Send to:

Choose Destination

SRX1081321: GSM1808017: Heart_1; Homo sapiens; RNA-Seq
1 ILLUMINA (Illumina HiSeq 2000) run: 27.6M spots, 5.5G bases, 2.4Gb downloads

Submitted by: NCBI (GEO)
Study: Transcriptomic variation of pharmacogenes in multiple human tissues and lymphoblastoid cell lines
show Abstracthide Abstract
Variation in the expression level and activity of genes involved in drug disposition and action (“pharmacogenes”) can affect drug response and toxicity, especially when in tissues of pharmacological importance. Previous studies have relied primarily on microarrays to understand gene expression differences, or have focused on a single tissue or small number of samples. The goal of this study was to use RNA-seq to determine the expression levels and alternative splicing of 389 PGRN pharmacogenes across four tissues (liver, kidney, heart and adipose) and lymphoblastoid cell lines (LCLs), which are used widely in pharmacogenomics studies. Analysis of RNA-seq data from different individuals across the 5 tissues (N = 139 samples) revealed substantial variation in both expression levels and splicing across samples and tissue types. This in-depth exploration also revealed 183 splicing events in pharmacogenes that were previously not annotated. Overall, this study serves as a rich resource for the research community to inform biomarker and drug discovery and use. Overall design: mRNA profile of 389 genes in 24 liver, 20 kidney (cortex), 25 heart (left ventricle), 25 adipose (subcutaneous) samples, and 45 lymphoblastoid cell lines (LCLs). The raw data for the LCL Samples will be available through dbGap under phs000481.
Sample: Heart_1
SAMN03840182 • SRS979159 • All experiments • All runs
Organism: Homo sapiens
Instrument: Illumina HiSeq 2000
Strategy: RNA-Seq
Selection: cDNA
Layout: PAIRED
Construction protocol: In brief, 0.5-1.0 µg of total RNA was twice selected for mRNA by oligo (dT) and then fragmented by heating. First strand cDNA was synthesized using Superscript III reverse transcriptase and random hexamer primers. After second strand synthesis by DNA polymerase I and with dUTP in place of dTTP, double stranded cDNA was end-repaired and A-tailed prior to ligation of Illumina adaptors including DNA indices. Libraries were made strand-specific by digestion with Uracil-DNA Glycosylase prior to PCR amplification. Bead-based clean-up was incorporated after each enzymatic reaction and libraries were checked by flash gel and Bioanalyzer analysis. Total RNA was isolated from tissues using TRIzol Reagent.
Runs: 1 run, 27.6M spots, 5.5G bases, 2.4Gb
Run# of Spots# of BasesSizePublished


Supplemental Content

Recent activity

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

See more...
Support Center