Computational protocol: Heart Mitochondrial Proteome Study Elucidates Changes in Cardiac Energy Metabolism and Antioxidant PRDX3 in Human Dilated Cardiomyopathy

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Protocol publication

[…] The initial whole transcriptome paired-end reads obtained from the sequencing were mapped against the latest version of the human genome (Version GRchr37/hg19) by using the Life Technologies mapping algorithm (http://www.lifetechnologies.com/). The aligned records were reported in the BAM/SAM format . Bad quality reads (Phred score <10) were eliminated using the Picard Tools software .The isoform and gene predictions were subsequently estimated using the cufflinks method , and the expression levels were calculated using the HTSeq software . The Edge method was applied to analyze the differential expression between conditions . This method relies on a Poisson model to estimate the RNAseq data variance for differential expression. We selected genes and isoforms that were calculated to exhibit p value<0.05 and fold-change >1.5. […]

Pipeline specifications

Software tools Picard, Cufflinks, HTSeq
Application RNA-seq analysis
Organisms Homo sapiens
Diseases Cardiomyopathy, Dilated, Heart Failure, Ventricular Dysfunction, Mitochondrial Diseases