iPSCORE Phenotype Metadata: Element Coordinate Bed Files

This directory contains 6 files for the genomic coordinates in the hg38 build for the genes, ATAC-seq peaks, and H3K27ac ChIP-seq peaks from three tissues from the iPSCORE Collection; induced pluripotent stem cells (iPSCs), iPSC-derived cardiovascular progenitor cells (CVPCs), and iPSC-derived pancreatic progenitor cells (PPCs).

Each file has a BED-like format. The five ATAC-seq and H3K27ac ChIP-seq peak files have a [tissue_phenotype_peaks.bed] labeling convention and have the same columns, including Chromosome, Start, End describing the genomic coordinates, Element_ID the identifier for the ATAC-seq or ChIP-seq peak, and Expressed TRUE/FALSE based on whether the peak is considered accessible/acetylated after filtering. To obtain the elements tested for QTLs, rows can be filtered by Expressed == "TRUE".

Since gene coordinates are fixed, the gene_info.txt.gz file contains information about which genes were considered expressed for all three tissues. The first three columns are the chromsome, start and end Gencode hg38 coordinates, the strand, gene ID and gene name are reported in the next three columns. The last three columns are iPSC_Expressed, CVPC_Expressed, and PPC_Expressed and indicate (TRUE/FALSE) whether the gene is expressed in the corresponding tissue and tested for QTLs.