Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Transcription profiling of Bacillus anthracis over 8 hours covering the entire life cycle

ABSTRACT: This is a series of expression measurements done during an 8 hour time course of B. anthracis growth in modified G medium. This time frame includes an entire life cycle.

ORGANISM(S): Bacillus anthracis

SUBMITTER: Amy Miyoshi

PROVIDER: E-MEXP-788 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Publications

Transcriptional profiling of the Bacillus anthracis life cycle in vitro and an implied model for regulation of spore formation.

Bergman Nicholas H NH Anderson Erica C EC Swenson Ellen E EE Niemeyer Matthew M MM Miyoshi Amy D AD Hanna Philip C PC

Journal of bacteriology 20060901 17

The life cycle of Bacillus anthracis includes both vegetative and endospore morphologies which alternate based on nutrient availability, and there is considerable evidence indicating that the ability of this organism to cause anthrax depends on its ability to progress through this life cycle in a regulated manner. Here we report the use of a custom B. anthracis GeneChip in defining the gene expression patterns that occur throughout the entire life cycle in vitro. Nearly 5,000 genes were expresse ...[more]

PMID: 16923876

Similar Datasets

Transcription profiling time series of Bacillus anthracis growing inside murine macrophages

Project description:This experiment follows gene expression within B. anthracis while the bacteria are growing inside murine macrophages, from 1-6 hours post-infection.

2007-05-11 | E-MEXP-1036 | biostudies-arrayexpress

Transcription profiling of Bacillus anthracis Sterne 34F2 cells and a sodA1 deletion mutant strain in reponse to different concentrations of paraquat and hydrogen peroxide

Project description:Bacillus anthracis Sterne 34F2 cells were grown in the absence of and in the presence of different concentrations of paraquat and hydrogen peroxide. Additionally, a deletion mutant strain lacking the sodA1 gene was also assayed with and without the addition of different concentrations of paraquat.

2007-04-12 | E-MEXP-1043 | biostudies-arrayexpress

Transcription profiling of C. elegans slr-2, C2H2 Zn-finger protein mutant to normal controls at L1 stage

Project description:Our slr-2 dataset showed strong overrepresentation of genes previously identified in a serial analysis of gene expression (SAGE) intestinal library (McGhee et al., 2006) (p << 0.01); 812 genes were common to both data sets. Consistent with the deregulation of intestinal genes, we observed repression of several important metabolic pathways, including the TOR and insulin signaling networks, suggesting that slr-2(ku297) mutants experience metabolic stress. We also compared differentially regulated genes in slr-2 and lin-35 single mutants. Again, we saw a statistically significant overlap (p-value < 0.01); 261 genes were present in both data sets. Strikingly, > 75% of genes common both datasets showed expression changes in the same direction, although the common dataset contained an approximately equal mixture of up and downregulated genes. Furthermore, more than fifty genes common to the lin-35 and slr-2 datasets are known to have intestinal-associated functions. That some of these common intestinal genes were absent from the gut SAGE library could be due to differences in the developmental stage of the animals assayed (adults versus L1s) as well as experimental approaches (SAGE versus microarrays) Experiment Overall Design: We compared transcriptome profiles of slr-2 mutants and control N2 worms at L1 stage stage. Experiment Overall Design: Each comparison was done in triplicate with independently grown and isolated animals. Experiment Overall Design: Data for N2 L1 stage were from our previous experiments (Series GSE6547) Experiment Overall Design: To achieve higher accuracy, RMA values were calculated on the basis of 21 microarray experiments (including data from Series GSE6547)

2008-06-16 | E-GEOD-9246 | biostudies-arrayexpress

Transcription profiling of C. elegans pocket protein ortholog, lin-35

Project description:LIN-35 is the single C. elegans ortholog of the mammalian pocket protein family members, pRb, p107, and p130. To gain insight into the roles of pocket proteins during development, a microarray analysis was performed with lin-35 mutants. Stage-specific regulation patterns were revealed, indicating that LIN-35 plays diverse roles at distinct developmental stages. LIN-35 was found to repress the expression of many genes involved in cell proliferation in larvae, an activity that is carried out in conjunction with E2F. In addition, LIN-35 was found to regulate neuronal genes during embryogenesis and targets of the intestinal-specific GATA transcription factor, ELT-2, at multiple developmental stages. Additional findings suggest that LIN-35 functions in cell cycle regulation in embryos in a manner that is independent of E2F. A comparison of LIN-35-regulated genes with known fly and mammalian pocket-protein targets revealed a high degree of overlap, indicating strong conservation of pocket protein functions in diverse phyla. Based on microarray results and our refinement of the C. elegans E2F consensus sequence, we were able to generate a comprehensive list of putative E2F-regulated genes in C. elegans. These results implicate a large number of genes previously unconnected to cell cycle control as having potential roles in this process. Experiment Overall Design: We compared transcriptom profiles of lin-35 mutants and control N2 worms at 3 developmental stages (embryonic, L1 and L4). Experiment Overall Design: Each comparison was done in triplicate on independently grown and isolated animals.

