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YylncT acts as a gatekeeper of the mesodermal transcriptional program by local modulation of DNMT3B [human_2]

ABSTRACT: Bidirectional transcription is a prevalent feature of eukaryotic promoters. The goal of this study is to identify novel divergent long-coding RNAs during differentiation of human ES to cardiomyocytes. Methods: Paired end RNA-Seq was performed on key time-points of human ES cell differentiation to cardiomyocytes. The time-points include day2, day4, day6 and day8. Results: Using an optimized data analysis workflow, we mapped about ~70 million sequence reads per sample to the human genome (build hg38) and identified 781 novel yylncRNAs during ES cell differentiation to cardiomyocytes. Expression kinetics of a subset of yylncRNAs identified from RNA-Seq had a linear relationship with qRT–PCR . Conclusions: Our study represents the detailed analysis of the genome wide identification of divergent long-coding RNA generated by paired end RNA-seq technology. Our results show that NGS offers a comprehensive and more accurate quantitative and qualitative evaluation of long-non coding RNA content within a cell. We conclude that RNA-seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biological functions.

ORGANISM(S): Homo sapiens

PROVIDER: GSE115663 | GEO | 2019/01/29

REPOSITORIES: GEO

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yylncT acts as a gatekeeper of the mesodermal transcriptional program by local modulation of DNMT3B [human_1]

Project description:Bidirectional transcription is a prevalent feature of eukaryotic promoters. The goal of this study is to identify novel divergent long-coding RNAs during differentiation of human ES to cardiomyocytes. Methods: Paired end RNA-Seq was performed on key time-points of human ES cell differentiation to cardiomyocytes. The time-points include day 0, day 1, day 2, day 4,day 6, day 8 and day 14. Results: Using an optimized data analysis workflow, we mapped about ~70 million sequence reads per sample to the human genome (build hg38) and identified 781 novel yylncRNAs during ES cell differentiation to cardiomyocytes. Expression kinetics of a subset of yylncRNAs identified from RNA-Seq had a linear relationship with qRT–PCR . Conclusions: Our study represents the detailed analysis of the genome wide identification of divergent long-coding RNA generated by paired end RNA-seq technology. Our results show that NGS offers a comprehensive and more accurate quantitative and qualitative evaluation of long-non coding RNA content in the process of cardiac differentitation. We conclude that RNA-seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biological functions.

2019-01-29 | GSE115575 | GEO

yylncT acts as a gatekeeper of the mesodermal transcriptional program by local modulation of DNMT3B [mouse]

Project description:Bidirectional transcription is a prevalent feature of eukaryotic promoters. The goal of this study is to identify novel divergent long-coding RNAs during differentiation of human ES to cardiomyocytes. Methods: Paired end RNA-Seq was performed on the tissue obtained from the cardiogenic region of the indicated embroynic stages of mice. Following stages of mouse development were used:- E8,E8.5,E9.5 and E14., Results: Using an optimized data analysis workflow, we mapped about ~70 million sequence reads per sample to the mouse genome (build mm10). Conclusions: Our study represents the detailed analysis of the genome wide identification of divergent long-coding RNA generated by paired end RNA-seq technology. Our results show that NGS offers a comprehensive and more accurate quantitative and qualitative evaluation of long-non coding RNA content within a cell. We conclude that RNA-seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biological functions.

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RNA-seq analysis of global RNA levels at 4 stages of directed cardiac differentiation of mouse embryonic stem cells

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