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Sample GSM1212732 Query DataSets for GSM1212732
Status Public on Oct 31, 2014
Title F2 ind25
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 SAMN02319495
SRA SRX337421

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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