility in microisolator caging on a 12-hour light-dark cycle.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA was isolated from liver tissue using standard TRIzol methods (Chomczynski and Sacchi 1987). RNA quality was determined via a BioAnalyzer 2100 (Agilent Technologies, Santa Clara, CA, USA), using an RIN threshold of 7.
RNA-Seq libraries were prepared with TruSeq RNA Sample Preparation Kits v2 (Illumina, San Diego, CA) according to manufacturer’s instructions.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Tophat (version 1.4.1) were used to map RNA-Seq reads to rat Ensembl transcripts first allowing up to 1 mismatch and the reads that were not fully mapped to the transcriptome will then be mapped to rat rn4 Ensembl genome allowing up to 2 mismatch.
Only the uniquely mapped read pairs were subjected to downstream analyses.
FPKMs (fragments per kb of exon per million sequence reads) were calculated using Cufflinks (version 2.0.0).
Genome_build: rn4
Supplementary_files_format_and_content: Supplemental excel file includes the FPKM values of all samples.
|
| |
|
| Submission date |
Aug 20, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Jinkai Wang |
| Organization name |
University of California, Los Angeles
|
| Street address |
650 Charles E. Young Drive South, CHS 33-228
|
| City |
Los Angeles |
| State/province |
CA |
| ZIP/Postal code |
90095-7278 |
| Country |
USA |
| |
|
| Platform ID |
GPL14844 |
| Series (1) |
| GSE50027 |
Systems biology with high-throughput sequencing revealed genetic mechanisms underlying the Metabolic Syndrome in the Lyon Hypertensive Rat |
|
| Relations |
| BioSample |
SAMN02319496 |
| SRA |
SRX337425 |
