Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

ABSTRACT: Butyrate HCT116 ATAC/RNA

PROVIDER: PRJNA715317 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR13998206_1.fastq.gz	Fastqsanger.gz
	SRR13998206_2.fastq.gz	Fastqsanger.gz
	SRR13998207_1.fastq.gz	Fastqsanger.gz
	SRR13998207_2.fastq.gz	Fastqsanger.gz
	SRR13998208_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 41

Similar Datasets

ncRNA DUBR RAP-MS in HCT116 cells

Project description:Non-coding RNAs (ncRNAs) are finely tuned cellular regulators important for human cell growth and cancer progression. DUBR (also known as linc00883) is a nuclear ncRNA first discovered in mice for its role in regulating myoblast differentiation through interactions with chromatin and DNA methyltransferases. High expression levels of this ncRNA are predictive of poor patient outcome in colon adenocarcinoma, suggesting that DUBR may be involved in controlling cancer growth. To elucidate its function, we used RAP-MS and RNA immunoprecipitation techniques which revealed its interaction with epigenetic maintenance proteins in the human colon cancer cell line HCT116. Further, ATAC-seq and RNA-seq were used to address its function in regulating the epigenome and transcriptome of HCT116 cells. Here we report that DUBR is a regulator of human colon cancer cell line HCT116 survival.

2025-05-07 | PXD057811 | Pride

The Warburg effect alters histone acetylation in cancer cells by influencing the utilization of HDAC and HAT mechanisms.

Project description:Microarray transcriptome analysis of siMock and siACL HCT116 cells treated with 0, 0.5, 2.0, and 5.0 mM butyrate over three days. Gene expression is measured at control cells (siMock) and ACL-depleted (siACL) cells with 4 dosages (0, 0.5, 2.0, and 5.0 mM) of butyrate treatments

2012-12-01 | E-GEOD-41113 | biostudies-arrayexpress

The Warburg effect alters histone acetylation in cancer cells by influencing the utilization of HDAC and HAT mechanisms.

Project description:Microarray transcriptome analysis of siMock and siACL HCT116 cells treated with 0, 0.5, 2.0, and 5.0 mM butyrate over three days.

2012-12-01 | GSE41113 | GEO

The diapause-like colorectal cancer cells induced by SMC4 attenuation are characterized by low proliferation and chemotherapy insensitivity [ATAC-seq]

Project description:ATAC-seq for HCT116 cells and its shSMC4.

2022-07-17 | GSE208201 | GEO

HCT116_SMARCA4 ATAC-seq

Project description:To investigate the effect of SMARCA4-R1157W mutant on chromatin accessibility, we performed ATAC-seq experiments in HCT116 cells.

2023-01-05 | GSE221947 | GEO

ATAC-seq of oxaliplatin resistant HCT116

Project description:ATAC-seq of oxaliplatin resistant HCT116

| PRJNA1269608 | ENA

EHF and CDX1 co-operate to drive extensive transcriptional reprogramming and chromatin remodelling in CRC cells [ATAC-seq]

Project description:EHF and CDX1 co-operate to drive differentation of CRC cells. To identify the change in chromatin remodelling induced by these transcription factors, EHF and CDX1 were stably re-expressed in poorly differentiated HCT116 CRC cells and ATAC-seq analysis performed.

2022-11-02 | GSE202072 | GEO

Project description:SAGA and ATAC are two related transcriptional coactivator complexes, sharing the same histone acetyltransferase (HAT) subunit. The HAT activities of SAGA and ATAC are required for metazoan development but the precise role of the two complexes in RNA polymerase II transcription in mammals is less understood. To determine whether SAGA and ATAC have redundant or specific functions dependent on their HAT activities, we compared the effects of HAT inactivation in each complex with that of inactivation of either SAGA or ATAC core subunits in mouse embryonic stem cells (ESCs). We show that core subunits of SAGA or ATAC subunits are required for complex assembly, mouse ESC growth and self-renewal. Additionally, ATAC, but not SAGA subunits are required for ESC viability by regulating the transcription of translation-related genes. Surprisingly, depletion of specific or shared HAT module subunits caused a global decrease in histone H3K9 acetylation, but did not result in significant phenotypic or transcriptional defects. Thus, our results indicate that SAGA and ATAC are differentially required for viability and self-renewal of mouse ESCs by regulating transcription through different pathways, in a HAT-independent manner.

2021-08-11 | PXD027026 | Pride

Genome-wide measurement of acetylated histone H3 in naÃ¯ve cells under Treg-inducing conditon

Project description:To investigate the molecular mechanism how butyrate promoter differentiation of naÃ¯ve T cells into regulatory T cells Examination of acetylated histone H3 during the differentiation of regulatory T cells in the presence or absence of butyrate

2013-11-20 | E-GEOD-49653 | biostudies-arrayexpress

Regulation of gene expression in enteroids by butyrate and IL-13

Project description:Expression in organoids dervied from the ileum of WT C57Bl/6 mice stimulated with butyrate, IL-13, or butyrate + IL-13. Intestinal organoids were stimulated with butyrate for 48hrs, then IL-13 for 72 hrs. RNA was isolated using RNeasy Kit (Qiagen). Sequencing was performed using the Illumina HiSeq2500. Reads were mapped to the mm10 genome using Bowtie.

2024-03-06 | GSE223822 | 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