RNA-seq analysis of single bovine blastocysts
Background: Use of RNA-Seq presents unique benefits in terms of gene expression analysis because of its wide dynamic range and ability to identify functional sequence variants. This technology provides the opportunity to assay the developing embryo, but the paucity of biological material available f...
| Autores principales: | , , , , |
|---|---|
| Formato: | info:ar-repo/semantics/artículo |
| Lenguaje: | Inglés |
| Publicado: |
BMC
2019
|
| Materias: | |
| Acceso en línea: | https://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2164-14-350 http://hdl.handle.net/20.500.12123/4368 https://doi.org/10.1186/1471-2164-14-350 |
| _version_ | 1855035309841973248 |
|---|---|
| author | Chitwood, James L. Rincon, Gonzalo Kaiser, German Gustavo Medrano, Juan F. Ross, Pablo J. |
| author_browse | Chitwood, James L. Kaiser, German Gustavo Medrano, Juan F. Rincon, Gonzalo Ross, Pablo J. |
| author_facet | Chitwood, James L. Rincon, Gonzalo Kaiser, German Gustavo Medrano, Juan F. Ross, Pablo J. |
| author_sort | Chitwood, James L. |
| collection | INTA Digital |
| description | Background: Use of RNA-Seq presents unique benefits in terms of gene expression analysis because of its wide dynamic range and ability to identify functional sequence variants. This technology provides the opportunity to assay the developing embryo, but the paucity of biological material available from individual embryos has made this a challenging prospect.
Results: We report here the first application of RNA-Seq for the analysis of individual blastocyst gene expression, SNP detection, and characterization of allele specific expression (ASE). RNA was extracted from single bovine blastocysts (n = 5), amplified, and analyzed using high-throughput sequencing. Approximately 38 million sequencing reads were generated per embryo and 9,489 known bovine genes were found to be expressed, with a high correlation of expression levels between samples (r > 0.97). Transcriptomic data was analyzed to identify SNP in expressed genes, and individual SNP were examined to characterize allele specific expression. Expressed biallelic SNP variants with allelic imbalances were observed in 473 SNP, where one allele represented between 65-95% of a variant’s transcripts.
Conclusions: This study represents the first application of RNA-seq technology in single bovine embryos allowing a representation of the embryonic transcriptome and the analysis of transcript sequence variation to describe specific allele expression. |
| format | info:ar-repo/semantics/artículo |
| id | INTA4368 |
| institution | Instituto Nacional de Tecnología Agropecuaria (INTA -Argentina) |
| language | Inglés |
| publishDate | 2019 |
| publishDateRange | 2019 |
| publishDateSort | 2019 |
| publisher | BMC |
| publisherStr | BMC |
| record_format | dspace |
| spelling | INTA43682019-01-31T13:45:33Z RNA-seq analysis of single bovine blastocysts Chitwood, James L. Rincon, Gonzalo Kaiser, German Gustavo Medrano, Juan F. Ross, Pablo J. Secuencia Nucleotídica ARN Embriones Animales Bovina Expresión Génica Nucleotide Sequence RNA Animal Embryos Bovinae Gene Expression Blastocistos Blastocysts Background: Use of RNA-Seq presents unique benefits in terms of gene expression analysis because of its wide dynamic range and ability to identify functional sequence variants. This technology provides the opportunity to assay the developing embryo, but the paucity of biological material available from individual embryos has made this a challenging prospect. Results: We report here the first application of RNA-Seq for the analysis of individual blastocyst gene expression, SNP detection, and characterization of allele specific expression (ASE). RNA was extracted from single bovine blastocysts (n = 5), amplified, and analyzed using high-throughput sequencing. Approximately 38 million sequencing reads were generated per embryo and 9,489 known bovine genes were found to be expressed, with a high correlation of expression levels between samples (r > 0.97). Transcriptomic data was analyzed to identify SNP in expressed genes, and individual SNP were examined to characterize allele specific expression. Expressed biallelic SNP variants with allelic imbalances were observed in 473 SNP, where one allele represented between 65-95% of a variant’s transcripts. Conclusions: This study represents the first application of RNA-seq technology in single bovine embryos allowing a representation of the embryonic transcriptome and the analysis of transcript sequence variation to describe specific allele expression. EEA Balcarce Fil: Chitwood, James L. University of California Davis. Department of Animal Science; Estados Unidos Fil: Rincon, Gonzalo. University of California Davis. Department of Animal Science; Estados Unidos Fil: Kaiser, German Gustavo. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Balcarce; Argentina Fil: Medrano, Juan F. University of California Davis. Department of Animal Science; Estados Unidos Fil: Ross, Pablo J. University of California Davis. Department of Animal Science; Estados Unidos 2019-01-31T13:44:15Z 2019-01-31T13:44:15Z 2013-05 info:ar-repo/semantics/artículo info:eu-repo/semantics/article info:eu-repo/semantics/publishedVersion https://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2164-14-350 http://hdl.handle.net/20.500.12123/4368 1471-2164 https://doi.org/10.1186/1471-2164-14-350 eng info:eu-repo/semantics/openAccess http://creativecommons.org/licenses/by-nc-sa/4.0/ Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0) application/pdf BMC BMC Genomics 14 : 350 (2013) |
| spellingShingle | Secuencia Nucleotídica ARN Embriones Animales Bovina Expresión Génica Nucleotide Sequence RNA Animal Embryos Bovinae Gene Expression Blastocistos Blastocysts Chitwood, James L. Rincon, Gonzalo Kaiser, German Gustavo Medrano, Juan F. Ross, Pablo J. RNA-seq analysis of single bovine blastocysts |
| title | RNA-seq analysis of single bovine blastocysts |
| title_full | RNA-seq analysis of single bovine blastocysts |
| title_fullStr | RNA-seq analysis of single bovine blastocysts |
| title_full_unstemmed | RNA-seq analysis of single bovine blastocysts |
| title_short | RNA-seq analysis of single bovine blastocysts |
| title_sort | rna seq analysis of single bovine blastocysts |
| topic | Secuencia Nucleotídica ARN Embriones Animales Bovina Expresión Génica Nucleotide Sequence RNA Animal Embryos Bovinae Gene Expression Blastocistos Blastocysts |
| url | https://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2164-14-350 http://hdl.handle.net/20.500.12123/4368 https://doi.org/10.1186/1471-2164-14-350 |
| work_keys_str_mv | AT chitwoodjamesl rnaseqanalysisofsinglebovineblastocysts AT rincongonzalo rnaseqanalysisofsinglebovineblastocysts AT kaisergermangustavo rnaseqanalysisofsinglebovineblastocysts AT medranojuanf rnaseqanalysisofsinglebovineblastocysts AT rosspabloj rnaseqanalysisofsinglebovineblastocysts |