Context
High-throughput transcriptome sequencing (RNA-Seq) has been widely applied in cattle studies. Public databases such as the National Center for Biotechnology Information (NCBI) contain large collections of gene expression data from various cattle tissues that can be used in gene expression analysis research
Aims
This study was conducted to investigate patterns of transcriptome variation across tissues of cattle through large-scale identification of housekeeping genes (i.e. those crucial to maintaining basic cellular activity) and tissue-specific genes in cattle tissues.
Methods
Using data available in the NCBI Sequence Read Archive database, we analysed 1377 transcriptome data sequences from 60 bovine tissue types, identified tissue-specific and housekeeping genes, and set up a web-based bovine gene expression analysis tool.
Key results
We found 101 genes widely expressed in almost all tissue and screened out five housekeeping genes: RPL35A, eIF4A2, GAPDH, IPO5 and PAK2. Focusing on 12 major organs, we found 861 genes specifically expressing in these tissues. Furthermore, 187 significantly differentially expressed genes were found among six types of muscle tissues. All expression data were made available at our new website http://cattleExp.org, which can be freely accessed for future gene expression analyses.
Conclusions
The housekeeping genes and tissue-specific genes identified will provide more information for researchers studying gene expression in cattle.
Implications
The web-based cattle gene expression analysis tool will make it easy for researchers to access large public datasets. Users can easily access all publicly available RNA data and upload their own RNA-Seq data.
Identification of reference genes for quantitative expression analysis using large-scale RNA-seq data of Arabidopsis thaliana and model crop plants