Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

10 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

ChIP-seq analysis of Escherichia coli sigma 38 binding in cells lacking H-NS

ABSTRACT: The experiment contains ChIP-seq data for Escherichia coli strain RPB104 hns::kan. The strain was grown at 37 degrees in LB medium to stationary phase and crosslinked with 1 % (v/v) formaldehyde. After sonication, to break open cells and fragment DNA, immunoprecipitations were done using anti-FLAG antibodies. Libraries were prepared using DNA remaining after immunoprecipitation.

INSTRUMENT(S): Illumina MiSeq

ORGANISM(S): Escherichia coli K-12

SUBMITTER: David Grainger

PROVIDER: E-MTAB-8778 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

ChIP-seq of the multiple antibiotic resistance repressor (MarR) protein of Enterotoxigenic Escherichia coli strain H10407

Project description:The experiment contains ChIP-seq data for Enterotoxigenic Escherichia coli strain H10407 transformed with plasmids pAMNF (encoding an N-terminal MarR-3xFLAG fusion) or pAMNM (encoding an N-terminal MarR-8xmyc fusion). The cells was cultured at 37 degrees in LB medium and crosslinked with 1 % (v/v) formaldehyde. After sonication, to break open cells and fragment DNA, immunoprecipitations were done using an anti-FLAG antibody (i.e. the strain encoding the MarR-8xmyc fusion was used as a control). Libraries were prepared using DNA remaining after immunoprecipitation.

2017-12-01 | E-MTAB-5591 | biostudies-arrayexpress

ChIP-seq of the multiple antibiotic resistance activator (MarA) protein and RNA polymerase sigma70 subunit of Enterotoxigenic Escherichia coli strain H10407

Project description:The experiment contains ChIP-seq data for Enterotoxigenic Escherichia coli strain H10407 transformed with plasmid pRGM9818. The strain was grown at 37 degrees in LB medium and crosslinked with 1 % (v/v) formaldehyde. After sonication, to break open cells and fragment DNA, immunoprecipitations were done using antibodies against MarA, MarR or the RNA polymerase sigma 70 subunit. Libraries were prepared using DNA remaining after immunoprecipitation. Note that the MarR immunoprecipitations were not successful but the data served as a useful control for non-specifically immunoprecipitated DNA sequences.

2017-09-30 | E-MTAB-5521 | biostudies-arrayexpress

ChIP-seq analysis of genome-wide DNA binding by transcription factors HapR and LuxO in Vibrio cholerae

Project description:The experiment contains ChIP-seq data for Vibrio cholerae strain E7946. The strain was grown at 37 degrees in LB medium and crosslinked with 1 % (v/v) formaldehyde. After sonication, to break open cells and fragment DNA, immunoprecipitations were done using anti-FLAG antibodies. Libraries were prepared using DNA remaining after immunoprecipitation.

2023-03-29 | E-MTAB-11906 | biostudies-arrayexpress

ChIP-seq analysis of MarA, SoxS, Rob and RamA biding across the Salmonella Typhimurium SL1344 genome

Project description:ChIP-seq data for Salmonella Typhimurium strain SL1344. The strain was grown at 37 degrees in LB medium and crosslinked with 1 % (v/v) formaldehyde. After sonication, to break open cells and fragment DNA, immunoprecipitations were done using anti-FLAG antibodies (for SoxS, Rob and RamA) or anti Myc (for MarA) antibodies. Libraries were prepared using DNA remaining after immunoprecipitation.

2023-03-29 | E-MTAB-12627 | biostudies-arrayexpress

ChIP-seq analysis of the Vibrio cholerae VpsT protein

2021-11-18 | E-MTAB-10829 | biostudies-arrayexpress

ChIP-seq of the cyclic-AMP Receptor Protein (CRP) and RNA polymerase sigma 70 subunit in Vibrio cholerae

Project description:The experiment contains ChIP-seq data for Vibrio cholerae strain N16961. The strain was grown at 37 degrees in M9 minimal medium and crosslinked with 1 % (v/v) formaldehyde. After sonication, to break open cells and fragment DNA, immunoprecipitations were done using no antibodies (mock immunoprecipitations) or antibodies against CRP or the RNA polymerase sigma 70 subunit. Libraries were prepared using DNA remaining after immunoprecipitation.

