Computational protocol: Dual specificity phosphatase 5 and 6 are oppositely regulated in human skeletal muscle by acute exercise

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Protocol publication

[…] RNA was isolated from biopsies of skeletal muscle and adipose tissue, reverse transcribed into cDNA and deep sequenced (Li et al. ). In brief, an Illumina HiSeq 2000 platform with multiplex design was used to amplify and deep sequence sonicated cDNA fragments with 51 bp nucleotides. Tophat 2.0.8 with Bowtie 2.1.0 was used with default settings (Langmead et al. ; Kim et al. ) to align the RNA‐seq reads against the UCSC hg19 annotated transcriptome and genome. Gene filtering and normalization were performed with EdgeR v3.4.2 (Robinson et al. ) using a negative binominal generalized linear model in R v3.0.3 (The R Foundation, Vienna, Austria). Normalized gene expression levels are presented in fragments per kB mapped reads (FPKM). […]

Pipeline specifications

Software tools TopHat, Bowtie, edgeR
Application RNA-seq analysis
Organisms Homo sapiens
Chemicals Dexamethasone