Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Transcription modulates chromatin dynamics and locus configuration sampling

ABSTRACT: Transcription modulates chromatin dynamics and locus configuration sampling

PROVIDER: PRJNA986010 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR24970924_1.fastq.gz	Fastqsanger.gz
	SRR24970924_2.fastq.gz	Fastqsanger.gz
	SRR24970925_1.fastq.gz	Fastqsanger.gz
	SRR24970925_2.fastq.gz	Fastqsanger.gz
	SRR24970926_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 32

Similar Datasets

Transcription modulates chromatin dynamics and locus configuration sampling

Project description:This SuperSeries is composed of the SubSeries listed below.

2023-06-21 | GSE235416 | GEO

Transcription modulates chromatin dynamics and locus configuration sampling.

Project description:In living cells, the 3D structure of gene loci is dynamic, but this is not revealed by 3C and FISH experiments in fixed samples, leaving a notable gap in our understanding. To overcome these limitations, we applied the highly predictive heteromorphic polymer (HiP-HoP) model to determine chromatin fiber mobility at the Pax6 locus in three mouse cell lines with different transcription states. While transcriptional activity minimally affects movement of 40-kbp regions, we observed that motion of smaller 1-kbp regions depends strongly on local disruption to chromatin fiber structure marked by H3K27 acetylation. This also substantially influenced locus configuration dynamics by modulating protein-mediated promoter-enhancer loops. Importantly, these simulations indicate that chromatin dynamics are sufficiently fast to sample all possible locus conformations within minutes, generating wide dynamic variability within single cells. This combination of simulation and experimental validation provides insight into how transcriptional activity influences chromatin structure and gene dynamics.

| S-EPMC10497412 | biostudies-literature

STAT3 Modulates CD4+ T Mitochondrial Dynamics and Function in Aging

Project description:STAT3 Modulates CD4+ T Mitochondrial Dynamics and Function in Aging

| PRJNA1008269 | ENA

Microbiota configuration dictates nutritional immune optimization

Project description:Microbiota configuration dictates nutritional immune optimization

| PRJNA928085 | ENA

C9ORF72 interaction with cofilin modulates actin dynamics in motoneurons

Project description:Intronic hexanucleotide expansions in C9ORF72 are common in ALS and FTLD, but it is unknown whether loss of function, toxicity by the expanded RNA or dipeptides from non ATG-initiated translation are responsible for the pathophysiology. We determined the interactome of C9ORF72 in motoneurons and found that C9ORF72 is present in a complex with cofilin and other actin binding proteins. Phosphorylation of cofilin is enhanced in C9ORF72 depleted motoneurons, in patient derived lymphoblastoid cells, iPS cell derived motoneurons and post-mortem brain samples from ALS patients. C9ORF72 modulates the activity of the small GTPases Arf6 and Rac1, resulting in enhanced activity of LIMK1/2. This results in reduced axonal actin dynamics in C9ORF72 depleted motoneurons. Dominant negative Arf6 rescues this defect, suggesting that C9ORF72 acts as a modulator of small GTPases in a pathway that regulates axonal actin dynamics.

2016-09-30 | PXD004913 | Pride

Endovascular Device for Endothelial Cell Sampling

Project description:We have developed an endovascular catheter-based device for sampling of the endothelium, intended for RNA-seq analysis. With an outer diameter of 0.23 mm it is capable of reaching peripheral vessels for endothelial sampling, and favourably compares to other approaches with stent retrievers or similar tools. Here, we have collected samples from liver and kidney vessels from swine and performed RNA-sequencing to validate the sample quality.

2022-08-21 | GSE197756 | GEO

A neuroprotective locus modulates ischemic stroke infarction independent of collateral vessel anatomy

Project description:A neuroprotective locus modulates ischemic stroke infarction independent of collateral vessel anatomy

| PRJNA707067 | ENA

Longitudinal wastewater sampling and untargeted metabolomics of three buildings

Project description:Direct sampling of building wastewater has the potential to enable precision public health observations and interventions. Temporal sampling offers additional dynamic information that can be used to increase the informational content of individual metabolic “features”, but few studies have focused on high-resolution sampling. Here, we sampled three spatially close buildings, revealing individual metabolomics features, retention time (rt) and mass-to-charge ratio (mz) pairs, that often possess similar stationary statistical properties, as expected from aggregate sampling. However, the temporal profiles of features—providing orthogonal information to physicochemical properties—illustrate that many possess different feature temporal dynamics (fTDs) across buildings, with large and unpredictable single day deviations from the mean. Internal to a building, numerous and seemingly unrelated features, with mz and rt differences up to hundreds of Daltons and seconds, display highly correlated fTDs, suggesting non-obvious feature relationships. Data-driven building classification achieves high sensitivity and specificity, and extracts building-identifying features found to possess unique dynamics. Analysis of fTDs from many short-duration samples allows for tailored community monitoring with applicability in public health studies.

2020-03-20 | ST001357 | MetabolomicsWorkbench

5C Chromatin interactions in the Igh locus in activated splenic B cells

Project description:These tracks include chromatin interaction data produced using the 5C (chromatin conformation capture carbon copy) method by the Kenter Lab located at the University of Illinois College of Medicine, Chicago, IL. These tracks show looping interactions across the Igh locus using alternating forward and reverse primer design scheme. The 3C method uses formaldehyde crosslinking to covalently associate interacting chromatin segments in intact cells. The cells are then lysed and chromatin is digested with the Hind III restriction enzyme. The digested fragments are ligated under dilute conditions to promote intra-molecular ligation. A genome-wide interaction library of ligation products corresponding to all possible chromatin interactions is produced by this method. In 5C assays, over 12,000 potential ligation products specific to the Igh locus are detected by PCR using multiplexed primer pairs. Here we focused on the 3’ end of the Igh locus to evaluate the status of the constant region domain of the locus in LPS+IL4 activated splenic B cells. We observe that the configuration of the 3’ end of the Igh locus spanning the CH region genes assumes a developmental stage specific configuration in B lineage B cells. We find that the interaction frequency and activation state of the 3’ enhancer increases as B cells mature.

2021-11-23 | GSE183195 | GEO

5C Chromatin interactions in the Igh locus in resting splenic B cells

2021-11-23 | GSE183574 | GEO