{"cohort":"GDC TCGA Breast Cancer (BRCA)","min":0.00000,"url":"https://gdc.cancer.gov/about-data/publications/ATACseq-AWG","probeMap":"brca/elmer.all.pairs.significant.probeMap","dataSubType":"DNA methylation","label":"Elmer enhancer results","max":1.00000,"name":"brca/TCGA-BRCA.methylation450.tsv","wrangling_procedure":"Beta_values are downloaded from GDC. Beta values from the same sample but from different vials/portions/analytes/aliquotes is averaged; beta_value from different samples is combined into genomicMatrix. <br>Probe to gene mapping is Elmer analysis performed on TCGA breast cancer samples using both supervised and unsupervised methods. Download BRCA_supervised_analaysis_molecular_subtypes_hg38_may_7.zip and BRCA_unsupervised_hg38.zip from synapse. Use all files getPair.*.pairs.significant.csv to generate probe to gene mapping.","type":"genomicMatrix","version":"2018-07-02","unit":"beta value","platform":"Illumina Human Methylation 450"}

{"name":"gencode.vM13.basic.gene","type":"probeMap","assembly":"mm10","version":"2017-04-25","url":"https://www.gencodegenes.org/mouse_releases/13.html, ftp://ftp.sanger.ac.uk/pub/gencode/Gencode_mouse/release_M13/gencode.vM13.basic.annotation.gtf.gz","notes":"grep '\t'gene'\t' gencode.vM13.basic.annotation.gtf |cut -f 1,4,5,7,9 | awk 'BEGIN {FS=\"\t\"; OFS=\"\t\"} {split($5,a,\";\"); split(a[1],id,\" \"); split(substr(id[2],2,length(id[2])-2), identifier,\".\"); split(a[3], name, \" \"); print identifier[1],substr(name[2],2,length(name[2])-2),$1,$2,$3,$4}' > gencode.vM13.basic.gene"}

{"name":"transpose_1M_neurons_filtered_gene_bc_matrices_h5.tsv","type":"genomicMatrix","cohort":"1.3 Million Brain Cells from E18 Mice","dataSubType":"single cell RNAseq gene expression","url":"https://support.10xgenomics.com/single-cell/datasets/1M_neurons","label":"1M neurons single cell RNAseq gene expression","probeMap":"gencode.vM13.basic.gene","colnormalization":"log2(x)","unit":"count"}

{"name":"1M_neurons_neuron20k.barcode","type":"clinicalMatrix","cohort":"1.3 Million Brain Cells from E18 Mice","dataSubType":"filter","url":"https://s3-us-west-2.amazonaws.com/10x.files/samples/cell/1M_neurons/1M_neurons_neuron20k.h5, https://support.10xgenomics.com/single-cell/datasets/1M_neurons","label":"20K cells"}