We made our efforts to utilize existing tools and data resources to avoid reinventing of wheels, standardize the nomenclatures and processes, so that our epi-data analysis can be performed for consistant and uniform outcomes that can be realiably used for comparisons.

• Public repositories

• Ensembl Expression Arlas
• FAANG Datasets
• NCBI - SRA

• Data sources used

• Genome build Bos taurus ARS-UCD1.2: https://ftp.ensembl.org/pub/release-110/fasta/bos_taurus/dna/Bos_taurus.ARS-UCD1.2.dna_sm.toplevel.fa.gz
• Transcriptome GTF file (NCBI – Bos taurus): https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/002/263/795/
• Transcriptome GTF file (Ensembl – Bos taurus): https://ftp.ensembl.org/pub/release-110/gtf/bos_taurus/

• Software employed

• Nextflow/rna-seq code: https://nf-co.re/rnaseq/3.12.0
• NF-core: https://nf-co.re/
• NF-core/rnaseq: https://github.com/nf-core/rnaseq

• Tissue ontology references

• Cell Line Ontology (CLO)
• Tissue / enzyme - BRENDA Tissue Ontology (BTO)
• Tissue - KB_Bio_101 (AURA)
• Tissue - Mouse gross anatomy and development, timed (EMAPA)
• Tissue - National Cancer Institute Thesaurus (NCIT)
• Tissue / organ / etc - Uber Anatomy Ontology (UBERON)