Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

58 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

SvenBldDChIPSeq

ABSTRACT: To examine the effects of cyclic-di-GMP on DNA binding by BldD in vivo, we manipulated the levels of c-di-GMP in Streptomyces venezuelae and monitored the effect on BldD binding to its target promoters in vivo by ChIP-seq, using a polyclonal BldD antibody. The degree of BldD binding was assayed at a single time point in wild-type (wt) S. venezuelae and the wt overexpressing either the diguanylate cyclase CdgB or the phosphodiesterase YhjH. A bldD null mutant was used a negative control.

INSTRUMENT(S): Illumina HiSeq 2000

ORGANISM(S): Streptomyces venezuelae

SUBMITTER: Govind Chandra

PROVIDER: E-MTAB-2196 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

SvenBldMWhiIChIPSeq

Project description:To determine the influence of BldM and WhiI on the binding of each other to their respective binding sites in the genome of Streptomyces venezuelae, ChIP-Seq experiments were carried out using polyclonal antibodies against the wild type proteins as well as anti-FLAG antibodies against FLAG-tagged proteins. Null mutants of Streptomyces venezuelae lacking WhiI or BldM were used as controls. The wild tpe strain was used as control in experiments using the anti-FLAG antibodies.

2015-05-19 | E-MTAB-2698 | biostudies-arrayexpress

Identification by ChIP-Seq of the binding sites of the developmental protein WhiH in the genome of Streptomyces venezuelae

Project description:The whiH gene is required for the differentiation of aerial hyphae into spores in Streptomyces species. It is a predicted member of the GntR family of transcription factors and has been shown to bind specifically to a sequence in its own promoter. This ChIP-Seq experiment was carried out to determine all the binding sites whiH binds to in the genome of Streptomyces venezuelae. A whiH deletion strain was made and a FLAG tagged whiH protein was expressed in it from a genome-integrated plasmid. Then anti-FLAG antibodies were used for chromatin immunoprecipitation followed by high throughput sequencing. The wild type Streptomyces venezuelae strain (ATCC 10712) was used as a negative control. For both the FLAG-WhiH strain and the WT strain, non-immunoprecipitated (total) DNA was also sequenced to arrive at a background enrichment which could be subtracted from the enrichment in the immunoprecipated sample.

2018-12-31 | E-MTAB-6702 | biostudies-arrayexpress

ChIP-Seq to determine binding sites of transcription factor BldO in the genome of Streptomyces venezuelae

Project description:The transcription factor BldO was identified as a target of WhiAB in an earlier ChIP-Seq experiment. This experiment was conducted to determine the targets of BldO in the Streptomyces venezuelae genome.

2021-03-31 | E-MTAB-10250 | biostudies-arrayexpress

Role of RccR in the transcriptional control of primary carbon metabolism in Pseudomonas

Project description:To characterise the RccR regulon, we performed a ChIP-seq assay using a polyclonal RccR antiserum on SBW25 WT/rccR strains grown in minimal pyruvate and glycerol media. We were able to identify 8 RccR binding sites from this experiment including one in the rccR promoter region itself. The peaks identified in our RccR ChIP-seq assays corresponded to strongly enriched regions relative to the respective rccR controls. All 8 peaks were localized in intergenic regions, upstream of one or more genes.

2017-08-24 | E-MTAB-5745 | biostudies-arrayexpress

Role of Fnr1 and Fnr3 in transcriptional regulation under oxygen limitation in Herbaspirillum seropedicae

Project description:To determine the direct promoter targets of Fnr proteins, we correlated transcriptional changes observed in single fnr1 and fnr3 mutants (E-MTAB-5741) with ChIP-Seq analysis, taking advantage of C-terminally 3xFlag fnr alleles engineered into the H. seropedicae genome. ChIP-seq data were obtained from cultures grown under limited oxygen availability. Using this approach, DNA-binding targets for the H. seropedicae Fnr1 and Fnr3 proteins were unambiguously revealed and correlated with transcript profiles to determine the specific regulons of each protein.

