Computational protocol: Eicosapentaenoic acid but not docosahexaenoic acid restores skeletal muscle mitochondrial oxidative capacity in old mice

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Protocol publication

[…] Total RNA was isolated using the TrueSeq method, and RNA libraries were prepared according to the manufacturer’s instructions for the TruSeq RNA Sample Prep Kit v2 (Illumina, Hayward, CA). Libraries were loaded onto paired end flow cells following the standard protocol for the Illumina cBot and cBot Paired end cluster kit version 3. Flow cells were sequenced as 51 × 2 paired end reads on an Illumina HiSeq 2000 using TruSeq SBS sequencing kit version 3 and hcs v2.0.12 data collection software. Base calling was performed using Illumina’s RTA version The RNA-Seq data were analyzed using map-rseq v.1.2.1 (Kalari et al., ), the Mayo Bioinformatics Core pipeline. MAP-RSeq consists of alignment with tophat 2.0.6 (Kim et al., , p.2) against the hg19 genome build and gene counts with the htseq software 0.5.3p9 ( using gene annotation files obtained from Illumina ( Normalization and differential expression analysis were performed using edgeR 2.6.2 (Robinson et al., ). […]

Pipeline specifications

Software tools MAP-RSEQ, TopHat, HTSeq, Cufflinks, edgeR
Databases iGenomes
Application RNA-seq analysis
Organisms Mus musculus
Diseases Mitochondrial Diseases
Chemicals Eicosapentaenoic Acid