Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Differences in RNA polymerase II complexes and their interactions with surrounding chromatin on human and cytomegalovirus genomes [Pro-seq]

ABSTRACT: Differences in RNA polymerase II complexes and their interactions with surrounding chromatin on human and cytomegalovirus genomes [Pro-seq]

PROVIDER: PRJNA770685 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR16301850_1.fastq.gz	Fastqsanger.gz
	SRR16301850_2.fastq.gz	Fastqsanger.gz
	SRR16301851_1.fastq.gz	Fastqsanger.gz
	SRR16301851_2.fastq.gz	Fastqsanger.gz
	SRR16301852_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 28

Similar Datasets

Differences in RNA polymerase II complexes and their interactions with surrounding chromatin on human and cytomegalovirus genomes [Pro-seq]

Project description:To characterize transcription throughout the HCMV infection, paired-end PRO-Seq was performed on human foreskin fibroblasts (HFF) infected with human cytomegalovirus (HCMV) for 4 h, 12 h, 24 h, 48 h, and 72 h using the TB40/e strain. Cells were treated with 1µM flavopiridol 1 hour prior to isolation. Additionally, PRO-Cap was performed on untreated HFFs after 72 h of infection. Each experiment was performed with adapters containing 8 nt of random sequence flanking both ends (16 total bases of randomness) to enable deduplication.

2022-02-17 | GSE185762 | GEO

Differences in RNA polymerase II complexes and their interactions with surrounding chromatin on human and cytomegalovirus genomes

Project description:Differences in RNA polymerase II complexes and their interactions with surrounding chromatin on human and cytomegalovirus genomes

| PRJNA770683 | ENA

Differences in RNA polymerase II complexes and their interactions with surrounding chromatin on human and cytomegalovirus genomes [ChIP-seq]

Project description:Differences in RNA polymerase II complexes and their interactions with surrounding chromatin on human and cytomegalovirus genomes [ChIP-seq]

| PRJNA770185 | ENA

Differences in RNA polymerase II complexes and their interactions with surrounding chromatin on human and cytomegalovirus genomes [ChIP-seq]

Project description:To investigate the chromatin structure surrounding human RNA polymerase II (Pol II) transcription on host and viral genomes, chromatin immunoprecipitation (ChIP) was performed following digestion of HCMV infected primary human foreskin fibroblasts (HFFs) with DNA Fragmentation Factor (DFF). DFF is a human endonuclease responsible for cleaving between nucleosomes during apoptosis. We found that utilizing DFF as the front end for ChIP-Seq in place of sonication or Micrococcal nuclease (MNase) offered new insights into the connections between active transcription and the local chromatin on the host and that these connections were completely absent on the HCMV genome.

2022-02-17 | GSE185618 | GEO

Differences in RNA polymerase II complexes and their interactions with surrounding chromatin on human and cytomegalovirus genomes.

Project description:Interactions of the RNA polymerase II (Pol II) preinitiation complex (PIC) and paused early elongation complexes with the first downstream (+1) nucleosome are thought to be functionally important. However, current methods are limited for investigating these relationships, both for cellular chromatin and the human cytomegalovirus (HCMV) genome. Digestion with human DNA fragmentation factor (DFF) before immunoprecipitation (DFF-ChIP) precisely revealed both similarities and major differences in PICs driven by TBP on the host genome in comparison with PICs driven by TBP or the viral-specific, late initiation factor UL87 on the viral genome. Host PICs and paused Pol II complexes are frequently found in contact with the +1 nucleosome and paused Pol II can also be found in a complex involved in the initial invasion of the +1 nucleosome. In contrast, viral transcription complexes have very limited nucleosomal interactions, reflecting a relative lack of chromatinization of transcriptionally active regions of HCMV genomes.

| S-EPMC9010409 | biostudies-literature

Differences in RNA polymerase II complexes and their interactions with surrounding chromatin on human and cytomegalovirus genomes

Project description:This SuperSeries is composed of the SubSeries listed below.

2022-02-17 | GSE185763 | GEO

Decoding murine cytomegalovirus

Project description:Decoding murine cytomegalovirus

| PRJNA874807 | ENA

Nucleotide resolution of RNA polymerase II transcription in human cytomegalovirus

Project description:We performed paired-end PRO-Seq and/or PRO-Cap on human foreskin fibroblasts (HFF) infected with human cytomegalovirus (HCMV) for 4 h (strain TB40/E) or 96 h (strain Towne varS). Each sample has matched uninfected controls. Towne experiments were also performed with adapters containing 4 nt of random sequence flanking both sides (8 total bases of randomness) to enable deduplication. Reads were first mapped to the human genome (hg38) (files available on GEO). Unmapped reads were then mapped to HCMV (Genbank FJ616285.1) (track hub available at https://github.com/P-TEFb/trackHub_HCMV).

2019-01-16 | GSE113394 | GEO

Murine Cytomegalovirus research reagents

Project description:Murine Cytomegalovirus pSM3fr

| PRJEB64494 | ENA

Cytomegalovirus infection

Project description:Comparison of gene expression profiles of human foreskin fibroblasts (HFF) infected with 3 clinical isolates of cytomegalovirus strains representing three glycoprotein B genotypes. Keywords: other

2003-07-16 | GSE501 | GEO

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