Supplementary data from:
"Fast and accurate differential splicing analysis across multiple conditions with replicates" Juan C. Entizne, Juan L. Trincado, Gerald Hysenaj, Babita Singh, Miha Skalic, David J. Elliott, Eduardo Eyras
Preprint available here: http://biorxiv.org/content/early/2016/11/10/086876
The supplementary_data is stuctured in the following way:
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annotation/: Ensembl and RefSeq files from hg19 and mm10 used for the quantification
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supplementary_data/busskamp: Commands used and events obtained with SUPPA, analyzing 4-day time-course data for the differentiation of human iPS cells into bipolar neurons[#express]
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supplementary_data/erythro: Commands used and events obtained comparing initial and final steps of differentiating human erythroblasts²
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supplementary_data/jurkat: Commands used and events obtained in the analysis of stimulated and unstimulated Jurkat T-cells³
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supplementary_data/mouse: Commands used and events obtained in the analyzed data from Cerebellum and Liver mouse tissues covering 8 different time points from 2 full circadian cycles⁴
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supplementary_data/simulated_reads: Commands and files necessary for the generation of the simulated reads, with 3 replicates of control cells from Best, A. et al⁵
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supplementary_data/tra2: Commands used and events obtained in the analysis on knockdown of TRA2A and TRA2B splicing regulators compared to controls⁵
[1] Busskamp, V. et al. Rapid neurogenesis through transcriptional activation in human stem cells. Mol. Syst. Biol. 10, 760 (2014).
[2] Pimentel, H. et al. A dynamic alternative splicing program regulates gene expression during terminal erythropoiesis. Nucleic Acids Res. 42, 4031–42 (2014).
[3] Cole, B. S. et al. Global analysis of physical and functional RNA targets of hnRNP L reveals distinct sequence and epigenetic features of repressed and enhanced exons. RNA 21, 2053–66 (2015).
[4] Zhang, R., Lahens, N. F., Ballance, H. I., Hughes, M. E. & Hogenesch, J. B. A circadian gene expression atlas in mammals: implications for biology and medicine. Proc. Natl. Acad. Sci. U. S. A. 111, 16219–24 (2014).
[5] Best, A. et al. Human Tra2 proteins jointly control a CHEK1 splicing switch among alternative and constitutive target exons. Nat. Commun. 5, 4760 (2014).