Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

10 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Transcription profiling by array of Bacillus thuringiensis Bt407 overexpressing transcriptional regulator MogR versus an empty vector (pHT304-Pxyl) control strain during late exponential growth

ABSTRACT: Comparison in late exponential phase (culture OD600 = 3) of global expression profiles from a Bacillus thuringiensis 407 strain overexpressing transcriptional regulator MogR from xylose inducible vector pHT304-Pxyl, versus an isogenic empty vector control strain, to analyze global expression changes resulting from MogR overexpression

ORGANISM(S): Bacillus thuringiensis

SUBMITTER: Ole Andreas Økstad

PROVIDER: E-MTAB-7633 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Transcription profiling by array of Bacillus thuringiensis Bt407 overexpressing the diguanylate cyclase CdgF (BTB_c06420) versus an empty vector (pHT304-Pxyl) control strain 2 hours into post-exponential growth

Project description:Comparison of global expression profiles from a Bacillus thuringiensis 407 strain overexpressing the diguanylate cyclase CdgF (BTB_c06420) from the xylose inducible vector pHT304-Pxyl, versus an isogenic empty vector control strain, to analyze global expression changes resulting from CdgF overexpression

2020-09-28 | E-MTAB-8898 | biostudies-arrayexpress

Transcription profiling of B. thuringiensis 407 nprA::lacZ and an isogenic delta-nprR-nprX strain

Project description:B. thuringiensis 407 nprA::lacZ strain was compared with an isogenic delta-nprR-nprX strain to explore the effects of nprR-nprX deletion. NprR is a transition state regulator which is activated towards the end of the exponential phase by a part of the signaling peptide NprX. We made direct comparisons of RNA from the two strains collected at T1 and T3, one and three hours after the transition to stationary phase, respectively. T1 was thought to be the early phase of NprR activation, while T3 was thought to be around the peak of NprR activation. All samples are biological replicates, and dye swap was performed between the different comparisons.

2010-09-10 | E-TABM-790 | biostudies-arrayexpress

Transcriptional analysis of quorum sensing null strain in Yersinia pestis CO92 at 30Â°C

Project description:Yersinia pestis is the etiology of plague that is able to sense cell density by quorum sensing. The function of quorum sensing in Y.pestis is not clear. Here, the process of quorum sensing was investigated by comparing transcript profiles when three quorum sensing synthase genes are knocked out. Two strains, â??pgm (pigmentation-negative) mutant R88 as treatment and 3XQS mutant with mutation (â??pgm, â??ypeIR, â??yspIR, and â??luxS) R115 as control are used in this analysis. Six independent RNA samples from R115 cultures were paired with six independent RNA samples from R88 cultures for hybridization to six two-color microarrays. Dye-swap design was used to remove the Cy5 and Cy3 dye bias.

2016-07-03 | E-GEOD-20217 | biostudies-arrayexpress

Gene expression changes in Corynebacterium glutamicum at increased growth temperature in the absence of PPIase FkpA

Project description:Comparative transcriptome analyses revealed 69 genes exhibiting ?2-fold mRNA level changes in C. glutamicum DfkpA.Overall, 34 genes exhibited ?2-fold increased and 35 genes at least 0.5-fold decreased mRNA levels in JVO1 DfkpA. About half of these genes (32) encode for hypothetical/putative proteins. LdhA encoding L-lactate dehydrogenase exhibited by far the strongest increased mRNA level (8.5-fold) in the absence of FkpA. Determination of the respective specific LdhA activities revealed about 2-fold increased activity in JVO1 DfkpA (0.73 ± 0.05 U/mg) compared to the reference JVO1 (0.41 ± 0.02 U/mg). Notably, the two short gene lists include four genes encoding transcriptional regulators exhibiting increased mRNA levels (farR, lexA, divS, znr) and two exhibiting decreased mRNA levels (ramB, mmpLR) in the absence of FkpA under the conditions tested. The mRNA level of cysK was increased (2.05-fold) which is repressed by RamB whose mRNA level was decreased (0.27-fold). In contrast, the mRNA level of RamB-repressed ald was decreased (0.31-fold) and not increased. To identify the influence of PPIase FkpA on global gene expression, DNA microarray analyses were performed with a ?fkpA mutant compared to the reference C. glutamicum JVO1. For this purpose RNA was isolated from exponentially growing cells cultivated in CgXII minimal medium with 4% glucose at increased temperature (35°C) above growth optimum of C. glutamicum. Two biological replicates were performed with each representing an intra-array duplicate.

2015-09-08 | E-GEOD-65294 | biostudies-arrayexpress

Transcriptional analysis of luxS-null strain in Yersinia pestis CO92 at 37M-BM-0C

Project description:Yersinia pestis, the etiological agent of plague, is able to sense cell density by quorum sensing. The function of quorum sensing in Y. pestis is not clear. Here, the process of autoinducer 2 (AI-2) quorum sensing was investigated by comparing transcript profiles when luxS gene was knocked out. The luxS gene encodes S-ribosylhomocysteinase which can produce DPD, a precursor of AI-2. The strain M-bM-^HM-^Fpgm (pigmentation-negative) mutant R88 was called wild type. The M-bM-^HM-^Fpgm M-bM-^HM-^FluxS mutant was called control. Six independent RNA samples from R88 were paired with six independent RNA samples from M-bM-^HM-^Fpgm M-bM-^HM-^FluxS mutant cultures for hybridization to six two-color microarrays. A dye-swap design was used to remove the Cy5 and Cy3 dye bias.

