Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

50 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

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.

ABSTRACT: 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.

INSTRUMENT(S): Illumina HiSeq 4000

ORGANISM(S): Streptomyces venezuelae

SUBMITTER: Govind Chandra

PROVIDER: E-MTAB-12832 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

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

RNA-Seq of Streptomyces venezuelae NRRL B65442 to compare global gene expression between the wild-type and bldB deletion strain and, wild-type and bldB plus whiJ9 double mutant after 14 hours growth in liquid medium.

Project description:Expression of iosA is greatly activated in the bldB deletion strain. whiJ9 is divergently transcribed from iosA and the double mutant (whiJ9 + bldB) was made to determine if WhiJ mediates the activation of iosA in the absence of BldB.

2023-04-14 | E-MTAB-12836 | biostudies-arrayexpress

RNA-Seq of Pseudomonas fluorescens SBW25 with and without the plasmid pQBR103 and with the rsmQ deleted from pQBR103 to determine the effect of the plasmid on global gene transcription.

Project description:Plasmids can affect expression of genes on the host chromosome. This experiment was carried out to determine the effect of the presence of the plasmid pQBR103 (with and without the rsmQ gene on it) on global gene expression in Pseudomonas fluorescens SBW25.

2022-12-15 | E-MTAB-11868 | 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

RNA-seq of human breast cancer cell lines characterized by ERalpha-LBD overexpression or knockdown, compared to control cells (with or without fulvestrant treatment)

Project description:RNA-seq analysis was carried out to study the effect on transcriptome of ERalpha-LDB gain/loss-of-function in different breast cancer models. Total RNA was extracted and processed for the analysis.

2022-08-29 | E-MTAB-10738 | 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 of Cluster situated regulators (ForJ, ForF and ForZ) of the formicamycin BGC in Streptomyces formicae

Project description:ForJ, ForF and ForZ are cluster situated regulators of the formicamycin biosynthetic gene cluster in Streptomyces forimcae. This ChIP Sequencing experiment was conducted to identify where in the genome these regulators bind in order to identify which transcripts they might regulate.

2019-05-31 | E-MTAB-8006 | biostudies-arrayexpress

Sorted tumor RNA-seq of syngeneic murine mutant IDH1 ICC tumor model treated with IDH1 inhibitor against vehicle

Project description:IDH1 is the most commonly mutated metabolic gene across human cancers, with the highest mutational frequency observed in AML, glioma, chondrosarcoma, and intrahepatic cholangiocarcinoma. Mutations of the hot spot R132 codon alter the activity of the IDH1 enzyme, resulting in the NADPH-dependent conversion of alpha-ketoglutarate to (R)-2-hydroxyglutarate [(R)-2HG], which accumulates to mM levels within tumors. (R)-2HG competitively inhibits a range of enzymes that utilize alpha-ketoglutarate. Targets include the JmjC family histone demethylases and TET family DNA demethylases whose inhibition is linked to the altered epigenetic state characteristic of many mIDH tumors. To gain insight into the mechanisms underlying the anti-tumor efficacy of inhibition of mutant IDH1 we conducted RNA-sequencing (RNA-seq) analysis of purified tumor cells. For these studies, the immune-competent 2205 subcutaneous allograft model was treated with AG120 or vehicle for 6 days and non-tumor cells were removed by magnetic bead sorting (negative selection for CD45+ immune cells, CD31+ endothelial cells, TER119+ erythrocytes, and CD90.2+ fibroblasts).

2021-11-23 | E-MTAB-11112 | biostudies-arrayexpress

Transcriptional profiles of primary macrophages incubated with the F-MLV env124-138-env548-567 and env124-138-env548-567:E561R/A567F peptides

Project description:The envelope glycoprotein of several retroviruses is postulated to encompass an immunosuppressive domain. Here, primary mouse macrophages were stimulated overnight with a peptide corresponding to the immunosuppressive domain, a peptide where critical residues in the immunosuppressive domain were mutated, or left untreated.

2016-11-24 | E-MTAB-5260 | biostudies-arrayexpress

Streptomyces coelicolor quantitative proteome and phosphoproteome analyses reveal proteins and phosphoproteins modulating differentiation and secondary metabolism

Project description:Investigation of proteome and phosphoproteome changes during Streptomyces coelictor life cycle using TMT tagging and calcium precipitation - titanium dioxide enrichment

2018-05-25 | PXD005558 | Pride

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