Computational protocol: Human DBR1 modulates the recycling of snRNPs to affect alternative RNA splicing and contributes to the suppression of cancer development

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Protocol publication

[…] The RNA sequencing results were read using TopHat (http://ccb.jhu.edu/software/tophat/index.shtml) to identify splice junctions between exons and to determine the skipping ratio of each exon (). A statistically significant change in the skipping ratio was used for all samples to subtract background noise (paired t-test, P<0.05). Two skipping ratios were determined for the same exon form DBR1-L and DBR1-N cells, and these two ratios are presented as a set of coordinates (x, y; with x representing the ratio derived from DBR1-N cells and y representing the same exon-skipping ratio from DBR1-L cells). [...] Laboratory quantification experiments, including mouse xenograft studies, underwent a sample size estimation for the t-test by SigmaPlot (Systat Software, San Jose, CA, USA) when designing experiments. In addition, all data were examined by the two-tailed t-test for statistical significance. […]

Pipeline specifications

Software tools TopHat, SigmaPlot
Applications Miscellaneous, RNA-seq analysis
Organisms Homo sapiens