Computational protocol: Comparative transcriptional profiling of renal cortex in rats with inherited stress-induced arterial hypertension and normotensive Wistar Albino Glaxo rats

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Protocol publication

[…] The collected samples of renal cortex were sent to JSC Genoanalytica (Moscow, Russia), where mRNA was extracted using Dynabeads mRNA Purification Kit (Ambion, USA). cDNA libraries were constructed using NEBNext mRNA Library Prep Reagent Set for Illumina (NEB, USA) following the manufacturer’s protocol and were subjected to Illumina single-end sequencing. Three renal cortex samples from ISIAH and three renal cortex samples from WAG rats were run as experimental replicates. The resulting fastq-formatted sequencing data were mapped to the RGSC Rnor_5.0\rn5 reference genome using Tophat2 aligner [] and NCBI RefSeq gene annotation. Quality assessment of the mapped data was performed using the module ‘CollectRnaSeqMetrics’ from Picard tools suite (http://broadinstitute.github.io/picard/). The summary statistics for each sequenced library is given in Additional file . The Cufflinks/Cuffdiff programs were then used to estimate gene expression levels in FPKM (fragments per kilobase of transcript per million mapped reads), and to perform differential expression analysis []. Genes were considered to be differentially expressed at q value < 0,05. […]

Pipeline specifications

Software tools TopHat, Picard, Cufflinks
Application RNA-seq analysis
Organisms Rattus norvegicus
Diseases Hypertension
Chemicals Calcium, Glutathione, Nitrogen, Steroids, Tryptophan