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.

本目录包含来自 iPSCORE 集合中三种组织（诱导多能干细胞（iPSCs）、iPSC 衍生的心血管祖细胞（CVPCs）和 iPSC 衍生的胰腺祖细胞（PPCs））的基因、ATAC-seq 峰和 H3K27ac ChIP-seq 峰的 hg38 构建基因组坐标的 6 个文件；每个文件均采用类似 BED 的格式。五个 ATAC-seq 和 H3K27ac ChIP-seq 峰文件遵循 [组织表型峰.tissue_phenotype_peaks.bed] 命名规范，并包含相同的列，包括染色体、起始点和终点，用以描述基因组坐标，Element_ID 表示 ATAC-seq 或 ChIP-seq 峰的标识符，以及根据峰在过滤后被认为可访问/乙酰化与否的 Expressed 真值/假值。要获取测试 QTL 的元素，可以通过 Expressed == "TRUE" 对行进行筛选。由于基因坐标固定不变，gene_info.txt.gz 文件包含关于哪些基因在所有三种组织中被认为表达的详细信息。前三个列是染色体、起始点和终点 Gencode hg38 坐标，接下来三列报告了链、基因 ID 和基因名称。最后三列是 iPSC 表达、CVPC 表达和 PPC 表达，它们指示（真/假）基因是否在相应的组织中表达并经过 QTL 测试。