Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

14 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Global profiling of gene expression in A signal mutants of Myxococcus xanthus

ABSTRACT: In response to starvation Myxococcus xanthus initiates a developmental program that culminates in the formation of fruiting bodies inside which the rod-shaped cells differentiate to spores. Fruiting body formation depends on intercellular communication and two intercellular signals are known, the A-signal and the C-signal. Five genes have been identified which are required for A-signal synthesis. To begin to understand the function of the genes required for A-signal synthesis, we have analysed gene expression in the asgA and the asgB mutant. Keywords: Vegetative cells of WT (DK1622) and AsgA mutant (DK5057) and AsgB mutant (DK4398) 3 biological replicates each; normalized ratios to vegetative cells of DK1622 (wt) Cy5

ORGANISM(S): Myxococcus xanthus

SUBMITTER: Lotte Sogaard-Andersen

PROVIDER: E-GEOD-18029 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Global profiling of gene expression in the ΔdigR and ΔsgmT mutant of Myxococcus xanthus

Project description:In Myxococcus xanthus 55% of the more than 250 two-component signal transduction systems (TCS) genes are orphan. We hypothesized that the histidine kinase SgmT and the response regulator DigR, which comprises a DNA binding domain of the HTH_Xer type, function together to regulate gene expression. We performed genome-wide expression profiling experiments to determine wether the same set of genes are differentially expressed in the ΔdigR and ΔsgmT mutants. 3 biological replicates each; normalized ratios to vegetative cells of DK1622 (wt) Cy5

2012-05-17 | E-GEOD-34408 | biostudies-arrayexpress

Global profiling of gene expression during glycerol-induced spore formation in Myxococcus xanthus

Project description:Myxococcus xanthus is a gram negative rod-shaped delta proteobacterium that differentiates into environmentally resistant spores in response to starvation. Little is known about the sporulation mechanism in part because sporulation occurs in a subpopulation of cells undergoing a lenghtly complex multicellular developmental program. This developmental program requires a solid surface, motility, a minimum population density and a sophisticated network of inter and intra-cellular signals which direct some cells first to aggregate into multicellular fruiting bodies and then to sporulate exclusively within these fruiting bodies. However, it has previously been demonstrated that synchronous conversion of vegetative cells into myxospores can also be triggered in nutrient-rich liquid medium by addition of glycerol to 0.5 M. Here, we took advantage of the glycerol-induced sporulation process to gain information about the core M. xanthus sprorulation mechanism. We determined changes in the global gene expression at 0.5, 1, 2, and 4 hours after glycerol induction compared to vegetative cells (wild-type DK1622). The expression of nearly 1,500 genes was found to be significantly altered at least two-fold within four hours of glycerol-induced development. Most of the known core sporulation marker genes were up-regulated, whereas most genes required for proper aggregation and fruiting body formation were not significantly regulated. Keywords: Time course of glycerol-induced (0.5 M final conc.) development with 4 time points referenced to vegetative cells 3 biological replicates each; normalized ratios to vegetative cells of DK1622 (wt) Cy3

2010-05-06 | E-GEOD-17912 | biostudies-arrayexpress

Global profiling of developmental gene expression in Myxococcus xanthus

Project description:In response to starvation, Myxococcus xanthus initiates a developmental program that results in the formation of spore-filled multicellular fruiting bodies. Here we have used cDNA microarray analysis to determine changes in the global gene expression at different time points of the developmental process. The expression of nearly 900 genes was found to be altered at least two-fold during development as compared to vegetative cells. Genes encoding proteins with typical vegetative functions such as protein synthesis and energy metabolism were transcriptionally down-regulated in the early stages of development. Among the 430 genes transcriptionally up-regulated during development genes with regulatory functions were overrepresented; underlining that fruiting body formation relies on a complex signalling network. Notably, almost 40% of all genes with increased expression at different stages of development encoded hypothetical proteins indicating a large unexplored potential of proteins important for fruiting body formation. Keywords: Time course of development with 9 time points 3 biological replicates each; normalized ratios to vegetative cells of DK1622 (wt) Cy5

