cGTEx_dataset:A multi-tissue atlas of regulatory variants in cattle

The files are raw data of the cGTEX dataset used in the publication https://doi.org/10.1038/s41588-022-01153-5. For details, please read the Methods section. 1. cGTEx_meta_data_8646sample.xlsx Metadata consists of sample names with their sample accession, including information such as data size, cleaned reads, mapping rate, and age. The data is extracted from SRA (https://www.ncbi.nlm.nih.gov/sra/) and BIGD (https://bigd.big.ac.cn/bioproject/) ( samples starting with CRS) 2. cGTEx_count_8646sample_27607gene.txt.gz Data consist of raw RNA-seq read count of 27607 genes (column names as Ensembl gene id )of 8646 samples (as row names) 3. cGTEx_TPM_8646sample_27607gene.txt.gz Data consist of TPM values of 27607 genes (column names as Ensembl gene id) in samples (8646 samples as row names) 4. cGTEx_imputed_vcf.tar.gz Imputed genotypes (SNP) of 7297 RNA-seq samples in 29 autosomes. 5. cGTEx_exon_junction_8646sample.tar.gz Exon junction files of 8646 files Note: Small discrepancies in some sample names or the absence of headers in some data sets compared to https://cgtex.roslin.ed.ac.uk/ are sorted out in this upload.

Liu, S., Gao, Y., Canela-Xandri, O., Wang, S., Yu, Y., Cai, W., Li, B., Xiang, R., Chamberlain, A. J., Pairo-Castineira, E., D'Mellow, K., Rawlik, K., Xia, C., Yao, Y., Navarro, P., Rocha, D., Li, X., Yan, Z., Li, C., … Fang, L. (2022). cGTEx_dataset:A multi-tissue atlas of regulatory variants in cattle [Data set]. In Nature Genetics (v.1.2, Vol. 54, pp. 1438–1447). Zenodo. https://doi.org/10.5281/zenodo.7560235