Journal: Cell reports

Article Title: Somatic Mutational Landscape of Splicing Factor Genes and Their Functional Consequences across 33 Cancer Types

doi: 10.1016/j.celrep.2018.01.088

Figure Lengend Snippet: KEY RESOURCES TABLE

Article Snippet: ​ REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Rabbit polyclonal anti-FUBP1 antibody Abcam Abcam# ab181111 Deposited Data Raw and analyzed data This paper GEO: {"type":"entrez-geo","attrs":{"text":"GSE100530","term_id":"100530"}} GSE100530 Human reference genome NCBI build 37, GRCh37 Genome Reference Consortium http://www.ncbi.nlm.nih.gov/projects/genome/assembly/grc/human/ GENCODE v19 GENCODE https://www.gencodegenes.org/releases/19.html RefSeq NCBI https://www.ncbi.nlm.nih.gov/refseq/ Raw TCGA and CCLE RNA-Seq data Genomic Data Commons https://gdc.cancer.gov/ Processed TCGA RNA-Seq data Omicsoft http://www.omicsoft.com/oncoland-service/ MutSigCV 2016_01_28 results The Broad Institute https://confluence.broadinstitute.org/display/GDAC/Dashboard-Analyses MC3 v0.2.8 MC3 https://gdc.cancer.gov/about-data/publications/mc3-2017 Experimental Models: Cell Lines Human: U87MG ATCC ATCC ® HTB-14 (TM) Oligonucleotides ON-TARGETplus Non-targeting siRNA Pool GE Dharmacon, Inc Cat# D-001810-10-05 ON-TARGETplus Human FUBP1 siRNA SMARTpool GE Dharmacon, Inc Cat# L-011548-00-0005 Software and Algorithms Kallisto Bray et al., 2016 https://pachterlab.github.io/kallisto/ Limma Ritchie et al., 2015 https://bioconductor.org/packages/release/bioc/html/limma.html STAR Dobin et al., 2013 https://github.com/alexdobin/STAR GSEA Subramanian et al., 2005 software.broadinstitute.org/gsea heatmap.3 https://github.com/obigriffith https://raw.githubusercontent.com/obigriffith/biostar-tutorials/master/Heatmaps/heatmap.3.R R R Development Core Team 2011 https://www.r-project.org/ Samtools Li et al., 2009 http://samtools.sourceforge.net Integrative Genomics Viewer (IGV) Robinson et al., 2011 http://software.broadinstitute.org/software/igv/ seaborn https://doi.org/10.5281/zenodo.883859 http://seaborn.pydata.org/ 20/20+ Tokheim et al., 2016 https://github.com/KarchinLab/2020plus Open in a separate window KEY RESOURCES TABLE 119 splicing factor genes carry putative driver mutations in one or more cancer types BLCA and UVM carry more driver splicing factor mutations than expected by chance Common splicing factor mutations associated with lineage-independent altered splicing Mutations are associated with deregulation of cell-autonomous pathways and immune infiltration

Techniques: Software