Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Protect-seq: Genome-wide profiling of nuclease inaccessible domains reveals physical properties of chromatin

ABSTRACT: We compare histone modifications, chromatin accessibility, and replication timing domain genome-wide in HCT116 colon cancer cells with its genetic derivative DKO cells which lack DNMT3B and DNMT1 activity and the fibrosarcoma cell line HT1080.

ORGANISM(S): Homo sapiens

PROVIDER: GSE135580 | GEO | 2019/11/25

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Protect-seq: genome-wide profiling of nuclease inaccessible domains reveals physical properties of chromatin.

Project description:In metazoan cell nuclei, heterochromatin constitutes large chromatin domains that are in close contact with the nuclear lamina. These heterochromatin/lamina-associated domains (LADs) domains are difficult to profile and warrants a simpler and direct method. Here we report a new method, Protect-seq, aimed at identifying regions of heterochromatin via resistance to nuclease degradation followed by next-generation sequencing (NGS). We performed Protect-seq on the human colon cancer cell line HCT-116 and observed overlap with previously curated LADs. We provide evidence that these protected regions are enriched for and can distinguish between the repressive histone modification H3K9me3, H3K9me2 and H3K27me3. Moreover, in human cells the loss of H3K9me3 leads to an increase in chromatin accessibility and loss of Protect-seq signal. For further validation, we performed Protect-seq in the fibrosarcoma cell line HT1080 and found a similar correlation with previously curated LADs and repressive histone modifications. In sum, Protect-seq is an efficient technique that allows rapid identification of nuclease resistant chromatin, which correlate with heterochromatin and radial positioning.

| S-EPMC7026637 | biostudies-literature

Protect-seq: Genome-wide profiling of nuclease inaccessible domains reveals physical properties of chromatin

Project description:Protect-seq: Genome-wide profiling of nuclease inaccessible domains reveals physical properties of chromatin

| PRJNA559362 | ENA

Expression analysis of human CRABP1 gene and R131A CRABP1 mutant in HT1080 cells

Project description:Investigation of whole genome gene expression level changes in HT1080 fibrosarcoma cell line after transfection CRABP1 gene and R131A CRABP1 mutant (arginine-alanine substitution in a protein active site, protein lacks the ability to interact with retinoic acid), compared to HT1080 line transfected with empty pLXSN vector. A twelve samples on one chip study using total RNA recovered from four separate cultures of HT1080 human fibrosarcoma cell line transfected with empty pLXSN vector, four HT1080 cell line cultures transfected with CRABP1 gene and four HT1080 cell line cultures transfected with R131A CRABP1 mutant. Each sample on a chip measures the expression level of 44,049 genes from human genome with three-fold technical redundancy.

2013-09-01 | E-GEOD-48673 | biostudies-arrayexpress

Expression analysis of human CRABP1 gene and R131A CRABP1 mutant in HT1080 cells

2013-09-01 | GSE48673 | GEO

Homo sapiens

Project description:Targets of cytostatic drugs in HT1080 fibrosarcoma

| PRJNA91501 | ENA

RNAi profiling of human fibrosarcoma cell line knocked down for MT1-MMP

Project description:To define the role of MT1-MMP in the tumor progression, we suppressed its expression in human fibrosarcoma cell line, HT1080, using RNAi technique. The gene expression pattern was then compared betweent the two experimental cell groups with contrasting MT1-MMP expression level.

2008-10-25 | E-GEOD-1774 | biostudies-arrayexpress

Homo sapiens

Project description:Expression data from RECK-overexpressing HT1080 fibrosarcoma cells

| PRJNA126575 | ENA

Genome binding profile of TFIIH helicases XPB and XPD in HT1080 cells

Project description:The conserved TFIIH helicases XPB and XPD play key roles in transcription initiation and DNA repair. To investigate the functions of these helicases on a genome-wide scale, we performed ChIP-seq of endogenous XPB and XPD in the HT1080 human fibrosarcoma cell line.

2014-02-18 | GSE44849 | GEO

Suppression of MT1-MMP in Human Fibrosarcoma Impair Tumor Angiogenesis and Enlargement

2008-09-01 | GSE1774 | GEO

Transcription profiling of human HT1080 fibrosarcoma cells treated with cytostatic drugs

Project description:HT1080 fibrosarcoma cells were treated with cytostatic drugs and analysed on Affymetrix microarray to identify genes and pathways regulated by these compounds. The array images were processed using Affymetrix MAS 5.0 software. and normalized by global scaling or scaled to a polyA+ spike mask

2008-04-01 | E-GEOD-2238 | biostudies-arrayexpress

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