Combination of novel and public RNA-seq datasets to generate an mRNA expression atlas for the domestic chicken
<strong>Background</strong> 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 type...
| Main Authors: | , , , , , , , , , , |
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| Format: | Journal article |
| Language: | English |
| Published: |
BioMed Central
2018
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| _version_ | 1826277490039980032 |
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| author | Bush, S Freem, L Maccallum, A O'Dell, J Wu, C Afrasiabi, C Psifidi, A Stevens, M Smith, J Summers, K Hume, D |
| author_facet | Bush, S Freem, L Maccallum, A O'Dell, J Wu, C Afrasiabi, C Psifidi, A Stevens, M Smith, J Summers, K Hume, D |
| author_sort | Bush, S |
| collection | OXFORD |
| description | <strong>Background</strong> 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. <strong>Results</strong> 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. <strong>Conclusion</strong> 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. |
| first_indexed | 2024-03-06T23:29:41Z |
| format | Journal article |
| id | oxford-uuid:6b99984e-7e8c-4aeb-9eb0-d46e2c0ccead |
| institution | University of Oxford |
| language | English |
| last_indexed | 2024-03-06T23:29:41Z |
| publishDate | 2018 |
| publisher | BioMed Central |
| record_format | dspace |
| spelling | oxford-uuid:6b99984e-7e8c-4aeb-9eb0-d46e2c0ccead2022-03-26T19:05:13ZCombination of novel and public RNA-seq datasets to generate an mRNA expression atlas for the domestic chickenJournal articlehttp://purl.org/coar/resource_type/c_dcae04bcuuid:6b99984e-7e8c-4aeb-9eb0-d46e2c0cceadEnglishSymplectic Elements at OxfordBioMed Central2018Bush, SFreem, LMaccallum, AO'Dell, JWu, CAfrasiabi, CPsifidi, AStevens, MSmith, JSummers, KHume, D<strong>Background</strong> 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. <strong>Results</strong> 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. <strong>Conclusion</strong> 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. |
| spellingShingle | Bush, S Freem, L Maccallum, A O'Dell, J Wu, C Afrasiabi, C Psifidi, A Stevens, M Smith, J Summers, K Hume, D Combination of novel and public RNA-seq datasets to generate an mRNA expression atlas for the domestic chicken |
| title | Combination of novel and public RNA-seq datasets to generate an mRNA expression atlas for the domestic chicken |
| title_full | Combination of novel and public RNA-seq datasets to generate an mRNA expression atlas for the domestic chicken |
| title_fullStr | Combination of novel and public RNA-seq datasets to generate an mRNA expression atlas for the domestic chicken |
| title_full_unstemmed | Combination of novel and public RNA-seq datasets to generate an mRNA expression atlas for the domestic chicken |
| title_short | Combination of novel and public RNA-seq datasets to generate an mRNA expression atlas for the domestic chicken |
| title_sort | combination of novel and public rna seq datasets to generate an mrna expression atlas for the domestic chicken |
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