Cattle GTEx (v1)

1. Introduction

Characterization of genetic regulatory variants acting on the transcriptome of livestock is essential for interpreting the molecular mechanisms underlying traits of economic value and for increasing the rate of genetic gain through artificial selection. Here we build a cattle Genotype-Tissue Expression atlas (cattleGTEx) as part of the pilot phase of Farm animal GTEx (FarmGTEx) project for the research community based on publicly available 7,180 RNA-Seq samples. We describe the landscape of transcriptome across over 100 tissues and report hundreds of thousands of genetic associations with gene expression and alternative splicing for 24 major tissues. We evaluate the tissue-sharing patterns of these genetic regulatory effects, and functionally annotate them using multi-omics data. Finally, we link gene expression in different tissues to 43 economically important traits using both transcriptome-wide association and colocalization analyses to decipher the molecular regulatory mechanisms underpinning such agronomic traits in cattle.

2. The main contents

There are mainly nine parts of analysis in our project.

Gene_expression_quantification

Includes gene expression quantification from RNA-seq.

DNA_methylation

Includes the analysis of WGBS data.

Tissue_specific_expression_splicing

Includes the detection of tissue specific expressed genes and spliced introns using the method illustrated in Finucane et al. (2018).

ASE

Includes the estimates of effect size (aFC) of requlatory variants using aggregated phASER haplotypic expression data using phASER and the correlation plot between top cis-eQTL slopes (from fastQTL).

SNP_calling_imputation

Includes the SNP calling from RNA-seq and imputation using Beagle 5.

cis-eQTL_detection

Includes the eQTL detection using fastQTL, effect size calculation using aFC and finemapping analysis using DAP-G

cis-sQTL_detection

Includes the eQTL detection using fastQTL.

Trans-eQTL_detection

Includes the trans-eQTL detection by a mixed linear model using mlma from GCTA with and without cis-eQTL adjustments.

GWAS_eQTLs

Includes the TWAS analysis using S-PrediXcan and MultiXcan from MetaXcan and Colocalization analysis using Coloc and fastENLOC.

HiC_analysis

Includes the HiC data processes using HiC-Pro(v2.11.4) and estimates of significant intra-chromosome contacts using FitHiC(v2.0.7).

Data availability

Gene expression data and cis-eQTLs/sQTLs have been uploaded to: https://figshare.com/articles/dataset/CattleGTEx-Gene_expression_data/21564780

https://figshare.com/articles/dataset/cis-eQTLs_for_24_tissues/22262575

and

https://cgtex.roslin.ed.ac.uk/