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Determine whether Streptomyces venezuelae protein SepH (vnz_27360) binds DNA and where

ABSTRACT: Determine whether Streptomyces venezuelae protein SepH (vnz_27360) binds DNA and where

PROVIDER: PRJEB38322 | ENA |

REPOSITORIES: ENA

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Determine whether Streptomyces venezuelae protein SepH (vnz_27360) binds DNA and where

Project description:SepH was identified having a potential role in sporulation following ChIP-seq analysis that showed the sepH gene is under the control of the WhiA and WhiB transcription factors (Bush et al., 2013; Bush et al., 2016). Since SepH has a helix-turn-helix motif, this ChIP-Seq experiment was carried out to determine whether SepH specifically binds DNA and if so, where.

2020-09-30 | E-MTAB-9064 | 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-chip to determine bldN binding sites in Streptomyces venezuelae

Project description:ChIP-chip of genomic DNA of Streptomyces venezuelae using polyclonal antibody against bldN

2013-04-30 | E-MTAB-1103 | 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

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

Identifying Lsr2 binding sites in Streptomyces venezuelae

Project description:The goal of this work was to determine where Lsr2 binds within the S. venezuelae chromosome, and to differentiate between direct versus indirect effects by comparing our ChIP-seq results with RNA-seq results

2018-06-09 | GSE115538 | GEO

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

Transcriptional changes over time in exploring cultures of Streptomyces venezuelae [three growth timepoints]

Project description:We isolated and sequenced mRNA from Streptomyces venezuelae grown on solid medium that promotes exploratory behaviour in this bacterial species. The data was analyzed using DeSeq2 to identify genes that undergo changes in expression over time.

2021-10-22 | GSE186259 | GEO

Transcriptional changes over time in exploring cultures of Streptomyces venezuelae

Project description:We isolated and sequenced mRNA from Streptomyces venezuelae grown on two different solid media that promote exploratory behaviour in this bacterial species. The data was analyzed using DeSeq2 to identify genes that undergo changes in expression over time as well as differences in gene expression patterns between the two media conditions.

2021-07-30 | GSE181041 | GEO

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