Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Effect of VirR/VirS-VR-RNA regulatory cascade on the expression of chromosomal genes of Clostridium perfringens

ABSTRACT: The microarrays were subjected to two-color hybridization using Cy5 and Cy3 dyes incorporated in the cDNAs synthesized from total RNA samples of strains. We compared each gene’s transcription level between the wild-type (WT) strain 13 (labeled by Cy5) and the VirR-mutant strain (TS133) or VR-RNA-mutant strain (TS140) (both labeled by Cy3) on a single DNA microarray. Keywords: gene regulation in time course

ORGANISM(S): Clostridium perfringens str. 13

PROVIDER: GSE12833 | GEO | 2009/09/17

SECONDARY ACCESSION(S): PRJNA111143

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Effect of VirR/VirS-VR-RNA regulatory cascade on the expression of chromosomal genes of Clostridium perfringens

Project description:The microarrays were subjected to two-color hybridization using Cy5 and Cy3 dyes incorporated in the cDNAs synthesized from total RNA samples of strains. We compared each geneâs transcription level between the wild-type (WT) strain 13 (labeled by Cy5) and the VirR-mutant strain (TS133) or VR-RNA-mutant strain (TS140) (both labeled by Cy3) on a single DNA microarray. Keywords: gene regulation in time course Each sample represent data calculated from 3 to 4 biological replicates of independent experiments. Each biological replicate contains duplicated data.

2010-05-05 | E-GEOD-12833 | biostudies-arrayexpress

Effect of virX regulator on the expression of chromosomal genes of Clostridium perfringens

2012-10-01 | GSE37998 | GEO

VirR and RevR regulate many Clostridium perfringens genes in a reciprocal manner

Project description:We further characterize the VirSR and RevR regulatory networks by profiling the C. perfringens strain JIR325 and its isogenic virR and revR regulatory mutants using strand-specific RNA-seq. Two independent biological replicates were sequenced for each strain, generating more than 90 million sequence reads for each RNA-seq library (wild type, 97,289,148 reads; virR mutant, 116,505,992 reads and revR mutant, 131,811,486 reads). Using the edgeR analysis package, 223 genes in the virR mutant and 88 genes in the revR mutant were found to be differentially expressed. Comparative transcriptomic analysis revealed that VirR acts as a global negative regulator, whilst RevR acts as a global positive regulator. Therefore, about 88% of the differentially expressed genes were up-regulated in the virR mutant, whereas 75% of the differentially expressed genes were down-regulated in the revR mutant. Importantly, we identified 22 genes that were regulated by both VirR and RevR. Of these genes, 18 or 82%, which included the sporulation-specific spoIVA, sigG and sigF genes, were regulated positively and negatively by RevR and VirR, respectively. Furthermore, mapped RNA-seq reads visualized as a user plot showed that there were 97 previously unannotated transcripts in the intergenic regions. These transcripts may potentially encode novel genes or small RNA molecules. This study has identified genes, antisense transcripts, and transcripts within intergenic regions and on the native plasmid, which are controlled by the VirSR or RevR regulatory system. The knowledge obtained will enable a more thorough annotation of the C. perfringens genome.

2016-08-03 | GSE72137 | GEO

Effect of virX regulator on the expression of chromosomal genes of Clostridium perfringens

Project description:The microarrays were subjected to two-color hybridization using Cy5 and Cy3 dyes incorporated in the cDNAs synthesized from total RNA samples of strains. We compared each geneM-bM-^@M-^Ys transcription level between the wild-type (WT) strain 13 (labeled by Cy5) and the virX-mutant strain (TS186) (labeled by Cy3) on a single DNA microarray. Total RNA was isolated from exponentially growing cells from thevirX mutant and the wild-type. Gene expression levels were compared between thevirX mutant and wild-type strain 13

2012-10-01 | E-GEOD-37998 | biostudies-arrayexpress

VirR and RevR regulate many Clostridium perfringens genes in a reciprocal manner

2016-08-03 | E-GEOD-72137 | biostudies-arrayexpress

Clostridium perfringens str. 13

Project description:Effect of VirR/VirS-VR-RNA regulatory cascade on the expression of chromosomal genes of Clostridium perfringens

| PRJNA111143 | ENA

Screening for candidate clock-controlled genes

Project description:Microarrays were hybridized with a mixture of solutions containing LL2 cDNA labeled with Cy3 or Cy5 (dye-swap) and LL14 cDNA labeled with Cy5 or Cy3 (dye-swap). Keywords: repeat sample

2004-12-29 | GSE2114 | GEO

Clostridium perfringens

Project description:VirR and RevR regulate many Clostridium perfringens genes in a reciprocal manner

| PRJNA293160 | ENA

Eucalyptus grandis BC progeny

Project description:The gene expression profiles of the differentiating xylem of 91 Eucalyptus grandis backcross individuals were characterized following a loop design (Churchill, G.A. Nat Genet. 2002 Dec;32 Suppl:490-5). In this design, RNA from genotype 1666 (labeled with Cy5) was hybridized with RNA from genotype 1667 (labeled with Cy3) on the first slide(GEO accession number GSM7637); the same genotype 1667 (now labeled with Cy5) was compared with genotype 1669 (Cy3) on the second slide (GSM7638), and so on. The loop was completed when genotype 1666 (Cy3) was contrasted to individual 1796 (Cy3) on slide GSM7727. Therefore, 91 individuals (genotypes) from the E. grandis backcross population were analyzed in two replicates, one with RNA labeled with Cy3 and the other with Cy5. Keywords = Eucalyptus, xylem, microarray Keywords: ordered

2003-07-16 | GSE502 | GEO

Prokaryotic expression profiling analysis for single or combined chaperones deletion

Project description:Chaperones have essential role in assist nascent peptides folding, prevent proteins aggregation and maintain cellular protein homeostasis. Considering spatial and temporal features of chaperones regulating in vivo, changes in single or combined chaperone-depleted E.coli strain is needed to be put into understand at transcriptional level. Here, we utilized expression microarrays to investigate global transcriptional response upon deletion of single or multiple chaperones in E. coli for understanding the transcriptional network affected by chaperones. To identify prokaryotic expression profiles in deletion of chaperones, several E.coli mutants were constructed in the following: Z116 (△tig 37℃), Z125(△dnaK37℃), Z625(△tig△dnaK 37℃ or 30℃), Z629(△tig△dnaK 30℃), NM (C-domain of tig was deleted 37℃), MC (N-domain of tig was deleted 37℃), NC (M-domain of tig was deleted 37℃). Two types of cDNA mixtures containing Cy3-labeled (or Cy5-labeled) control DNA (from BW25113) and Cy5-labeled (or Cy3-labeled) DNA targets (from mutant strain) were hybridized with E.coli microarrays in a dye-swap strategy.

2015-06-18 | GSE69912 | GEO

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