ArticleBMC genomics2018
Combination of novel and public RNA-seq datasets to generate an mRNA expression atlas for the domestic chicken.
Article in BMC genomics, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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Who cites it
24 citing papers in PubMed.
- Genome-Wide Association Studies Reveal Key Candidate Genes for Egg Weight and Quality Components in an FVeterinary sciences · 2026Article
- Transcriptome sequencing reveals the regulatory mechanisms during the development of small white follicles to small yellow follicles in laying hens.Poultry science · 2026Article
- Discordant effects of maternal age on the human MII oocyte transcriptome.Molecular human reproduction · 2025Article
- An mRNA expression atlas for the duck with public RNA-seq datasets.BMC genomics · 2025Article
- Catalogue of LPS-induced transcriptional changes across vertebrates identifies syntenically conserved human long non-coding RNAs that regulate the innate immune response.Frontiers in immunology · 2025Article
- The first chicken oocyte nucleus whole transcriptomic profile defines the spectrum of maternal mRNA and non-coding RNA genes transcribed by the lampbrush chromosomes.Nucleic acids research · 2024Article
- Runs of homozygosity and selection signature analyses reveal putative genomic regions for artificial selection in layer breeding.BMC genomics · 2024Article
- The relationship between extreme inter-individual variation in macrophage gene expression and genetic susceptibility to inflammatory bowel disease.Human genetics · 2024Article
- Cysteine Enrichment Mediates Co-Option of Uricase in Reptilian Skin and Transition to Uricotelism.Molecular biology and evolution · 2023Article
- Genetic architecture and key regulatory genes of fatty acid composition in Gushi chicken breast muscle determined by GWAS and WGCNA.BMC genomics · 2023Article
- Article
- Generation and network analysis of an RNA-seq transcriptional atlas for the rat.NAR genomics and bioinformatics · 2022Article
- Development of novel reagents to chicken FLT3, XCR1 and CSF2R for the identification and characterization of avian conventional dendritic cells.Immunology · 2022Article
- An Interaction-Based Method for Refining Results From Gene Set Enrichment Analysis.Frontiers in genetics · 2022Article
- Network analysis of transcriptomic diversity amongst resident tissue macrophages and dendritic cells in the mouse mononuclear phagocyte system.PLoS biology · 2020Article
- Regulation and function of macrophage colony-stimulating factor (CSF1) in the chicken immune system.Developmental and comparative immunology · 2020Article
- Pattern Recognition Receptor Signaling and Innate Responses to Influenza A Viruses in the Mallard Duck, Compared to Humans and Chickens.Frontiers in cellular and infection microbiology · 2020Review
- Species-Specificity of Transcriptional Regulation and the Response to Lipopolysaccharide in Mammalian Macrophages.Frontiers in cell and developmental biology · 2020Article
- Avian Expression Patterns and Genomic Mapping Implicate Leptin in Digestion and TNF in Immunity, Suggesting That Their Interacting Adipokine Role Has Been Acquired Only in MammalsInternational journal of molecular sciences · 2019Article
- Analysis of the Progeny of Sibling Matings Reveals Regulatory Variation Impacting the Transcriptome of Immune Cells in Commercial Chickens.Frontiers in genetics · 2019Article
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Authors and funding
11 authors.
Funding
Abstract
backgroundThe 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.
resultsRandomly 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.
conclusionExpression 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.
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