2019-02-04 | E-MTAB-6472 | biostudies-arrayexpress

ChIP-seq analysis of the Vibrio cholerae AphA protein

2019-10-21 | E-MTAB-7953 | biostudies-arrayexpress

Study of APOL1-containing complexes in podocytes

Project description:The C-terminal variants G1 and G2 of apolipoprotein L1 (APOL1) confer human resistance to the sleeping sickness parasite Trypanosoma rhodesiense, but also increase the risk of developing kidney disease. APOL1 and APOL3 are death-promoting proteins associated with endoplasmic reticulum and Golgi membranes. We report that in podocytes, either expression of APOL1 devoid of C-terminal helix (APOL1) or deletion of APOL3 (APOL3 KO) induce actomyosin reorganization linked to inhibition of phosphatidylinositol-4-phosphate (PI(4)P) synthesis by the Golgi PI(4)-kinase IIIB (PI4KB). Both APOL1 and APOL3 form K+ channels, but only APOL3 exhibited Ca2+-dependent binding to neuronal calcium sensor-1 (NCS-1), promoting NCS-1/PI4KB interaction that strongly activates PI(4)P synthesis. APOL1 C-terminal deletion or mutations increased APOL1 binding to APOL3, affecting APOL3 interaction with NCS-1. Since podocytes of G1 and G2 patients exhibited an APOL1/APOL3KO-like phenotype, APOL1 C-terminal variants may induce kidney disease by preventing APOL3 from activating PI4KB, resulting in actomyosin reorganization of podocytes.

2020-03-19 | PXD016851 | Pride

ChIP-seq of E. coli to identify H-NS and Fis binding at multiple time-points during growth in rich medium

Project description:Among the most important regulators of gene expression in bacteria are 'nucleoid-associated proteins'. These proteins alter the topology of the bound DNA by bending, wrapping or bridging it, thus having multiple effects, including transcriptional regulation, on the bacterial cell. Among the best-studied nucleoid proteins are H-NS and Fis, which bind to specific sequences on the DNA. H-NS is a global repressor of gene expression. Fis alters the global conformation of the DNA by introducing branched structures in it; but its effect on gene expression on a genomic scale remains largely unclear.<br><br>Several bacterial transcriptional regulators including H-NS and Fis have been studied using ChIP-chip. However, the higher resolution and dynamic range offered by ChIP-Seq have not been exploited for any bacterial species. By performing ChIP-Seq of these two proteins, we present the first such study in a bacterium. In addition to providing a proof-of-principle for the use of this technology for bacteria, we perform our study at multiple time-points during growth in rich medium, thus generating new insights into how these proteins function under different cellular conditions. Further, by analysing our data in conjunction with newly-generated gene expression and RNA polymerase-chromosome interaction data we provide new interpretation of the genome-scale patterns of the interactions of these proteins to the DNA.

2010-09-01 | E-MTAB-332 | biostudies-arrayexpress

Histone-like family of nucleoid structuring protein of A. actinomycetemcomitans promotes biofilm formation and alters protein dynamics of other species within multi-species biofilm

Project description:Aggregatibacter actinomycetemcomitans is a Gram-negative organism, strongly associated with aggressive forms of periodontitis. An important virulence property of A. actinomycetemcomitans is its ability to form tenacious biofilms that can attach to abiotic as well as biotic surfaces. The histone-like (H-NS) family of nucleoid structuring proteins act as transcriptional silencers in many Gram-negative bacteria. To evaluate the role of H-NS in A. actinomycetemcomitans, hns mutant derivatives of the serotype a strain D7S were generated. Characteristics of the hns mutant phenotype included shorter and fewer pili, which were accompanied by substantially lower biofilm formation relative to the wild type. In accordance with this observation, the D7S hns mutant exhibited significantly reduced growth within a seven-species biofilm model. However, no apparent difference was observed regarding the numbers and proportions of the remaining six species in the biofilm regardless co-cultivated with D7S hns or its parental strain. Proteomics analysis of the strains grown in monocultures confirmed the role of H-NS as a repressor of gene expression in A. actinomycetemcomitans. Interestingly, proteomics analysis of the multispecies biofilms indicated that the A. actinomycetemcomitans wildtype and hns mutant imposed different regulatory effects on the pattern of protein expression in the other species, i.e. mainly Streptococcus spp., Fusobacterium nucleatum, and Veillonella dispar. Gene ontology analysis revealed that a large portion of the differentially regulated proteins was related to translational activity. Taken together, our data suggest that, apart from being a negative regulator of gene expression in A. actinomycetemcomitans, H-NS promotes biofilm formation and may be an important factor for survival of this species within a multispecies biofilm.

2018-06-05 | PXD008444 | Pride

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

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