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Analysis of transcriptome complexity through RNA sequencing in normal and failing murine hearts.

Publication ,  Journal Article
Lee, J-H; Gao, C; Peng, G; Greer, C; Ren, S; Wang, Y; Xiao, X
Published in: Circ Res
December 9, 2011

RATIONALE: Accurate and comprehensive de novo transcriptome profiling in heart is a central issue to better understand cardiac physiology and diseases. Although significant progress has been made in genome-wide profiling for quantitative changes in cardiac gene expression, current knowledge offers limited insights to the total complexity in cardiac transcriptome at individual exon level. OBJECTIVE: To develop more robust bioinformatic approaches to analyze high-throughput RNA sequencing (RNA-Seq) data, with the focus on the investigation of transcriptome complexity at individual exon and transcript levels. METHODS AND RESULTS: In addition to overall gene expression analysis, the methods developed in this study were used to analyze RNA-Seq data with respect to individual transcript isoforms, novel spliced exons, novel alternative terminal exons, novel transcript clusters (ie, novel genes), and long noncoding RNA genes. We applied these approaches to RNA-Seq data obtained from mouse hearts after pressure-overload-induced by transaortic constriction. Based on experimental validations, analyses of the features of the identified exons/transcripts, and expression analyses including previously published RNA-Seq data, we demonstrate that the methods are highly effective in detecting and quantifying individual exons and transcripts. Novel insights inferred from the examined aspects of the cardiac transcriptome open ways to further experimental investigations. CONCLUSIONS: Our work provided a comprehensive set of methods to analyze mouse cardiac transcriptome complexity at individual exon and transcript levels. Applications of the methods may infer important new insights to gene regulation in normal and disease hearts in terms of exon utilization and potential involvement of novel components of cardiac transcriptome.

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Published In

Circ Res

DOI

EISSN

1524-4571

Publication Date

December 9, 2011

Volume

109

Issue

12

Start / End Page

1332 / 1341

Location

United States

Related Subject Headings

  • Transcription, Genetic
  • Sequence Analysis, RNA
  • Molecular Sequence Data
  • Mice, Inbred C57BL
  • Mice
  • Male
  • High-Throughput Nucleotide Sequencing
  • Heart Failure
  • Heart
  • Gene Expression Regulation
 

Citation

APA
Chicago
ICMJE
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Lee, J.-H., Gao, C., Peng, G., Greer, C., Ren, S., Wang, Y., & Xiao, X. (2011). Analysis of transcriptome complexity through RNA sequencing in normal and failing murine hearts. Circ Res, 109(12), 1332–1341. https://doi.org/10.1161/CIRCRESAHA.111.249433
Lee, Jae-Hyung, Chen Gao, Guangdun Peng, Christopher Greer, Shuxun Ren, Yibin Wang, and Xinshu Xiao. “Analysis of transcriptome complexity through RNA sequencing in normal and failing murine hearts.Circ Res 109, no. 12 (December 9, 2011): 1332–41. https://doi.org/10.1161/CIRCRESAHA.111.249433.
Lee J-H, Gao C, Peng G, Greer C, Ren S, Wang Y, et al. Analysis of transcriptome complexity through RNA sequencing in normal and failing murine hearts. Circ Res. 2011 Dec 9;109(12):1332–41.
Lee, Jae-Hyung, et al. “Analysis of transcriptome complexity through RNA sequencing in normal and failing murine hearts.Circ Res, vol. 109, no. 12, Dec. 2011, pp. 1332–41. Pubmed, doi:10.1161/CIRCRESAHA.111.249433.
Lee J-H, Gao C, Peng G, Greer C, Ren S, Wang Y, Xiao X. Analysis of transcriptome complexity through RNA sequencing in normal and failing murine hearts. Circ Res. 2011 Dec 9;109(12):1332–1341.

Published In

Circ Res

DOI

EISSN

1524-4571

Publication Date

December 9, 2011

Volume

109

Issue

12

Start / End Page

1332 / 1341

Location

United States

Related Subject Headings

  • Transcription, Genetic
  • Sequence Analysis, RNA
  • Molecular Sequence Data
  • Mice, Inbred C57BL
  • Mice
  • Male
  • High-Throughput Nucleotide Sequencing
  • Heart Failure
  • Heart
  • Gene Expression Regulation