Computational protocol: Loss of Free Fatty Acid Receptor 2 leads to impaired islet mass and beta cell survival

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Protocol publication

[…] Total cellular RNA was extracted from isolated islets (pooled from 2 mice) using an RNeasy Mini kit (QIAGEN, Venlo, Linburg). Experiments were run in triplicate for each genotype. RNA seq and data analyses were carried out by the Next Generation Sequencing Core, Center for Genetic Medicine, Northwestern University. Briefly, alignment and expression analysis were performed using TopHat (v2.0.8b) and Cufflinks (v2.1.1). Differential expression was determined by cuffdiff using an FDR cutoff value of 0.05. The results of the differential expression analysis were processed with the R package, cummerbund (http://compbio.mit.edu/cummeRbund/) to obtain up-and down-regulated genes. […]

Pipeline specifications

Software tools TopHat, Cufflinks, CummeRbund
Applications RNA-seq analysis, Transcriptome data visualization
Organisms Mus musculus
Chemicals Fatty Acids, Fatty Acids, Nonesterified