Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

RNA content of transcription factories

ABSTRACT: RNA content of transcription factories

PROVIDER: PRJEB7531 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	ERR655280.fastq.gz	Fastqsanger.gz
	ERR655281.fastq.gz	Fastqsanger.gz
	ERR655282.fastq.gz	Fastqsanger.gz
	ERR655283.fastq.gz	Fastqsanger.gz
	ERR655284.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 18

Similar Datasets

RNA content of transcription factories

Project description:We have develop a simple fact method to isolate transcription factories and analyzed their RNA content as compared to total poly(A)+ and chromatin associated RNA fractions in presence or absence of pro-inflammatory cytokine.

2015-10-30 | E-MTAB-3020 | biostudies-arrayexpress

In vivo live imaging of RNA polymerase II transcription factories in primary cells

Project description:Transcription steps are marked by different modifications of the C-terminal domain of RNA polymerase II (RNAPII). Phosphorylation of Ser5 and Ser7 by cyclin-dependent kinase 7 (CDK7) as part of TFIIH marks initiation, whereas phosphorylation of Ser2 by CDK9 marks elongation. These processes are thought to take place in localized transcription foci in the nucleus, known as ‘‘transcription factories,’’ but it has been argued that the observed clusters/foci are mere fixation or labeling artifacts. We show that transcription factories exist in living cells as distinct foci by live-imaging fluorescently labeled CDK9, a kinase known to associate with active RNAPII. These foci were observed in different cell types derived from CDK9-mCherry knock-in mice. We show that these foci are very stable while highly dynamic in exchanging CDK9. Chromatin immunoprecipitation (ChIP) coupled with deep sequencing (ChIP-seq) data show that the genome-wide binding sites of CDK9 and initiating RNAPII overlap on transcribed genes. Immunostaining shows that CDK9- mCherry foci colocalize with RNAPII-Ser5P, much less with RNAPII-Ser2P, and not with CDK12 (a kinase reported to be involved in the Ser2 phosphorylation) or with splicing factor SC35. In conclusion, transcription factories exist in living cells, and initiation and elongation of transcripts takes place in different nuclear compartments.

2013-05-13 | GSE46849 | GEO

In vivo live imaging of RNA polymerase II transcription factories in primary cells

Project description:Transcription steps are marked by different modifications of the C-terminal domain of RNA polymerase II (RNAPII). Phosphorylation of Ser5 and Ser7 by cyclin-dependent kinase 7 (CDK7) as part of TFIIH marks initiation, whereas phosphorylation of Ser2 by CDK9 marks elongation. These processes are thought to take place in localized transcription foci in the nucleus, known as M-bM-^@M-^XM-bM-^@M-^Xtranscription factories,M-bM-^@M-^YM-bM-^@M-^Y but it has been argued that the observed clusters/foci are mere fixation or labeling artifacts. We show that transcription factories exist in living cells as distinct foci by live-imaging fluorescently labeled CDK9, a kinase known to associate with active RNAPII. These foci were observed in different cell types derived from CDK9-mCherry knock-in mice. We show that these foci are very stable while highly dynamic in exchanging CDK9. Chromatin immunoprecipitation (ChIP) coupled with deep sequencing (ChIP-seq) data show that the genome-wide binding sites of CDK9 and initiating RNAPII overlap on transcribed genes. Immunostaining shows that CDK9- mCherry foci colocalize with RNAPII-Ser5P, much less with RNAPII-Ser2P, and not with CDK12 (a kinase reported to be involved in the Ser2 phosphorylation) or with splicing factor SC35. In conclusion, transcription factories exist in living cells, and initiation and elongation of transcripts takes place in different nuclear compartments. Examination of genome occupancy of CDK9 and RNAPII that was performed by ChIP-seq in the MEL cell line as described (Soler et al. 2010, 2011) using CDK9 C20 antibody (Santa Cruz Biotechnology, C20, sc-484) and RNA Pol II antibody (Santa Cruz Biotechnology, N20, sc899),

2013-05-13 | E-GEOD-46849 | biostudies-arrayexpress

Dissecting the nascent human transcriptome by analysing the RNA content of transcription factories.

Project description:While mapping total and poly-adenylated human transcriptomes has now become routine, characterizing nascent transcripts remains challenging, largely because nascent RNAs have such short half-lives. Here, we describe a simple, fast and cost-effective method to isolate RNA associated with transcription factories, the sites responsible for the majority of nuclear transcription. Following stimulation of human endothelial cells with the pro-inflammatory cytokine TNFα, we isolate and analyse the RNA content of factories by sequencing. Comparison with total, poly(A)(+) and chromatin RNA fractions reveals that sequencing of purified factory RNA maps the complete nascent transcriptome; it is rich in intronic unprocessed transcript, as well as long intergenic non-coding (lincRNAs) and enhancer-associated RNAs (eRNAs), micro-RNA precursors and repeat-derived RNAs. Hence, we verify that transcription factories produce most nascent RNA and confer a regulatory role via their association with a set of specifically-retained non-coding transcripts.

| S-EPMC4538806 | biostudies-literature

Mimivirus Replication Factories

Project description:Proteomic analysis of isolated viral factories along a timeline after infection of the amoeba Acanthamoeba polyphaga by the giant Mimivirus

2018-10-26 | PXD004203 | Pride

Chromatin architecture in hexaploid wheat is hierarchically organized around genome territories and transcription factories

Project description:Chromatin architecture in hexaploid wheat is hierarchically organized around genome territories and transcription factories

| PRJNA552868 | ENA

CpG islands and GC content dictate nucleosome depletion in a transcription independent manner at mammalian promoters

Project description:This SuperSeries is composed of the following subset Series: GSE38560: CpG islands and GC content dictate nucleosome depletion in a transcription independent manner at mammalian promoters (RNA-seq) GSE38561: CpG islands and GC content dictate nucleosome depletion in a transcription independent manner at mammalian promoters (ChIP-seq) GSE38562: CpG islands and GC content dictate nucleosome depletion in a transcription independent manner at mammalian promoters (genomic SEQ) GSE38563: CpG islands and GC content dictate nucleosome depletion in a transcription independent manner at mammalian promoters (MNase-seq) GSE38564: CpG islands and GC content dictate nucleosome depletion in a transcription independent manner at mammalian promoters (5) Refer to individual Series

2012-06-11 | E-GEOD-38577 | biostudies-arrayexpress

Air and dust from pharmaceutical factories

Project description:Air and dust from pharmaceutical factories Metagenome

| PRJNA1004882 | ENA

RNA content of yeast nuclear mRNPs

Project description:RNA content of yeast nuclear mRNPs

| PRJNA941889 | ENA

Chromatin architecture in hexaploid wheat is hierarchically organized around genome territories and transcription factories (Wheat_ChIP)

Project description:Chromatin architecture in hexaploid wheat is hierarchically organized around genome territories and transcription factories (Wheat_ChIP)

| PRJNA552870 | ENA

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data