REAGENT or RESOURCE	SOURCE	IDENTIFIER
Deposited data
Bovine in vivo RNAseq raw data	Gene Expression Omnibus (GEO) Jiang et al., 2014	GSE59186
Bovine in vitro RNAseq raw data	Gene Expression Omnibus (GEO) Chitwood et al., 2013 and Graf et al., 2014a	GSE44023, GSE121227∗ and GSE52415
Mouse in vivo RNAseq raw data	Gene Expression Omnibus (GEO) Wang et al., 2018 and Wu et al., 2018	GSE97778 and GSE113164
Mouse in vitro RNAseq raw data	Gene Expression Omnibus (GEO)	GSE159484∗
Human in vitro RNAseq raw data	Gene Expression Omnibus (GEO) Xue et al., 2013 and Dang et al., 2016	GSE44183 and GSE71318
Software and algorithms
R software	R Core Team (2020)	https://www.R-project.org/
Raw data importing, genome alignment and counting using Galaxy by NetworkAnalyst 3.0 web browser	Zhou et al., 2019	https://galaxy.networkanalyst.ca/
RNAseq quantification using Galaxy by NetworkAnalyst 3.0 web browser function Kallisto	Bray et al., 2016	https://galaxy.networkanalyst.ca/
Limma analysis using R	Ritchie et al., 2015	R package limma
ROAST analysis using R	Wu et al., 2010	mroast() function from the limma R package
PQN analysis using R	Dieterle et al., 2006	DOI: https://doi.org/10.1021/ac051632c
Random Forest model analysis using R	Ho, 1995	R package randomForest (ver. 4.6-14; RColorBrewer)
Other
Compilation of genes part of Reactome metabolic and epigenetic pathways	Jassal et al., 2020	https://reactome.org/
R code necessary to reproduce RNAseq and Pearson correlations analyses	This paper	Data S6

∗Unpublished