Computational protocol: Inflammatory and apoptotic remodeling in autonomic nervous system following myocardial infarction

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Protocol publication

[…] Transcriptomes were analyzed using the tuxedo suite of tools. Briefly, bases with poor quality scores were eliminated from the analysis using the fastq_quality_trimmer tool, and reads with fewer than 50 remaining bases were removed from the analysis. Remaining reads for each sample were mapped to the Sscrofa10.2 genome using Tophat 2.1.1 and counted, annotated and compared using cufflinks 2.2.1. Hierarchical Clustering was used to determine that one sample (204 LSG) was an outlier with no similarity to any other sample (), and it was removed from further analyses. Left and right SG/DRG were treated as individual samples. In all cases an FDR of 5% was used. Cuffdiff was used to calculate statistical differences coming from RNA-seq as previously described[]. […]

Pipeline specifications

Software tools Tuxedo, TopHat, Cufflinks
Application RNA-seq analysis
Organisms Sus scrofa
Diseases Heart Diseases, Cardiomyopathies, Myocardial Infarction