| Deposited data |
|
| RNA-seq data |
This study |
NCBI SRA BioProject accessions: PRJNA392196, PRJNA616134, PRJNA305942, PRJNA392196, PRJNA917329 |
| Linear mixed model-based Summary statistics of mapped eQTLs and sQTLs from each of the 16 tissue and the multi-tissue analysis |
This study |
https://melbourne.figshare.com/articles/dataset/eQTL_and_sQTL_from_16_cattle_tissues_linear_mixed_model_/19793047 (https://doi.org/10.26188/19793047) |
| Cattle GTEx RNA-seq data and summary stats |
Liu et al.8
|
http://cgtex.roslin.ed.ac.uk/ |
| DNA sequence of 1000 Bull Genome |
Daetwyler et al.1,2
|
https://www.ebi.ac.uk/eva/?eva-study=PRJEB42783 |
|
| Software and algorithms |
|
| Customsed code related to heritability analyses |
This study |
https://github.com/rxiangr/e-sQTL_h2 (https://sandbox.zenodo.org/account/settings/github/repository/rxiangr/e-sQTL_h2 or https://doi.org/10.5072/zenodo.1219141) |
| Code to implement Coloc by Cattle GTEx |
Liu et al.8
|
https://github.com/shuliliu/cattleGTEx/tree/master/GWAS_eQTLs/Coloc (https://zenodo.org/badge/latestdoi/484289386) |
| Coloc |
Giambartolomei et al.29
|
https://cran.r-project.org/web/packages/coloc/vignettes/a01_intro.html |
| PLINK |
Chang et al.43
|
https://www.cog-genomics.org/plink/ |
| GCTA |
Yang et al.3
|
https://yanglab.westlake.edu.cn/software/gcta/#Overview |
| BayesRC |
MacLeod et al.4
|
https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-016-2443-6 |
| METAL |
Willer et al.44
|
https://genome.sph.umich.edu/wiki/METAL_Documentation |
| LDSC |
Finucane et al.20
|
https://github.com/bulik/ldsc |
| FastQTL |
Ongen et al.45
|
https://github.com/francois-a/fastqtl |
