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RNA-seq analysis of bovine intramuscular, subcutaneous and perirenal adipose tissues

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Abstract

The deposition of intramuscular fat is an important factor affecting the beef quality, such as flavour and palatability. In this study, for further identifying the differential molecular mechanisms regulating the deposition of fat between intramuscular and external adipose tissues, particularly subcutaneous and perirenal adipose tissues, it was designed to obtain transcript sequence data and compare the transcriptomes among intramuscular, subcutaneous, and perirenal adipose tissues by RNA-Seq. A total of 66,206,912, 55,114,070 and 67,320,426 fragments were sequenced for the intramuscular (IAT), subcutaneous (SAT), and perirenal adipose tissue (PAT) respectively. Among them, total 953, 1,534, 2,026 genes showing differential expression between IAT and SAT, IAT and PAT, SAT and PAT, were identified respectively (FDR < 0.05). When these data had been mixed and analyzed together, 110 genes were differentially expressed among these three adipose tissues. Using GO enrichment analysis, multiple biological pathways were found to be significantly enriched for differentially expressed genes (FDR < 0.01), including cellular process, biological regulation, and metabolic process. In addition, total 4,625, 4,775 and 4,147 alternative splicing events occurred in IAT, SAT, and PAT, had also been detected respectively. Thus, our results logically provide the evidence for further understanding the bovine fat deposition, especially intramuscular fat, at a fine scale.

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Acknowledgments

This work was supported by Grants from Beijing Natural Science Foundation (Grant No. 6132003), the science and technology project of Beijing Municipal Commission of Education (Grant No. PXM 2014_014207_000001), the Project of Construction of Innovative Teams and Teacher Career Development for Universities and Colleges Under Beijing Municipality (PXM2013_014207_000067), National Natural Science Foundation of China (Grant No. 31272526, Grant No. 31072185), and Beijing University of Agriculture Funding to improve research quality (Grant No. GJB2012002).

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Authors and Affiliations

  1. College of Animal Science and Technology, Beijing University of Agriculture, Beijing, 102206, China

    Xihui Sheng, Hemin Ni, Yunhai Liu & Yong Guo

  2. Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China

    Junya Li & Lupei Zhang

Authors
  1. Xihui Sheng
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  2. Hemin Ni
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  3. Yunhai Liu
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  4. Junya Li
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  5. Lupei Zhang
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  6. Yong Guo
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Correspondence to Xihui Sheng or Yong Guo.

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Xihui Sheng and Hemin Ni have contributed equally to this work.

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11033_2013_3010_MOESM1_ESM.xlsx

Table S1. The FPKM value of annotated genes in bovine intramuscular, subcutaneous and perirenal adipose tissues. (XLSX 1034 kb)

Table S2. The different expressed genes detected among three adipose tissues. (XLS 37 kb)

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Sheng, X., Ni, H., Liu, Y. et al. RNA-seq analysis of bovine intramuscular, subcutaneous and perirenal adipose tissues. Mol Biol Rep 41, 1631–1637 (2014). https://doi.org/10.1007/s11033-013-3010-8

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  • DOI: https://doi.org/10.1007/s11033-013-3010-8

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