Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

ATAC-seq_experiment in RKO cell line under low replication stress

ABSTRACT: RKO cells were treated with low doses of aphidicolin (0.2µM) that inhibit replicative DNA polymerases and induce a mild replication stress. ATAC-seq data were analysed on control cells (DMSO) and after 16h of treatment with aphidicolin

ORGANISM(S): Homo sapiens

PROVIDER: GSE156552 | GEO | 2021/05/19

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Microarray gene expression in RKO cell line under low replication stress

Project description:RKO cells were treated with low doses of aphidicolin (0,2µM) that inhibit replicative DNA polymerases and induce a mild replication stress. Expression data were analysed on control cells (DMSO), 16h of treatment (t0) and after release in complete new culture medium of 13h (N+1) using microarray (affymetrix Clarion S) We used microarray to analyse the impact of low replication stress on gene expression comparing DMSO or aphidicolin-treated cells at the end of the treatment (t0) and in daughter cells released from the replication stress (N+1).

2021-05-19 | GSE156521 | GEO

Genome-wide replication dynamics quantification reveals stress-induced delayed/under-replication as a hallmark of CFSs

Project description:We report Repli-Seq analysis of the replication program in human lymphoblasts grown in the absence or in the presence of aphidicolin, an inhibitor of replicative DNA polymerases used in vitro to destabilize CFSs. We identified regions displaying specific replication delay upon aphidicolin treatment, resulting in under-replication. We then further study the mechanisms leading to such specific delayed/under-replication within CFSs and show that transcription-dependent segregation of initiation events out of the gene body generates long-traveling forks in large transcribed domains, which elicits the replication timing delay responsible for CFS instability upon replication stress.

2019-12-29 | GSE134709 | GEO

Expression data from RKO cells transfected with SPARCL1 and vector control

2011-09-30 | GSE31440 | GEO

Expression data from RKO cells transfected with SPARCL1 and vector control

Project description:Colon cancer cell line RKO grown on Matrigel form a luminal-like structure after the transfection of SPARCL1 gene, which may imply the differentiation of the cells. To indentify genes regulated by SPARCL1, we built two stable cell lines: RKO with pLXSN-SPARCL1 plasmid (RKO-SPARCL1) and RKO with pLXSN plasmid (RKO-pLXSN). Then we cultured these two cell lines on both plastic dish and dish cover with a layer of Matrigel. We used microarrays to undentify global gene expression change in RKO cells after the tranfection of SPARCL1. Four samples including RKO-pLXSN cells cultured on plastic, RKO-pLXSN cells cultured on Matrigel, RKO-SPARCL1 cells cultured on plastic and RKO-SPARCL1 cells cultured on Matrigel were trypsinized and collected for RNA extraction and hybridization on Affymetrix microarray U133plus2.0. Supplementary files: * RLvsRP: up and down regulated genes comparing with RKO-SPARCL1(RL) and RKO-pLXSN(RP) cells cultured on plastic * RLMvsRPM: up and down regulated genes comparing with RKO-SPARCL1(RL) and RKO-pLXSN(RP) cells cultured on Matrigel

2011-09-29 | E-GEOD-31440 | biostudies-arrayexpress

A global profile of replication polymerase usage

Project description:We have established a novel sequencing approach to characterise usage of replicative DNA polymerases in S. pombe. This approach allows us to determine the roles of DNA polymerase delta and epsilon in lagging strand and leading strand DNA synthesis, respectively in genome-wide scale. Utilising the dataset of usage of these polymerases, we also successfully identified DNA replication initiation sites at high resolution. Furthermore, our informatics analysis establishes genome-wide datasets of fork direction rates, replication timing and the probability of replication termination. We mapped ribonucleotide-incorporation by the mutated DNA polymerase delta and epsilon at single-nucleotide resolution and subsequent informatics analysis was performed to generate datasets listed here.

2015-02-03 | E-GEOD-62108 | biostudies-arrayexpress

ChIP-seq of MYST acetyltransferases in RKO cell line

Project description:Genome-wide mapping of MYST acetyltransferase subunit BRPF3 in RKO synchronised cells. Genome-wide mapping of MYST acetyltransferase subunit BRPF3 in RKO synchronised cells.

2016-02-05 | E-GEOD-63722 | biostudies-arrayexpress

A global profile of replication polymerase usage

2015-02-03 | GSE62108 | GEO

RNA-seq of Colo-205 and RKO colon adenocarcinoma cell lines treated with Novel 2-Acetamido, 6-Carboxamide Substituted Benzothiazole Derivatives as Potential BRAFV600E Inhibitors and PLX4720

Project description:Two human colorectal adenocarcinoma cell lines (Colo-205 and RKO) were treated with PLX4720 and newly synthesized 2-Acetamido, 6-Carboxamide Substituted Benzothiazole Derivatives, as potential BRAF V600E inhibitors; IDK142, IDK145, IDK133 and DMSO as control.

2023-12-19 | E-MTAB-13097 | biostudies-arrayexpress

Methylation analysis of normal lymphocytes, HCT116, RKO and SW480

Project description:Methylation analysis of normal lymphocytes, HCT116, RKO and SW480

2013-08-30 | GSE50511 | GEO

Methylation analysis of normal lymphocytes, HCT116, RKO and SW480

Project description:Methylation analysis of normal lymphocytes, HCT116, RKO and SW480 In vitro methylated DNA (IVD) generated from normal lymphocytes, HCT116, RKO and SW480 genomic DNA was subjected to sodium bisulfite treatment and the DNA was analyzed for CpG methylation using the Infinium Methylation Array.

2013-08-30 | E-GEOD-50511 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

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