Combination of novel and public RNA-seq datasets to generate an mRNA expression atlas for the domestic chicken.

BMC Genomics 2018 Aug 7;19(1):594. Epub 2018 Aug 7.

The Roslin Institute, University of Edinburgh, Easter Bush Campus, Edinburgh, Midlothian, EH25 9RG, UK.

Background: The domestic chicken (Gallus gallus) is widely used as a model in developmental biology and is also an important livestock species. We describe a novel approach to data integration to generate an mRNA expression atlas for the chicken spanning major tissue types and developmental stages, using a diverse range of publicly-archived RNA-seq datasets and new data derived from immune cells and tissues.

Results: Randomly down-sampling RNA-seq datasets to a common depth and quantifying expression against a reference transcriptome using the mRNA quantitation tool Kallisto ensured that disparate datasets explored comparable transcriptomic space. The network analysis tool Graphia was used to extract clusters of co-expressed genes from the resulting expression atlas, many of which were tissue or cell-type restricted, contained transcription factors that have previously been implicated in their regulation, or were otherwise associated with biological processes, such as the cell cycle. The atlas provides a resource for the functional annotation of genes that currently have only a locus ID. We cross-referenced the RNA-seq atlas to a publicly available embryonic Cap Analysis of Gene Expression (CAGE) dataset to infer the developmental time course of organ systems, and to identify a signature of the expansion of tissue macrophage populations during development.

Conclusion: Expression profiles obtained from public RNA-seq datasets - despite being generated by different laboratories using different methodologies - can be made comparable to each other. This meta-analytic approach to RNA-seq can be extended with new datasets from novel tissues, and is applicable to any species.

Download full-text PDF

Source
http://dx.doi.org/10.1186/s12864-018-4972-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6081845PMC
August 2018

Publication Analysis

Top Keywords

rna-seq datasets
16
expression atlas
12
public rna-seq
8
generate mrna
8
mrna expression
8
domestic chicken
8
expression
6
rna-seq
6
datasets
6
atlas
5
implicated regulation
4
regulation associated
4
associated biological
4
biological processes
4
factors implicated
4
transcription factors
4
cell-type restricted
4
restricted contained
4
contained transcription
4
processes cell
4

Altmetric Statistics

Similar Publications