Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Topo1cc siganls are presented at the KCl induced acutely activated enhancers [CUT&RUN]

ABSTRACT: Topo1cc siganls are serving as the marker for the KCl induced acutely enhancer activation in cortical neurons.

ORGANISM(S): Mus musculus

PROVIDER: GSE185649 | GEO | 2022/08/04

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Ku70/HP1g are presented at the KCl induced acutely activated enhancers [ChIP-seq]

Project description:Ku70/HP1g are serving as the marker for the KCl induced acutely enhancer activation in cortical neurons.

2022-08-04 | GSE185648 | GEO

Phosphoproteome of five-minute KCl-depolarised mouse cultured hippocampal neurons

Project description:Cultured hippocampal neurons from mice were treated with high concentration KCl for five minutes to depolarise the plasma membrane and model sustained brain activity. A high KCl condition was compared to low KCl using phosphoproteomics. Phosphopeptides were enriched from trypsin digested bio-replicates of the high and low KCl conditions and analysed by mass spectrometry. Approximately 20,000 phosphopeptides were identified enabling a comparison of the relative level of phosphorylation in response to depolarisation.

2023-10-15 | PXD020232 | Pride

KCl Stress in Desulfovibrio vulgaris Hildenborough (Series 1)

2006-03-22 | GSE4515 | GEO

Comparison of gene regulation by Gcn5 under KCl stress in S. cerevisiae and S. pombe

Project description:This is parallel comparison of gene regulation by Gcn5 in evolutionarily divergent yeasts S. pombe and S. cerevisiae. Our study showed Gcn5 is required for a similar spectrum of stress responses in both organisms, including the response to KCl. This DNA microarray studies is to find conserved or diverged gene regulation pattern under KCl stress condition in the two yeasts. There are 6 subsets in total, 3 subsets in each evolutionarily divergent yeasts including the following: 1 gcn5 mutant compared to wt under rich medium without treatment, 2 gcn5 mutant compared to wild type both under KCl treatment, 3 wild type strains under KCl treatment compared to wild type without treatment. Keywords: stress response, Gcn5, Comparative genomics, Transcriptional co-activator

2010-01-01 | GSE5218 | GEO

Improved CUT&RUN chromatin profiling tools.

Project description:Previously, we described a novel alternative to chromatin immunoprecipitation, CUT&RUN, in which unfixed permeabilized cells are incubated with antibody, followed by binding of a protein A-Micrococcal Nuclease (pA/MNase) fusion protein (Skene and Henikoff, 2017). Here we introduce three enhancements to CUT&RUN: A hybrid protein A-Protein G-MNase construct that expands antibody compatibility and simplifies purification, a modified digestion protocol that inhibits premature release of the nuclease-bound complex, and a calibration strategy based on carry-over of E. coli DNA introduced with the fusion protein. These new features, coupled with the previously described low-cost, high efficiency, high reproducibility and high-throughput capability of CUT&RUN make it the method of choice for routine epigenomic profiling.

| S-EPMC6598765 | biostudies-other

KCl Stress in Desulfovibrio vulgaris Hildenborough (Series 1)

Project description:Increased salinity constitutes an important and frequent fluctuation faced by D. vulgaris in its natural habitat. Using data from microarray experiments, we investigated the effects of excess KCl on D. vulgaris. Keywords: stress response, time course Comparison of cells treated with 250mM KCl to untreated cells at times of 0, 30, 60, 120, and 240 min. See also Series GSE4447: http://www.ncbi.nlm.nih.gov/projects/geo/query/acc.cgi?acc=GSE4447

2010-06-11 | E-GEOD-4515 | biostudies-arrayexpress

Identification of calcineurin-dependent, Crz1-independent gene expression changes in response to chronic KCl stress

Project description:Gene expression was quantified in S. cerevisae cells after 48 hours of treatment with KCl. crz1 and crz1 cnb1 mutant strains were compared to allow the identification of calcineurin-dependent gene expression changes that are independent of the downstream transcription factor Crz1. We find that calcineurin has very little effect on gene expression in response to KCl.

2024-03-19 | GSE254554 | GEO

High-Resolution Chromatin Profiling Using CUT&RUN.

Project description:Determining the genomic location of DNA-binding proteins is essential to understanding their function. Cleavage Under Targets and Release Using Nuclease (CUT&RUN) is a powerful method for mapping protein-DNA interactions at high resolution. In CUT&RUN, a recombinant protein A-microccocal nuclease (pA-MN) fusion is recruited by an antibody targeting the chromatin protein of interest; this can be done with either uncrosslinked or formaldehyde-crosslinked cells. DNA fragments near sites of antibody binding are released from the insoluble bulk chromatin through endonucleolytic cleavage and used to build barcoded DNA-sequencing libraries that can be sequenced in pools of at least 30. Therefore, CUT&RUN provides an alternative to ChIP-seq approaches for mapping chromatin proteins, which typically have relatively high signal-to-noise ratios, while using fewer cells and at a lower cost. Here, we describe the methods for performing CUT&RUN, generating DNA-sequencing libraries, and analyzing the resulting datasets. © 2019 by John Wiley & Sons, Inc.

| S-EPMC6422702 | biostudies-literature

CUT&RUNTools: a flexible pipeline for CUT&RUN processing and footprint analysis.

Project description:We introduce CUT&RUNTools as a flexible, general pipeline for facilitating the identification of chromatin-associated protein binding and genomic footprinting analysis from antibody-targeted CUT&RUN primary cleavage data. CUT&RUNTools extracts endonuclease cut site information from sequences of short-read fragments and produces single-locus binding estimates, aggregate motif footprints, and informative visualizations to support the high-resolution mapping capability of CUT&RUN. CUT&RUNTools is available at https://bitbucket.org/qzhudfci/cutruntools/ .

| S-EPMC6734249 | biostudies-literature

Chronic potassium chloride (KCl) treatment induced gene expression changes in Drosophila head

Project description:We have recently developed a Drosophila behavioral- and transcriptomic- based (systems) model of chronic pentylenetetrazole induced locomotor plasticity. Pharmacological validation at behavioral level and at the level of fly head microarray gene expression shows that the model is of potential value in screening of compounds for detecting antiepileptic, antiepileptogenic, disease-modifying and neuroprotective activities. While screening compounds using this model at behavioral level, potassium chloride (KCl) was identified as having therapeutic potential. Examination of transcriptomic changes induced by KCl in fly head further supports its potential use as a therapeutic agent in neurological and neuropsychiatric conditions. Keywords: Drug Response

2008-03-18 | GSE10808 | 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