TCGA stomach adenocarcinoma (STAD) somatic mutation (bcm automated)

{"start_index":1,"owner":"TCGA","longTitle":"TCGA stomach adenocarcinoma (STAD) somatic mutation (bcgsc automated)","cohort":"TCGA Stomach Cancer (STAD)","url":"https://tcga-data.nci.nih.gov/tcgafiles/ftp_auth/distro_ftpusers/anonymous/tumor/stad/gsc/bcgsc.ca/illuminahiseq_dnaseq_automated/mutations/","dataSubType":"somatic mutation (SNPs and small INDELs)","security":"public","label":"bcgsc automated","method":"BCGSC pipeline","tags":["cancer","gastric cancer"],"path":"data/public/TCGA/STAD/mutation_bcgsc","anatomical_origin":["Stomach"],"name":"TCGA.STAD.sampleMap/mutation_bcgsc","dataproducer":"Michael Smith Genome Sciences Centre (British Columbia Genome Sciences Centre, BCGSC)","wrangling_procedure":"Download .maf file from TCGA DCC, removed any calls from WGS samples, processed into UCSC Xena mutation format, stored in the UCSC Xena repository","sample_type":["tumor"],"assembly":"hg19","redistribution":true,"domain":"TCGA","type":"mutationVector","wrangler":"TCGAscript maf processed on 2017-09-08","version":"2017-09-08","gdata_tags":["Michael Smith Genome Sciences Centre (British Columbia Genome Sciences Centre, BCGSC)"],"primary_disease":"stomach adenocarcinoma","platform":"IlluminaHiSeq","description":"TCGA stomach adenocarcinoma (STAD) somatic mutation data. Sequencing data are generated on a IlluminaHiSeq system. The calls are generated at Michael Smith Genome Sciences Centre (British Columbia Genome Sciences Centre, BCGSC) using the BCGSC pipeline method.","wholegenome":true}

TCGA stomach adenocarcinoma (STAD) somatic mutation (bcgsc automated)

TCGA stomach adenocarcinoma (STAD) gene expression by RNAseq (polyA+ IlluminaHiSeq BC)

{"longTitle":"TCGA stomach adenocarcinoma (STAD) gene-level nonsilent somatic mutation (wustl_hiseq automated)","cohort":"TCGA Stomach Cancer (STAD)","url":"https://tcga-data.nci.nih.gov/tcgafiles/ftp_auth/distro_ftpusers/anonymous/tumor/stad/gsc/genome.wustl.edu/illuminahiseq_dnaseq_automated/mutations/","probeMap":"probeMap/hugo_gencode_good_hg19_V24lift37_probemap","dataSubType":"somatic non-silent mutation (gene-level)","security":"public","label":"wustl_hiseq automated","method":"WashU pipeline","tags":["cancer","gastric cancer"],"path":"data/public/TCGA/STAD/mutation_wustl_hiseq_gene","anatomical_origin":["Stomach"],"name":"TCGA.STAD.sampleMap/mutation_wustl_hiseq_gene","dataproducer":"Genome Institute at Washington University Sequencing Center","wrangling_procedure":"Download .maf file from TCGA DCC, processed into gene by sample matrix at UCSC, stored in the UCSC Xena repository","sample_type":["tumor"],"redistribution":true,"type":"genomicMatrix","wrangler":"xena TCGAscript maf processed on 2018-01-10","version":"2018-01-10","gdata_tags":["Genome Institute at Washington University Sequencing Center"],"unit":"binary non-silent mutation","primary_disease":"stomach adenocarcinoma","platform":"IlluminaHiSeq","description":"TCGA stomach adenocarcinoma (STAD) somatic mutation data.  Sequencing data are generated on a IlluminaHiSeq system. The calls are generated at Genome Institute at Washington University Sequencing Center using the WashU pipeline method. <br><br> Red (=1) indicates that a non-silent somatic mutation (nonsense, missense, frame-shif indels, splice site mutations, stop codon readthroughs, change of start codon, inframe indels) was identified in the protein coding region of a gene, or any mutation identified in a non-coding gene. White (=0) indicates that none of the above mutation calls were made in this gene for the specific sample.<br><br>"}