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Biology of reproduction2014; 90(3); 61; doi: 10.1095/biolreprod.113.113928

RNA-seq transcriptome profiling of equine inner cell mass and trophectoderm.

Abstract: Formation of the inner cell mass (ICM) and trophectoderm (TE) marks the first differentiation event in mammalian development. These two cell types have completely divergent fates for the remainder of the developmental process. The molecular mechanisms that regulate ICM and TE formation are poorly characterized in horses. The objective of this study was to establish the transcriptome profiles of ICM and TE cells from horse blastocysts using RNA sequencing (RNA-seq). A total of 12 270 genes were found to be expressed in either lineage. Global analysis of the transcriptome profiles by unsupervised clustering indicated that ICM and TE samples presented different gene expression patterns. Statistical analysis indicated that 1662 genes were differentially expressed (adjusted P 2) between ICM and TE. Genes known to be specific to the ICM and TE were expressed primarily in their respective tissue. Transcript abundance for genes related to biological processes important for horse blastocyst formation and function is presented and discussed. Collectively, our data and analysis serve as a valuable resource for gene discovery and unraveling the fundamental mechanisms of early horse development.
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Publication Date: 2014-03-20 PubMed ID: 24478389PubMed Central: PMC4435230DOI: 10.1095/biolreprod.113.113928Google Scholar: Lookup
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  • Journal Article
  • Research Support
  • N.I.H.
  • Extramural
  • Research Support
  • Non-U.S. Gov't

Summary

This research summary has been generated with artificial intelligence and may contain errors and omissions. Refer to the original study to confirm details provided. Submit correction.

The research study used RNA sequencing to compare and analyze gene expressions in inner cell mass and trophectoderm cells, two early developmental cell types in horses, to help shed light on the biological processes important for horse embryo development.

Objective of the Study

  • The main objective of this research study was to understand the transcriptome profiles of the inner cell mass (ICM) and the trophectoderm (TE) cells in horse blastocysts. These are two critical cell types that form during the early stages of mammalian development and have completely different evolutionary paths throughout the rest of the development process.

Methodology

  • The researchers used a method called RNA sequencing (RNA-Seq) to accurately establish the transcriptome profiles of the ICM and TE cells.
  • A global analysis of the transcriptome profiles followed by unsupervised clustering was carried out to understand the expression patterns of genes in these cells.
  • Statistical analysis was performed to identify differentially expressed genes between ICM and TE.

Findings

  • Through this research, the team identified a total of 12,270 genes that were expressed in either the ICM or TE lineage.
  • The unsupervised clustering of the global transcriptome profiles revealed distinct gene expression patterns in the ICM and TE samples.
  • The statistical analysis indicated a significant number—1,662 genes—were differentially expressed between ICM and TE, with an adjusted P-value less than 0.05 and fold change greater than 2, two common statistics indicating significant differences.
  • Furthermore, it was found that genes specific to either the ICM and TE were mainly expressed in their respective tissue, further corroborating distinct roles and functions of these two cell types during development.

Conclusion

  • The overall results of the study and subsequent analysis provide much-needed understanding of gene expression in early horse development.
  • The research not only increases knowledge in this area but also serves as an extensive resource for gene discovery and understanding the core mechanisms that drive early development in horses.

Cite This Article

APA
Iqbal K, Chitwood JL, Meyers-Brown GA, Roser JF, Ross PJ. (2014). RNA-seq transcriptome profiling of equine inner cell mass and trophectoderm. Biol Reprod, 90(3), 61. https://doi.org/10.1095/biolreprod.113.113928

Publication

Biology of reproduction
ISSN: 1529-7268
NlmUniqueID: 0207224
Country: United States
Language: English
Volume: 90
Issue: 3
Pages: 61
PII: 61

Researcher Affiliations

Iqbal, Khursheed
  • Department of Animal Science, University of California Davis, Davis, California.
Chitwood, James L
    Meyers-Brown, Geraldine A
      Roser, Janet F
        Ross, Pablo J

          MeSH Terms

          • Animals
          • Blastocyst / physiology
          • Blastocyst / ultrastructure
          • Blastocyst Inner Cell Mass / cytology
          • Blastocyst Inner Cell Mass / physiology
          • Chromosome Mapping
          • Embryonic Development / genetics
          • Embryonic Development / physiology
          • Female
          • Gene Amplification
          • Gene Expression Regulation, Developmental / genetics
          • Gene Expression Regulation, Developmental / physiology
          • Horses / physiology
          • Multigene Family
          • Pregnancy
          • RNA / genetics
          • Real-Time Polymerase Chain Reaction
          • Transcriptome / genetics
          • Transcriptome / physiology

          Grant Funding

          • R01 HD070044 / NICHD NIH HHS
          • R01HD070044 / NICHD NIH HHS

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