{"cohort":"PCAWG (specimen centric)","url":"https://www.synapse.org/#!Synapse:syn5878064, https://www.synapse.org/#!Synapse:syn5842981","dataSubType":"miRNA expression","label":"UQ normalized, filtered","name":"x3t2m1.mature.UQ.mirna.matrix.log","wrangling_procedure":"miRNA matrix data (x3t2m1.mature.UQ.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-uq+0.1)","colnormalization":true,"description":"PCAWG-14 miRNA expression. UQ 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 ."}

{"name":"TCGA_ATAC_peak.promoter.probeMap","type":"probeMap","version":"2018-07-05","wrangling_procedure":"peak summit within -1000 to 100bp from TSS site","url":"https://www.synapse.org/#!Synapse:syn12511521","assembly":"hg38"}

{"cohort":"GDC Pan-Cancer (PANCAN)","url":"https://gdc.cancer.gov/about-data/publications/ATACseq-AWG","probeMap":"TCGA_ATAC_peak.promoter.probeMap","dataSubType":"ATAC-seq","label":"Promoter peak signal","name":"TCGA_ATAC_peak_Log2Counts_dedup_promoter","wrangling_procedure":"Normalized count matrix: a prior count of 5 is added to the raw counts, then put into a \"counts per million\", then log2 transformed, then quantile normalized, the result is TCGA_ATAC_Log2Counts_Matrix.180608.txt.gz.  We download TCGA_ATAC_Log2Counts_Matrix.180608.txt.gz from synapse, average the values in the file (i.e. log2(count+5)-qn values) across all technical replicates and all biospecimens belong to the same TCGA sample. The result is the genomic matrix TCGA_ATAC_peak_Log2Counts_dedup_promoter.<br>Promoter region is defined as within -1000 to 100bp to TSS sites. The promoter peak to gene mapping information is dervied from if a peak summit locates within the promoter region of a gene. Peak location information is from the file TCGA_ATAC_Log2Counts_Matrix.180608.txt.gz.","type":"genomicMatrix","version":"2018-06-25","unit":"log2((count+5)PM)-qn","colnormalization":true}