Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Gene expression and chromatin accessibility of iLSCs vs iBlasts cells

ABSTRACT: Gene expression and chromatin accessibility of iLSCs vs iBlasts cells

PROVIDER: PRJNA514713 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR8435060_1.fastq.gz	Fastqsanger.gz
	SRR8435060_2.fastq.gz	Fastqsanger.gz
	SRR8435070_1.fastq.gz	Fastqsanger.gz
	SRR8435070_2.fastq.gz	Fastqsanger.gz
	SRR8435080.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 72

Similar Datasets

Gene expression and chromatin accessibility of iLSCs vs iBlasts cells

Project description:Gene expression and chromatin accessibility of iLSCs vs iBlasts cells

| PRJNA514716 | ENA

Gene expression and chromatin accessibility of iLSCs vs iBlasts cells

Project description:Gene expression and chromatin accessibility of iLSCs vs iBlasts cells

| PRJNA514717 | ENA

Chromatin accessibility changes of Fli1ko vs WT in CD8 T cells

Project description:Chromatin accessibility changes of Fli1ko vs WT in CD8 T cells

| PRJNA630255 | ENA

Acute BAF perturbation causes immediate changes in chromatin accessibility

Project description:Loss-of-function mutations in genes coding for subunits of the large, multifarious BRG1/BRM associated factor (BAF) chromatin remodeling complexes are frequently causative for cancer or developmental diseases1-5. Cells lacking the most frequently mutated subunits like the ATPase SMARCA4 typically exhibit drastic chromatin accessibility changes, especially of important regulatory regions6-12. However, so far it remains unknown how these changes are established over time, and whether they are causative for intra-complex synthetic lethalities abrogating the formation (SMARCC1-SMARCC2)8,13,14 or activity (SMARCA4-SMARCA2)15-17 of BAF complexes. Here, we utilize the dTAG system18 to induce acute degradation of BAF subunits in wild-type and BAF mutant backgrounds and analyze the resulting chromatin accessibility changes with high kinetic resolution. We observe that chromatin alterations are established faster than the duration of one cell cycle and that maintaining genome accessibility requires constant ATP-dependent remodeling. Completely abolishing BAF complex function by acute degradation of a synthetic lethal subunit in a paralog-deficient background results in a near-complete loss of chromatin accessibility at BAF-controlled sites, especially at super-enhancers, providing a mechanism for intra-complex synthetic lethalities.

2020-12-23 | PXD018381 | Pride

Chromatin accessibility changes caused by expression of histone 3.3(K9M) in A375 cells

Project description:We use ATAC-seq to examine chromatin accessibility changes in A375 cells after expression of mScarlet tagged H3.3(wildtype) vs. H3.3(K9M)

2022-02-25 | GSE194422 | GEO

Gene Expression and Chromatin Accessibility of Nephron Progenitor Cells in Mice

Project description:Gene Expression and Chromatin Accessibility of Nephron Progenitor Cells in Mice

| PRJNA1027873 | ENA

Chromatin accessibility and gene expression maps of Plasma Cells and Myeloma Plasma Cells

Project description:Chromatin accessibility and gene expression maps of Plasma Cells and Myeloma Plasma Cells

| PRJNA642172 | ENA

Chromatin Accessibility Profiling of Osteoclasts Precursor Cells

Project description:Chromatin Accessibility Profiling of Osteoclasts Precursor Cells

| PRJNA839624 | ENA

Functional DNA methylation is accompanied by chromatin accessibility [gene expression]

Project description:Analysis of nucleosome positioning and chromatin state by using CpG methyltransferase M.SssI to methylate nuclei. Unmethylated regions that gain methylation (low to high beta value) are known to be accessible and nucleosome depleted. Method used to study changes after epigenetic drug treatments identified that majority of demethylation events are not accompanied by chromatin accessibility changes. RNA harvested from cells post epigenetic drug treatment, with 5-Aza-CdR or SAHA

2013-03-08 | E-GEOD-43852 | biostudies-arrayexpress

Single-minded homolog 2 resides in the chromatin protein network of androgen receptor and modulates gene expression in prostate cancer cells Single-minded homolog 2 resides in the chromatin protein network of androgen receptor and modulates gene expression in prostate cancer cells

Project description:We investigated the composition of chromatin protein network around endogenous androgen receptor (AR) in VCaP castration resistant prostate cancer cells using recently developed chromatin-directed proteomic approach called ChIP-SICAP . The androgen-induced AR chromatin protein network contained expected TFs, e.g. HOXB13, chromatin remodeling proteins, e.g. SMARCA4, and several novel candidates not previously associated with AR, e.g. prostate cancer biomarker SIM2. Based on these findings, the role of SMARCA4 and SIM2 was further characterized at AR chromatin domains . Silencing of SIM2 altered chromatin accessibility at a similar number of AR-binding sites as SMARCA4, an established ATPase subunit of the BAF chromatin remodeling complex, often aberrantly expressed in prostate cancer. Despite the wide co-occurrence on chromatin of SMARCA4 and AR, depletion of SMARCA4 influenced chromatin accessibility and expression of a restricted set of AR target genes, in particular those involved in cell morphogenetic changes in epithelial-mesenchymal transition. Silencing of SIM2, in turn, affected the expression of a much larger group of androgen-regulated genes, e.g. those involved in cellular responses to external stimuli and steroid hormone stimulus. The silencing also reduced proliferation of VCaP cells and tumor size in chick embryo chorioallantoic membrane assay, further suggesting the importance of SIM2 in the regulation prostate cancer cells.

2021-06-17 | PXD025193 | Pride

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