Supplementary data from:
"SUPPA2 provides fast, accurate, and uncertainty-aware differential splicing analysis across multiple conditions" Juan L. Trincado, Juan C. Entizne, Gerald Hysenaj, Babita Singh, Miha Skalic, David J. Elliott, Eduardo Eyras
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 neurons¹
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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).