{"cohort":"PCAWG (specimen centric)","url":"https://www.synapse.org/#!Synapse:syn5553991,https://www.synapse.org/#!Synapse:syn3104297,https://www.synapse.org/#!Synapse:syn2364711","probeMap":"gencode.v19.annotation.gene.probemap","dataSubType":"gene expression RNAseq","label":"normalized (fpkm-uq)","name":"tophat_star_fpkm_uq.v2_aliquot_gl.sp.log","type":"genomicMatrix","version":"2017-01-18","unit":"log2(fpkm-uq+0.001)","colnormalization":true,"description":"PCAWG-3 gene expression quantification (averaged from TopHat2 and STAR alignment derived gene expression estimations) in gene-level fpkm upper quartile normalized (FPKM-UQ) values, log2(x+0.001) transformed. FPKM-UQ has been shown to be a better normalization approach. The PCAWG-3 group recommends using FPKM-UQ values for gene expression quantification. Please see the PCAWG-3 wiki page for more information on normalization: https://wiki.oicr.on.ca/display/PANCANCER/Gene+expression+normalization. <br><br> RNAseq data are mapped from aliquote uuid to ICGC specimen ids using http://pancancer.info/data_releases/may2016/pcawg_sample_sheet.v1.4.2016-09-14.tsv from https://wiki.oicr.on.ca/display/PANCANCER/Available+PCAWG+Data#AvailablePCAWGData-May2016Dataset,Version1.4 ."}

{"cohort":"PCAWG (specimen centric)","url":"https://www.synapse.org/#!Synapse:syn5878059, https://www.synapse.org/#!Synapse:syn5842981","dataSubType":"miRNA expression","label":"raw, unfiltered","name":"x3t2m1.mature.mirna.all.matrix.log","wrangling_procedure":"miRNA matrix data (x3t2m1.mature.mirna.all..matrix) are downloaded from synapse, mapped from submitter uuid (all from TCGA) to ICGC specimen id using https://raw.githubusercontent.com/isb-cgc/readthedocs/master/docs/include/LATEST_MANIFEST.tsv.","type":"genomicMatrix","version":"2017-02-23","unit":"log2(cpm+1)","colnormalization":true,"description":"PCAWG-14 miRNA expression. The unfiltered raw miRNA expression matrix of the complete list of 5806 total mature miRNA genes"}

{"cohort":"PCAWG (specimen centric)","url":"https://www.synapse.org/#!Synapse:syn5878067, https://www.synapse.org/#!Synapse:syn5842981","dataSubType":"miRNA expression","label":"TMM normalized, filtered","name":"x3t2m1.mature.TMM.mirna.matrix.log","wrangling_procedure":"miRNA matrix data (x3t2m1.mature.TMM.mirna.matrix) are downloaded from synapse, mapped from submitter uuid (all from TCGA) to ICGC specimen id using https://raw.githubusercontent.com/isb-cgc/readthedocs/master/docs/include/LATEST_MANIFEST.tsv.","type":"genomicMatrix","version":"2017-02-23","unit":"log2(cpm-TMM+0.1)","colnormalization":true,"description":"PCAWG-14 miRNA expression. TMM normalized miRNA expression matrices. Those contain results for 1864 of 5806 total mature miRNA genes that have passed various filtering steps that are described at https://www.synapse.org/#!Synapse:syn5842981 ."}