2013-09-05 | E-GEOD-22849 | biostudies-arrayexpress

Global gene expression analysis of Yersinia pestis Ype AHL quorum sensing at 30Â°C

Project description:Quorum sensing is a cell to cell communication process that involves chemical signaling. Yersinia pestis, the agent of plague, has two functional AHL quorum sensing systems Ysp and Ype. For several reasons, it was not clear what effect AHL pathways have on virulence gene expression and survival in the two different hosts, flea and human. To investigate to what effect AHL quorum sensing has on gene expression, we conducted microarray studies comparing Yersinia pestis CO92 (â??pgm) to a double AHL mutant strain (â??pgm Î?ypeIR) at 30Â°C. Six independent RNA samples from Y. pestis CO92 Î?pgm Î?ypeIR cultures were paired with six independent RNA samples from control Y. pestis CO92 R88 cultures for hybridization to six two-color microarrays. For three arrays, the control RNA sample was labeled with Alexa 555 dye and the experimental RNA sample was labeled with Alexa 647 dye; the dyes were reversed for the other three arrays to account for any dye bias.

2016-07-03 | E-GEOD-30332 | biostudies-arrayexpress

Global gene expression analysis of Yersinia pestis Ysp AHL quorum sensing at 37Â°C

Project description:Quorum sensing is a cell to cell communication process that involves chemical signaling. Yersinia pestis, the agent of plague, has two functional AHL quorum sensing systems Ysp and Ype. For several reasons, it was not clear what effect AHL pathways have on virulence gene expression and survival in the two different hosts, flea and human. To investigate to what effect Ysp AHL quorum sensing has on gene expression, we conducted microarray studies comparing Yersinia pestis CO92 (âpgm) to a single AHL mutant strain (âpgm ÎyspI) at 37Â°C. Six independent RNA samples from Y. pestis CO92 Îpgm ÎyspI cultures were paired with six independent RNA samples from control Y. pestis CO92 R88 cultures for hybridization to six two-color microarrays. For three arrays, the control RNA sample was labeled with Alexa 555 dye and the experimental RNA sample was labeled with Alexa 647 dye; the dyes were reversed for the other three arrays to account for any dye bias.

2016-07-03 | E-GEOD-30328 | biostudies-arrayexpress

Global gene expression analysis of Yersinia pestis Ysp AHL quorum sensing at 30Â°C

Project description:Quorum sensing is a cell to cell communication process that involves chemical signaling. Yersinia pestis, the agent of plague, has two functional AHL quorum sensing systems Ysp and Ype. For several reasons, it was not clear what effect AHL pathways have on virulence gene expression and survival in the two different hosts, flea and human. To investigate to what effect Ysp AHL quorum sensing has on gene expression, we conducted microarray studies comparing Yersinia pestis CO92 (âpgm) to a single AHL mutant strain (âpgm ÎyspI) at 30Â°C. Six independent RNA samples from Y. pestis CO92 Îpgm ÎyspI cultures were paired with six independent RNA samples from control Y. pestis CO92 R88 cultures for hybridization to six two-color microarrays. For three arrays, the control RNA sample was labeled with Alexa 555 dye and the experimental RNA sample was labeled with Alexa 647 dye; the dyes were reversed for the other three arrays to account for any dye bias.

2016-07-03 | E-GEOD-30329 | biostudies-arrayexpress

Global gene expression analysis of Yersinia pestis AHL quorum sensing at 37Â°C

Project description:Quorum sensing is a cell to cell communication process that involves chemical signaling. Yersinia pestis, the agent of plague, has two functional AHL quorum sensing systems Ysp and Ype. For several reasons, it was not clear what effect AHL pathways have on virulence gene expression and survival in the two different hosts, flea and human. To investigate to what effect AHL quorum sensing has on gene expression, we conducted microarray studies comparing Yersinia pestis CO92 (âpgm) to a double AHL mutant strain (âpgm ÎypeIR ÎyspIR) at 37Â°C. Six independent RNA samples from Y. pestis CO92 R114 AHL deficient cultures were paired with six independent RNA samples from control Y. pestis CO92 R88 cultures for hybridization to six two-color microarrays. For three arrays, the control RNA sample was labeled with Alexa 555 dye and the experimental RNA sample was labeled with Alexa 647 dye; the dyes were reversed for the other three arrays to account for any dye bias.

2016-07-03 | E-GEOD-30331 | biostudies-arrayexpress

Yersinia pestis uses AHL-based quorum sensing to regulate metabolic functions likely to be important for flea colonization

Project description:The etiologic agent of bubonic plague, Yersinia pestis, senses cell density-dependent chemical signals to synchronize transcription between cells of the population in a process named quorum sensing. Though the closely related enteric pathogen Y. pseudotuberculosis uses quorum sensing system to regulate motility, the role of quorum sensing in Y. pestis has been unclear. In this study we performed transcriptional profiling experiments to identify Y. pestis quorum sensing regulated functions. Our analysis revealed that acyl-homoserine lactone based quorum sensing controls the expression of several metabolic functions. Maltose fermentation and the glyoxylate bypass are induced by acyl-homoserine lactone signaling. This effect was seen to be temperature conditional. Metabolism is unresponsive to quorum sensing regulation at mammalian body temperature, indicating a potential role for quorum sensing regulation of metabolism specifically during colonization of the flea vector. It is proposed that utilization of alternative carbon sources may enhance growth and/or survival during prolonged flea colonization, contributing to maintenance of plague in nature. Six independent RNA samples from Y. pestis CO92 R114 AHL deficient cultures were paired with six independent RNA samples from control Y. pestis CO92 R88 cultures for hybridization to six two-color microarrays. For three arrays, the control RNA sample was labeled with Alexa 555 dye and the experimental RNA sample was labeled with Alexa 647 dye; the dyes were reversed for the other three arrays to account for any dye bias.

2016-07-03 | E-GEOD-29240 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

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