Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Candidate silencer elements in the human and mouse genome

ABSTRACT: Candidate silencer elements in the human and mouse genome

PROVIDER: PRJNA596216 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR10721036.fastq.gz	Fastqsanger.gz
	SRR10721037.fastq.gz	Fastqsanger.gz
	SRR10721038.fastq.gz	Fastqsanger.gz
	SRR10721039.fastq.gz	Fastqsanger.gz
	SRR10721040.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 10

Similar Datasets

Candidate silencer elements in the human and mouse genome

Project description:STARR-seq assay performed on uncharacterized cis-regulatory elements to find candidate silencer elements in K562 cells.

2019-12-18 | GSE142207 | GEO

Candidate silencer elements for the human and mouse genomes.

Project description:The study of gene regulation is dominated by a focus on the control of gene activation or increase in the level of expression. Just as critical is the process of gene repression or silencing. Chromatin signatures have identified enhancers, however, genome-wide identification of silencers by computational or experimental approaches are lacking. Here, we first define uncharacterized cis-regulatory elements likely containing silencers and find that 41.5% of ~7500 tested elements show silencer activity using massively parallel reporter assay (MPRA). We trained a support vector machine classifier based on MPRA data to predict candidate silencers in over 100 human and mouse cell or tissue types. The predicted candidate silencers exhibit characteristics expected of silencers. Leveraging promoter-capture HiC data, we find that over 50% of silencers are interacting with gene promoters having very low to no expression. Our results suggest a general strategy for genome-wide identification and characterization of silencer elements.

| S-EPMC7044160 | biostudies-literature

Short tandem repeats are important contributors to silencer elements in T cells

Project description:Short tandem repeats are important contributors to silencer elements in T cells

2023-02-28 | GSE219157 | GEO

Short tandem repeats are important contributors to silencer elements in T cells

Project description:Short tandem repeats are important contributors to silencer elements in T cells

| PRJNA836547 | ENA

Short tandem repeats are important contributors to silencer elements in T cells

Project description:Short tandem repeats are important contributors to silencer elements in T cells

| PRJNA907272 | ENA

An anti-silencer- and SATB1-dependent chromatin hub regulates Rag1 and Rag2 gene expression during thymocyte development

Project description:Rag1 and Rag2 gene expression in CD4+CD8+ double positive (DP) thymocytes depends on the activity of a distant anti-silencer element (ASE) that counteracts the activity of an intergenic silencer. However, the mechanistic basis for ASE activity is unknown. Here we show that the ASE physically interacts with the distant Rag1 and Rag2 gene promoters in DP thymocytes, bringing the two promoters together to form an active chromatin hub. Moreover, we show that the ASE functions as a classical enhancer that can potently activate these promoters in the absence of the silencer or other locus elements. In thymocytes lacking the chromatin organizer SATB1, we identified a partial defect in Tcra gene rearrangement that was associated with reduced expression of Rag1 and Rag2 at the DP stage. SATB1 binds to the ASE and Rag promoters, facilitating inclusion of Rag2 in the chromatin hub and the loading of RNA polymerase II to both the Rag1 and Rag2 promoters. Our results provide a novel framework for understanding ASE function and demonstrate a novel role for SATB1 as a regulator of Rag locus organization and gene expression in DP thymocytes. Sequencing of Satb1-ChIP and input control from 6 wk old thymus

2015-02-25 | E-GEOD-66248 | biostudies-arrayexpress

Mouse SINE B2 elements function as IFN-inducible enhancer elements

Project description:Mouse SINE B2 elements function as IFN-inducible enhancer elements

| PRJNA836589 | ENA

Identification of candidate enhancer elements in unstimulated and stimulated dendritic cells and fibroblasts

Project description:To identify candidate enhancer elements we analyzed the distribution of two histone modifications associated with enhancers - H3K4me1 and H3K27ac - and one histone modification associated with active transcription - H4 acetylation.

2012-11-19 | GSE32380 | GEO

Expression of candidate genes in Celiac Disease - Associated genes and regulatory elements (part 1)

Project description:Celiac disease is a chronic immune-mediated disorder with an important genetic component. We analyzed the expression of candidate genes and regulatory elements in biopsies from duodenum.

2018-09-28 | GSE87457 | GEO

mouse liver concatenated tandem array of consensus TF response elements (catTFRE) with H2O2

Project description:a pull-down assay using a concatenated tandem array of consensus TF response elements (catTFRE) to trap the TFs expressed in mouse livers following treatment with or without H2O2

2019-08-31 | PXD015265 |

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