Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

33 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Transcriptional profiling of the developmental gene whiG deletion mutant of Streptomyces venezuelae ATCC 10712 at 7 time points from 8 to 20 hours of growth.

ABSTRACT: WhiG is a sigma factor found in Streptomyces species. It has a central role in sporulation in these bacteria. Although mutants in whiG are able to form aerial mycelia, these fail to differentiate into spores. The aim of this transcription profiling experiment was to measure genome wide transcript levels in the wild type and the whiG deletion mutant at 7 time points from 8 to 20 hours during the growth cycle of Streptomyces venezuelae.

ORGANISM(S): Streptomyces venezuelae

SUBMITTER: Maureen Bibb

PROVIDER: E-MTAB-8114 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Transcriptional profiling of the developmental gene whiA deletion mutant of Streptomyces venezuelae ATCC 10712 at 7 time points from 8 to 20 hours of growth.

Project description:WhiA is an unusual transcriptional regulator found in Streptomyces species related to eukaryotic homing endonucleases. It plays a central role in sporulation in these bacteria. The aim of this transcription profiling experiment was to measure genome wide transcript levels in the wild type and the whiA deletion mutant at 7 time points from 8 to 20 hours during the growth cycle of Streptomyces venezuelae.

2020-12-11 | E-MTAB-9728 | biostudies-arrayexpress

Transcriptional profiling of the developmental gene whiB deletion mutant of Streptomyces venezuelae ATCC 10712 at 7 time points from 8 to 20 hours of growth

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 and play key roles in diverse aspects of the biology of actinomycetes, including pathogenesis, antibiotic resistance, and the control of development. In Streptomyces, WhiB is essential for the process of developmentally controlled cell division that leads to sporulation. The aim of this transcription profiling experiment was to measure genome wide transcript levels in the wild type and the whiB deletion mutant at 7 time points from 8 to 20 hours during the growth cycle of Streptomyces venezuelae.

2021-06-30 | E-MTAB-10631 | biostudies-arrayexpress

Transcriptional profiling of the sigma factor sigE deletion mutant of Streptomyces coelicolor (J2130) at 0, 30, 60 and 90 minutes after treatment with sub-lethal concentration of vancomycin.

Project description:SigE is a sigma factor found in Streptomyces species and is the key regulator of cell envelope stress response in Streptomyces coelicolor. To determine the regulon of SigE under conditions of cell envelope stress, 10 ug / ml vancomycin was used to induce cell envelope stress in the wild type and a sigE deletion strain of S. coelicolor. Samples were taken 0, 30, 60 and 90 minutes after addition of vancomycin and subjected to transcriptional profiling using Affymetrix arrays. Note – equivalent data for wild type Streptomyces coelicolor M600 is submitted as part of E-MEXP-3032. The data for both M600 (E-MEXP-3032) and J2130 (this submission) were generated at the same time employing the same protocols.

2019-04-24 | E-MTAB-7814 | biostudies-arrayexpress

Differential gene expression analysis by RNA-Seq for the bldC deletion strain and the wild type of Streptomyces venezuelae strain NRRL B-65442 after 10 and 14 hours of culture

Project description:The BldC gene is required for the formation of aerial hyphae in Streptomyces venezuelae. It is a 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 RNA-Seq experiment was carried out to determine and quantify effect of BldC on the expression of all genes in the S. venezuelae genome after 10 and 14 hours of culture.

2019-01-14 | E-MTAB-7457 | 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

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

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

RNA-Seq of Streptomyces venezuelae to compare global gene expression between the wild-type and BldB deletion strains after 10, 14 and 22 hours of growth.

Project description:BldB is a regulatory protein in Streptomyces and most species have a number of paralogs in their genomes. Deletion of BldB leads to a developmental deficiency and the colonies fail to produce aerial mycelium. In this experiment global gene expression was compared between the WT and BldB deletion strain of Streptomyces venezuelae NRRL B65442 after 10, 14 and 22 hours of growth in liquid cultures.

2023-04-14 | E-MTAB-12832 | biostudies-arrayexpress

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

RNA-Seq of Streptomyces venezuelae grown overnight (14 hrs) with Mitomycin-C against untreated controls.

Project description:Mitomycin C is a DNA crosslinking agent. This experiment was carried out to determine the effect of Mitomycin C on genome wide transcription in Streptomyces venezuelae NRRL B65442.

2022-07-06 | E-MTAB-11556 | 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