Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

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

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 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.

ORGANISM(S): Mus musculus

PROVIDER: GSE115670 | GEO | 2019/01/29

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

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

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 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.

2019-01-29 | GSE115663 | GEO

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

Transcriptome profiling of various organs at different developmental stages in rice (paired-end)

2015-11-25 | GSE56462 | GEO

RNA-seq on developing mouse heart

Project description:In order to compehensively determine long non-coding RNAs (lncRNAs) expressed in the mouse heart, we conducted RNA-seq on heart ventricles at three stages. We found that although lncRNAs are generally at a distance from protein-coding genes, cardiac transcription factor genes have lncRNAs in their proximity. Detailed examination revealed that many of these ln cRNAs were transcribed from the neighboring genes' promoter in a head-to-head divergent manner.

2017-08-01 | GSE93324 | GEO

RNA-seq analysis of SKMEL28 melanoma cells following DIRC3 and IGFBP5 ASO knockdown

Project description:We identified genes regulated by the DIRC3 long non-coding RNA and its neighbouring tumour suppressor gene IGFBP5 and determined common targets. DIRC3 and IGFBP5 were knocked down by transient transfection of antisense oligonucleotides (ASOs) in the human melanoma cell line Sk-Mel-28. RNA was extracted 72 hours after transfection and polyA selected 150-bp paired end RNA sequencing was performed on the Illumina HiSeq4000 .

2019-11-08 | GSE129467 | GEO

Transcriptome profiling of various organs at different developmental stages in rice (paired-end)

Project description:To identificate long noncoding RNAs in rice, we profiled transcriptome of various organs at different developmental stages using nondirectional paired-end RNA-seq based on poly(A) selection. Transcriptom profiling in flower buds, flowers, flag leaves and roots sampled before flowering and after flowering, milk grains and mature seeds.

2015-11-25 | E-GEOD-56462 | biostudies-arrayexpress

ChIP-seq analysis of Rpb1 from 12hr conjugating Oxytricha trifallax cells

Project description:To study the biogenesis of long non-coding RNAs transcribed during genome rearrangements in Oxytricha development, genome-wide localization pattern of Rpb1 (RNA Pol-II largest subunit) was studied from Oxytricha cells undergoing conjugation. Chromatin from 12hr conjugating O.trifallax cells was subjected to chromatin immunoprecipitation (ChIP) followed by sequencing of Input and ChIP samples via Illumina paired-end sequencing.

2014-03-08 | E-GEOD-55703 | biostudies-arrayexpress

Transcriptomic analysis of zebrafish during development and homeostasis

Project description:Sequencing libraries were generated from total RNA samples following the mRNAseq protocol for the generation of single end (16-36 hpf, 5 day larvae, adult head and adult tail) or paired end (24 hpf) libraries (Illumina). Single end reads of 36 nucleotides and paired end reads (2 x 76 nucleotides) were obtained with a GAIIx (Illumina). Gene expression at the different stages/tissu was assessed by cufflinks and HTseq.

2013-07-27 | GSE39703 | GEO

Mus musculus

Project description:Long non-coding RNAs from divergent transcription of protein-coding genes

| PRJNA156995 | ENA

Paired-end RNA-seq in HepG2 cells

Project description:Paired-end RNA-seq in HepG2 cells

| PRJNA547628 | ENA