Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Analysis of genome wide changes in RNA polymerase II occupancy in murine cells during heat shock and recovery

ABSTRACT: Analysis of genome wide changes in RNA polymerase II occupancy in murine cells during heat shock and recovery

PROVIDER: PRJNA422767 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR6384680.fastq.gz	Fastqsanger.gz
	SRR6384681.fastq.gz	Fastqsanger.gz
	SRR6384682.fastq.gz	Fastqsanger.gz
	SRR6384683.fastq.gz	Fastqsanger.gz
	SRR6384684.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 6

Similar Datasets

Analysis of genome wide changes in RNA polymerase II occupancy in murine cells during heat shock and recovery

Project description:The goal of this study was to reveal changes in genome-bound RNA polymerase II in response to heat shock, and monitor the recovery of bound RNA polymerase II as cells return to homeostasis.

2018-07-04 | GSE108185 | GEO

Genome-wide occupancy of RNA polymerase II before and after heat shock in mouse cells

Project description:The goal of this study was to understand changes that occur in RNA polymerase II occupancy upon heat shock using ChIP-seq in mouse cells.

2015-12-30 | GSE66513 | GEO

Chromatin accessibility in human K562 erythroleukemia cells profiled upon heat shock, recovery, and heat-induced transcriptional memory

Project description:ATAC-seq in human K562 erythroleukemia cells that were either unconditioned (s_uC and HSS_uC), preconditioned with a single heat shock exposure (s_pC), or preconditioned with multiple heat exposures (HSS_pC). After two day recovery from the preconditioning, during which the cells underwent two mitotic divisions, the cells were additionally subjected to a single heat shock to analyze heat-induced changes in chromatin accessibility in unconditioned versus preconditioned cells.

2021-04-01 | GSE154744 | GEO

Transriptional profiling upon heat shock and recovery in cells deficient for FBXW7 and their wild type counterpart.

2015-02-20 | GSE57397 | GEO

Transriptional profiling upon heat shock and recovery in cells deficient for FBXW7 and their wild type counterpart.

Project description:FBXW7 modulates stress response by post-translational modification of HSF1 HSF1 orchestrates the heat-shock response upon exposure to heat stress and activates a transcriptional program vital for cancer cells. Genes positively regulated by HSF1 show increeased expression during heat shock while their expression is reduced during recovery. Genes negatively regulated by HSF1 show the opposite pattern. In this study we utilized the HCT116 FBXW7 KO colon cell line and its wild type counterpart to monitor gene expression changes during heat shock (42oC, 1 hour) and recovery (37oC for 2 hours post heat shock) using RNA sequencing. These results revealed that the heat-shock response pathway is prolonged in cells deficient for FBXW7. Whole RNA was extracted from 1 million HCT116 WT or FBXW7KO cells using the RNAeasy kit (Qiagen) according to the manufacturer’s protocol. Poly-A+ (magnetic oligodT-containing beads (Invitrogen)) or Ribominus RNA was used for library preparation. cDNA preparation and strand-specific library construction was performed using the dUTP method. Libraries were sequenced on the Illumina HiSeq 2000 using 50bp single-read method. Differential gene expression analysis was performed for each matched recovery versus heat-shock pairs, separately in each biological replicate and cell line (WT or KO). Two types of comparisons were tested: (a) WT recovery vs WT heat shock, (b) FBXW7 KO recovery vs heat shock.

2015-02-20 | E-GEOD-57397 | biostudies-arrayexpress

Systemic Comparison of Heat Shock Response Induced by Heat Shock and a Proteasome Inhibitor in Mouse Fibrosarcoma Cells and Their Thermotolerant Counterparts

Project description:Heat shock response (HSR) is a cellular defense mechanism against various stresses. Both heat shock and proteasome inhibitor MG132 cause the induction of heat shock proteins, a distinct feature of HSR. To better understand the molecular basis of HSR, we subjected the mouse fibrosarcoma cell line, RIF-1, and its thermotolerant variant, TR-RIF-1 cells, to heat shock and MG132. We compared mRNA expressions using microarray analysis during recovery after heat shock and MG132 treatment. This study led us to group the 3,245 up-regulated genes by heat shock and MG132 into three families: genes regulated 1) by both heat shock and MG132 (e.g. chaperones); 2) by heat shock (e.g. DNA-binding proteins including histones); and 3) by MG132 (e.g. innate immunity and defense-related molecules).

2011-11-09 | GSE24197 | GEO

Systemic Comparison of Heat Shock Response Induced by Heat Shock and a Proteasome Inhibitor in Mouse Fibrosarcoma Cells and Their Thermotolerant Counterparts

2011-11-09 | E-GEOD-24197 | biostudies-arrayexpress

Heat shock response of HsfA2 knockout plants

Project description:The expression of heat-shock proteins (Hsps) induced by a non-lethal heat treatment confers acquired thermotolerance (AT) to organisms against a subsequent challenge of otherwise lethal temperature. After stress signal lifted, AT gradually decayed with the decline of Hsps during recovery period. The duration of AT may be critical for sessile organisms, such as plants, to survive repeated heat stress in the environment. To identify heat-induced genes involved in duration of AT, we took a reverse-genetics approach by screening for Arabidopsis T-DNA insertion mutants that show decreased thermotolerance after a long recovery at non-stress condition following a conditioning treatment. Among the tested mutants corresponding to 47 genes, only the HsfA2 knockout mutant showed significant phenotype. The mutant plants were more sensitive to severe heat stress than the wild type after long but not short recovery following a pretreatment at 37oC, which can be complemented by introducing a wild-type copy of the gene. Quantitative hypocotyl elongation assay also revealed that AT decayed faster in the absence of HsfA2. Significant decline of the transcript levels of several highly heat-induced genes was observed in the HsfA2 knockout plants after a 4-h recovery or after 2 h of prolonged heat stress. Immunoblot anlysis showed that Hsa32 and class I small Hsp were lower in the mutant than in the wild type after a long recovery. Our results suggest that HsfA2 as a heat-induced transactivator sustains the post-stress expression of Hsp genes and extends the duration of AT in Arabidopsis. Keywords: heat shock response

2006-11-01 | GSE4760 | GEO

The heat shock response of killifish (Fundulus heteroclitus): candidate gene and heterologous microarray approaches.

Project description:Subspecies of the Atlantic killifish, Fundulus heteroclitus, differ in their maximum thermal tolerance. To determine whether there is a link between the heat shock response (HSR) and maximum thermal tolerance, we exposed 20ºC acclimated killifish from these subspecies to a 2hr heat shock at 34ºC and examined gene expression during heat shock and recovery using real time quantitative PCR and a heterologous cDNA microarray designed for salmonid fishes. Keywords: Expression profiling by array

2009-10-30 | GSE18792 | GEO

Fcp1 dephosphorylation of the RNA polymerase II C-terminal domain required for efficient transcription of heat shock genes

Project description:RNA polymerase II is decreased on heat shock-induced genes when the CTD phosphatase Fcp1 is knocked down in Drosophila S2 cells. We examined transcriptionally-engaged Pol II genome-wide with GRO-seq to determine if other genes are similarly affected.

2012-06-29 | GSE38748 | 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