2008-06-14 | E-GEOD-6547 | biostudies-arrayexpress

Transcription profiling of Bacillus anthracis Sterne during iron starvation

Project description:Effects of iron starvation on the transcriptional profile of Bacillus anthracis

2010-07-22 | E-MEXP-2272 | biostudies-arrayexpress

Bacillus anthracis Stern 34F2 sporulation

Project description:Timecourse from log phase growth to sporulation in Bacillus anthracis Stern 34F2 Keywords: time-course

2004-01-08 | GSE840 | GEO

Transcription profiling of S. cerevisiae histone mutants H3,K4,79R and H3,K4,36,79R (at 0, 6, and 9 hours) Mutations

Project description:This SuperSeries is composed of the following subset Series:; GSE6319: Histone H3 K4,79R; GSE6326: Histone H3 K4,36,79R 0 hr; GSE6327: Histone H3 K4,36,79R 6 hr; GSE6328: Histone H3 K4,36,79R 9 hr Experiment Overall Design: Refer to individual Series

2008-06-14 | E-GEOD-6331 | biostudies-arrayexpress

Laboratory adaptation of Bacillus anthracis

Project description:The spore forming pathogen Bacillus anthracis is the etiologic agent of anthrax in humans and animals. It cycles through infected hosts as vegetative cells and is eventually introduced into the environment where it generates an endospore resistant to many harsh conditions. The endospores are subsequently ingested by the next host to begin the next cycle. Outbreaks of anthrax occur regularly worldwide in wildlife and livestock, and the potential for human infection exists whenever humans encounter infected animals. It is also possible to encounter intentional releases of anthrax spores, as was the case in October 2001. Consequently, it is important to be able to rapidly establish the provenance of infectious strains of B. anthracis. Here, we compare protein expression in seven low-passage wild isolates and four laboratory strains of B. anthracis grown under identical conditions using LC-MS/MS proteomic analysis. Of the 1,023 total identified proteins, 96 had significant abundance differences between wild and laboratory strains. Of those, 28 proteins directly related to sporulation were upregulated in wild isolates, with expression driven by Spo0A, CodY, and AbrB/ScoC. In addition, we observed evidence of changes in cell division and fatty acid biosynthesis between the two classes of strains, despite being grown under identical experimental conditions. These results suggest wild B. anthracis cells are more highly tuned to sporulate than their laboratory cousins, and this difference should be exploited as a method to differentiate between laboratory adapted cultures and low passage wild strains isolated during an anthrax outbreak. This knowledge should distinguish between intentional releases and exposure to strains in nature providing a basis for the type of response by public health officials and investigators.

2018-12-04 | PXD010120 | Pride

Transcription profiling of S. cerevisiae Histone H3 K4,79R mutant vs. wild type

Project description:Total RNA from three replicate cultures of wild-type and mutant strains was isolated and the expression profiles were determined using Affymetrix arrays. Comparisons between the sample groups allow the identification of genes regulated by H3 K4,79R mutant. Experiment Overall Design: Comparison of genes whose mRNA levels are affected in a histone H3 K4,79R mutant yeast strain compared to wild-type yeast strain.

2008-06-14 | E-GEOD-6319 | biostudies-arrayexpress

Identification of Bacillus anthracis genes differentially expressed in human serum

Project description:Bacillus anthracis causes anthrax infections in mammals. Large-scale mortality resulting from the intentional release of B. anthracis spores represents a potential bioterrorism threat. Inhalational anthrax almost invariably proceeds to fatal systemic infection, characterized by massive bacteremia. A better understanding of host-pathogen interactions is urgently needed for effective treatment of this lethal disease. However, virulence mechanisms used by B. anthracis to survive and multiply in human blood are not completely understood. Identification of genes that are differentially expressed during the growth of B. anthracis in human serum can elucidate how this pathogen successfully colonizes the bloodstream. We compared the transcriptional profile of B. anthracis growing in heat-inactivated human serum to that in LB medium. Genes involved in the biosynthesis of purines, certain amino acids and riboflavin and lipid metabolism, genes encoding ABC transporters, respiratory enzymes and several genes with hypothetical function were identified as being upregulated during growth in serum.

2022-12-01 | GSE97567 | 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