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BMC Genomics. 2018 Aug 7;19(1):594. doi: 10.1186/s12864-018-4972-7.

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

Author information

1
The Roslin Institute, University of Edinburgh, Easter Bush Campus, Edinburgh, Midlothian, EH25 9RG, UK.
2
Present address: Nuffield Department of Clinical Medicine, University of Oxford, John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK.
3
Present address: Rivers and Lochs Institute, Inverness College, University of the Highlands and Islands, Research Hub, 1 Inverness Campus, Inverness, IV2 5NA, UK.
4
Department of Integrative and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA, 92037, USA.
5
Present address: The Royal Veterinary College, Hawkshead Lane, Hatfield, Hertfordshire, AL9 7TA, UK.
6
Present address: Mater Research-University of Queensland, Translational Research Institute, 37 Kent Street, Woolloongabba, QLD, 4102, Australia.
7
The Roslin Institute, University of Edinburgh, Easter Bush Campus, Edinburgh, Midlothian, EH25 9RG, UK. david.hume@uq.edu.au.
8
Present address: Mater Research-University of Queensland, Translational Research Institute, 37 Kent Street, Woolloongabba, QLD, 4102, Australia. david.hume@uq.edu.au.

Abstract

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.

KEYWORDS:

Chicken; Expression atlas; Gallus gallus; Network graph; RNA-seq

PMID:
30086717
PMCID:
PMC6081845
DOI:
10.1186/s12864-018-4972-7
[Indexed for MEDLINE]
Free PMC Article

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