2018-02-26 | E-MTAB-6395 | biostudies-arrayexpress

Identification by ChIP-Seq of the binding sites of the developmental protein BldC in the genome of Streptomyces venezuelae

Project description:The BldC gene is required for the formation of aerial hyphae Streptomyces venezuelae. It is 68 amino acid DNA-binding protein related to the MerR family of transcription factors. BldC deletion strains are bald because they initiate sporulation prematurely, omitting the formation of aerial hyphae altogether. This ChIP-Seq experiment was carried out to determine all the binding sites BldC binds to in the genome of Streptomyces venezuelae. Anti-BldC antibodies were used for ChIP-Seq of the wild type (WT) strain after 10 and 14 hours of growth in shaken cultures. A BldC deletion strain was made and anti-BldC antibodies were used for ChIP-Seq in the deletion strain after 14 hours of growth in shaken cultures. This was used as the negative control and enrichment in this ChIP-Seq was subtracted from the enrichment in the WT strain.

2019-01-14 | E-MTAB-7450 | biostudies-arrayexpress

ChIP-Seq to determine the binding sites of the transcription factor WhiB in the genome of Streptomyces venezuelae

Project description:WhiB is the founding member of a family of proteins (the WhiB-like [Wbl] family) that carry a [4Fe-4S] iron-sulfur cluster. It is essential for the process of developmentally controlled cell division leading to sporulation in Streptomyces species. This ChIP-Sea was carried out to determine unambiguously if WhiB functions as a transcription factor in Streptomyces venezuelae and also to determine its regulon.

2021-06-25 | E-MTAB-10648 | biostudies-arrayexpress

WhiA and WhiB of Streptomyces venezuelae depend on each other for binding DNA

Project description:WhiB regulon, as determined by ChIP-Seq turned out to be identical to the WhiA regulon leading to the speculation that the two proteins might be required to work together to bind DNA. In this experiment WhiA ChIP-Seq was done in a whiB deletion background and, WhiB ChIP-Seq was done in a whiA deletion background to show that the two proteins do indeed fail to bind DNA in the absence of one another.

2021-07-01 | E-MTAB-10673 | biostudies-arrayexpress

Mutation of the cysteine residues that coordinate the WhiB [4Fe-4S] cluster prevents in vivo DNA binding by both WhiB and WhiA

Project description:The purpose of this experiment was to show that the iron-sulphur cluster ([4Fe-4S]) of whiB is essential for the DNA binding by WhiB and WhiA. The \\"serine version of whiB\\" mentioned below is a whiB in which the 4 cysteine residues which coordinate the [4Fe-4S] cluster were mutated to serines. ChIP-Seq using anti-FLAG anitbodies was performed in the following: 1. A whiB deletion strain expressing the FLAG-tagged serine version of WhiB (WhiBFLAG-Ser). 2. A whiB and whiA deletion strain expressing the FLAG-tagged serine version of WhiB (delAB_WhiBFLAG-Ser). 3. A whiB and whiA deletion strain expressing the serine version of WhiB and FLAG-tagged whiA (delAB_WhiAFLAG_WhiBcomp-Ser).

2021-08-16 | E-MTAB-10818 | biostudies-arrayexpress

Identification by ChIP-Seq of the binding sites of the sigma factor WhiG in the genome of Streptomyces venezuelae

Project description:The WhiG sigma factor gene is required for spore formation is Streptomyces venezuelae. It is similar to the FliA sigma factor of E. coli. WhiG deletion strains are able to make aerial hyphae but are defective in the spore maturation. This ChIP-Seq experiment was carried out to determine all the binding sites WhiG binds to in the genome of Streptomyces venezuelae. Anti-WhiG polyclonal antibodies were used for ChIP-Seq of the wild type (WT) strain after 34 hours of growth in shaken cultures. A WhiG deletion strain was made and anti-WhiG antibodies were used for ChIP-Seq in the deletion strain after 34 hours of growth in shaken cultures. This was used as the negative control and ChIP-Seq peak positions in this were disregarded in the WT.

2019-08-01 | E-MTAB-8160 | biostudies-arrayexpress

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