2008-01-31 | E-GEOD-9477 | biostudies-arrayexpress

Myxococcus xanthus

Project description:VP963/DK1622

| PRJNA93997 | ENA

Myxococcus xanthus

Project description:Nla18/DK1622

| PRJNA93361 | ENA

Myxococcus xanthus

Project description:DK5653/DK1622 Vegetative

| PRJNA107417 | ENA

Mapping Epigenomic Type-Specific Differences Occurring During Hematopoiesis

Project description:Formation of the blood from self-renewing hematopoietic stem cells to terminal lineages necessarily involves epigenomic modifications of the genome to control regulator and signature gene expression. By analysing the global expression profiles of hematopoietic stem cells (HSCs), in vivo differentiated CD4+ T cells and CD19+ B cells as well as in vitro differentiated erythrocyte precursor cells, we identified hundreds of transcripts showing type-specific expression in these cell types. To understand the epigenomic changes related to tissue-specific expression during HSC differentiation, we examined the genome-wide distribution of H3K4me1, H3K4me3, H3K27me1, H3K27me3, histone variant H2A.Z, chromatin remodeler BRG1, and RNA Polymerase II in the same four cell types, as well as embryonic stem cells. Analysis of these datasets revealed that numerous key differentiation genes are primed for expression by Brg1 and Pol II binding, as well as bivalent modifications in the HSCs prior to their expression in downstream differentiated cell types. Much of this bivalency in HSC is retained from embryonic stem cells. After differentiation, these modified regions resolve to active chromatin modification configuration in the specific lineage, while in parallel differentiated lineages the bivalent modification remains; Pol II and Brg1 are lost in closer lineages but bivalency resolves to silent monovalency in more distant lineages. Correlation of tissue-specific gene expression with the epigenomic changes predicts tens of thousands of potential common enhancers and tissue-specific enhancers, which may critically contribute to the expression patterns. We provide a valuable dataset for further understanding the regulatory mechanisms of differentiation and function of blood lineages. This SuperSeries is composed of the SubSeries listed below. Refer to individual Series.

2013-03-25 | E-GEOD-39229 | biostudies-arrayexpress

Mapping Epigenomic Type-Specific Differences Occurring During Hematopoiesis [ChIP-Seq]

Project description:Formation of the blood from self-renewing hematopoietic stem cells to terminal lineages necessarily involves epigenomic modifications of the genome to control regulator and signature gene expression. By analysing the global expression profiles of hematopoietic stem cells (HSCs), in vivo differentiated CD4+ T cells and CD19+ B cells as well as in vitro differentiated erythrocyte precursor cells, we identified hundreds of transcripts showing type-specific expression in these cell types. To understand the epigenomic changes related to tissue-specific expression during HSC differentiation, we examined the genome-wide distribution of H3K4me1, H3K4me3, H3K27me1, H3K27me3, histone variant H2A.Z, chromatin remodeler BRG1, and RNA Polymerase II in the same four cell types, as well as embryonic stem cells. Analysis of these datasets revealed that numerous key differentiation genes are primed for expression by Brg1 and Pol II binding, as well as bivalent modifications in the HSCs prior to their expression in downstream differentiated cell types. Much of this bivalency in HSC is retained from embryonic stem cells. After differentiation, these modified regions resolve to active chromatin modification configuration in the specific lineage, while in parallel differentiated lineages the bivalent modification remains; Pol II and Brg1 are lost in closer lineages but bivalency resolves to silent monovalency in more distant lineages. Correlation of tissue-specific gene expression with the epigenomic changes predicts tens of thousands of potential common enhancers and tissue-specific enhancers, which may critically contribute to the expression patterns. We provide a valuable dataset for further understanding the regulatory mechanisms of differentiation and function of blood lineages. ChIP-Seq: profiling of DNA-associated proteins in blood cell subsets.

2013-03-25 | E-GEOD-39538 | biostudies-arrayexpress

Expression data from human bronchial airway smooth muscle (ASM) cells

Project description:Interleukin (IL)-17 plays an important and protective role in host defence and has been demonstrated to orchestrate airway inflammation by cooperating with and inducing proinflammatory cytokines. Mircoarrays were used to identify immediate-early/ primary response IL-17A-dependent gene transcripts in primary human bronchial ASM cells from mild asthmatic and healthy individuals. To evaluate IL-17A-inducible gene transcripts, primary human bronchial ASM cells from 3 mild asthmatic and 3 healthy donors were treated for 2h with IL-17 [10ng/ml] and were probed with the Affymetrix GeneChip array. The 2h time point was carefully chosen in order to identify primary response gene targets and to avoid confounding autocrine mechanisms mediating indirect, or late-phase gene expression responses. Non-stimulated ASM cells from the same patients were used as controls.

2012-02-09 | E-GEOD-35643 | biostudies-arrayexpress

Analysis of M.xanthus boundary by nano-LC-MS/MS

Project description:Investigation of different proteins that play role in the formation of boundary between DK1622 and the incompatible mutant strain via proteomics approach.

2019-11-13 | PXD012532 | Pride

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