RNA-seq analysis of single bovine blastocysts

Autores
Chitwood, James L.; Rincon, Gonzalo; Kaiser, German Gustavo; Medrano, Juan F.; Ross, Pablo J.
Año de publicación
2013
Idioma
inglés
Tipo de recurso
artículo
Estado
versión publicada
Descripción
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
Fuente
BMC Genomics 14 : 350 (2013)
Materia
Secuencia Nucleotídica
ARN
Embriones Animales
Bovina
Expresión Génica
Nucleotide Sequence
RNA
Animal Embryos
Bovinae
Gene Expression
Blastocistos
Blastocysts
Nivel de accesibilidad
acceso abierto
Condiciones de uso
http://creativecommons.org/licenses/by-nc-sa/4.0/
Repositorio
INTA Digital (INTA)
Institución
Instituto Nacional de Tecnología Agropecuaria
OAI Identificador
oai:localhost:20.500.12123/4368
Acceder
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oai_identifier_str oai:localhost:20.500.12123/4368
network_acronym_str INTADig
repository_id_str l
network_name_str INTA Digital (INTA)
spelling RNA-seq analysis of single bovine blastocystsChitwood, James L.Rincon, GonzaloKaiser, German GustavoMedrano, Juan F.Ross, Pablo J.Secuencia NucleotídicaARNEmbriones AnimalesBovinaExpresión GénicaNucleotide SequenceRNAAnimal EmbryosBovinaeGene ExpressionBlastocistosBlastocystsBackground: 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 BalcarceFil: Chitwood, James L. University of California Davis. Department of Animal Science; Estados UnidosFil: Rincon, Gonzalo. University of California Davis. Department of Animal Science; Estados UnidosFil: Kaiser, German Gustavo. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Balcarce; ArgentinaFil: Medrano, Juan F. University of California Davis. Department of Animal Science; Estados UnidosFil: Ross, Pablo J. University of California Davis. Department of Animal Science; Estados UnidosBMC2019-01-31T13:44:15Z2019-01-31T13:44:15Z2013-05info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfhttps://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2164-14-350http://hdl.handle.net/20.500.12123/43681471-2164https://doi.org/10.1186/1471-2164-14-350BMC Genomics 14 : 350 (2013)reponame:INTA Digital (INTA)instname:Instituto Nacional de Tecnología Agropecuariaenginfo:eu-repo/semantics/openAccesshttp://creativecommons.org/licenses/by-nc-sa/4.0/Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)2025-10-16T09:29:26Zoai:localhost:20.500.12123/4368instacron:INTAInstitucionalhttp://repositorio.inta.gob.ar/Organismo científico-tecnológicoNo correspondehttp://repositorio.inta.gob.ar/oai/requesttripaldi.nicolas@inta.gob.arArgentinaNo correspondeNo correspondeNo correspondeopendoar:l2025-10-16 09:29:26.35INTA Digital (INTA) - Instituto Nacional de Tecnología Agropecuariafalse
dc.title.none.fl_str_mv RNA-seq analysis of single bovine blastocysts
title RNA-seq analysis of single bovine blastocysts
spellingShingle RNA-seq analysis of single bovine blastocysts
Chitwood, James L.
Secuencia Nucleotídica
ARN
Embriones Animales
Bovina
Expresión Génica
Nucleotide Sequence
RNA
Animal Embryos
Bovinae
Gene Expression
Blastocistos
Blastocysts
title_short 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_sort RNA-seq analysis of single bovine blastocysts
dc.creator.none.fl_str_mv Chitwood, James L.
Rincon, Gonzalo
Kaiser, German Gustavo
Medrano, Juan F.
Ross, Pablo J.
author Chitwood, James L.
author_facet Chitwood, James L.
Rincon, Gonzalo
Kaiser, German Gustavo
Medrano, Juan F.
Ross, Pablo J.
author_role author
author2 Rincon, Gonzalo
Kaiser, German Gustavo
Medrano, Juan F.
Ross, Pablo J.
author2_role author
author
author
author
dc.subject.none.fl_str_mv Secuencia Nucleotídica
ARN
Embriones Animales
Bovina
Expresión Génica
Nucleotide Sequence
RNA
Animal Embryos
Bovinae
Gene Expression
Blastocistos
Blastocysts
topic Secuencia Nucleotídica
ARN
Embriones Animales
Bovina
Expresión Génica
Nucleotide Sequence
RNA
Animal Embryos
Bovinae
Gene Expression
Blastocistos
Blastocysts
dc.description.none.fl_txt_mv 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
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.
publishDate 2013
dc.date.none.fl_str_mv 2013-05
2019-01-31T13:44:15Z
2019-01-31T13:44:15Z
dc.type.none.fl_str_mv info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
http://purl.org/coar/resource_type/c_6501
info:ar-repo/semantics/articulo
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv 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
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
identifier_str_mv 1471-2164
dc.language.none.fl_str_mv eng
language eng
dc.rights.none.fl_str_mv 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)
eu_rights_str_mv openAccess
rights_invalid_str_mv http://creativecommons.org/licenses/by-nc-sa/4.0/
Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)
dc.format.none.fl_str_mv application/pdf
dc.publisher.none.fl_str_mv BMC
publisher.none.fl_str_mv BMC
dc.source.none.fl_str_mv BMC Genomics 14 : 350 (2013)
reponame:INTA Digital (INTA)
instname:Instituto Nacional de Tecnología Agropecuaria
reponame_str INTA Digital (INTA)
collection INTA Digital (INTA)
instname_str Instituto Nacional de Tecnología Agropecuaria
repository.name.fl_str_mv INTA Digital (INTA) - Instituto Nacional de Tecnología Agropecuaria
repository.mail.fl_str_mv tripaldi.nicolas@inta.gob.ar
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score 12.712165

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