Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

34 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

The GtaR quorum-sensing protein negatively regulates a capsular polysaccharide gene transfer agent (RcGTA) receptor on Rhodobacter capsulatus cells

ABSTRACT: Expression profiles of wild type and gtaI mutant in logarithmic and stationary phase of growth. The objective was to search for differentially regulated genes potentially associated with EPS production in R. capsulatus. A single sample of each strain in both growth phases for basic comparison of expression profiles.

ORGANISM(S): Rhodobacter capsulatus

SUBMITTER: Ryan Mercer

PROVIDER: E-GEOD-41014 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

DNA packaging bias and differential expression of gene transfer agent genes within a population during production and release of the Rhodobacter capsulatus gene transfer agent, RcGTA

Project description:Rhodobacter capsulatus produces a gene transfer agent (GTA) called RcGTA. RcGTA is a phage-like particle that packages R. capsulatus DNA and transfers it to other R. capsulatus cells. Low-resolution techniques suggested RcGTA packages random DNA. Analysis of the RcGTA terminase sequence revealed a distant relationship to the phage T4 terminase protein, which can also perform sequence-independent packaging. We quantified the relative frequency of packaging for each gene in the genome by hybridization of DNA from RcGTA particles to an R. capsulatus microarray. All genes were found within the RcGTA particles, and random packaging was observed at a genome-wide scale. However, the genes encoding the RcGTA particle were under-packaged compared to other regions. Single-cell expression analysis demonstrated that RcGTA gene expression is not uniform within a culture. We propose a mechanism by which high levels of RcGTA gene transcription in the most active RcGTA producing cells hinders access of the packaging machinery to these genes, which causes a reduction in their packaging frequency. This sub-population gene expression phenomenon likely explains the lack of observed cell lysis in RcGTA producing cultures. DNA extracted from within RcGTA particles produced by DE442, an RcGTA overproducer, was hybridized to an Affymetrix genechip custom array in order to quantify the relative frequency with which any given gene was packaged within the particles. These data were MAS5 normalized. An underlying packaging bias was suspected to be transcription related, so these frequencies were compared to expression levels within the population, as determined by hybridization of late-stationary RNA samples of DE442 and of the wildtype (SB1003) to the same custom array. These data were RMA normalized.

2012-05-21 | E-GEOD-33176 | biostudies-arrayexpress

Gene Co-Expression Network Analysis in Rhodobacter capsulatus and Application to Comparative Expression Analysis of Rhodobacter sphaeroides

Project description:Transcriptomic data has been previously used to determine expression patterns in various R. capsulatus strains using custom made Affymetrix microarrays. Additional expression analyses have since been carried out to obtain preliminary data on certain wild type and mutant strains that have not been reported on. We used all current microarray expression data available and constructed an R. capsulatus gene co-expression network and performed functional analysis of identified gene modules. RNA was harvested from various wild type and mutant R. capsulatus strains grown under photoheterotrophic conditions to different growth phases. The samples were hybridized to custom made R. capsulatus Affymetrix microarrays according to manufacturers recommendations. The raw data was RMA normalized and log transformed.

2014-09-08 | E-GEOD-53636 | biostudies-arrayexpress

Differences in gene expression of delta-fmt and wild-type Staphylococcus aureus RN4220

Project description:Formyltransferase lacking mutants exhibit reduced growth rates in exponential phase indicating that the function of certain proteins depends on formylated N-termini but it has remained unclear, which cellular processes are abrogated by the lack of formylation. In order to elucidate how global metabolic processes are affected by the absence of formylated proteins the transcription of the fmt mutant was compared with that of the parental strain. Bacteria were grown under aerobic and anaerobic conditions and harvested in the exponential growth phase. Here we have expected the most effects of lacking formyltransferase.

2013-05-31 | E-GEOD-41713 | biostudies-arrayexpress

Gene expression in synthetic nasal medium

Project description:Staphylococcus aureus prefers the human anterior nares as its habitat, but nothing is known about the nutritional situation in this ecological niche. Analysis of nasal secretions showed a complex mixture of nutrients at low concentration. Based on these findings a synthetic nasal medium (SNM) was composed, mimicking nasal secretions. We used microarrays in order to investigate pathways and expression patterns important in a synthetic medium mimicking nasal secretions compared to standard laboratory complex medium Staphylococcus aureus USA300 was inoculated in complex medium (BM) or synthetic nasal medium (SNM) to an OD578nm of 0.005 and grown under aerobic conditions until OD578nm of 0.02. RNA was stabilized and extracted at this early growth phase and hybridization was made on Affymetrix microarrays. The aim was to identify genes which are important during growth under the limited conditions present during colonization of human nares

2013-04-10 | E-GEOD-43712 | biostudies-arrayexpress

Transcription profiling by array of human bone marrow from acute myeloid leukemia patients and healthy donors.

Project description:AC133+ cell fractions were isolated from bone marrow of 33 acute myeloid leukemia patients and 10 healthy donors and their transcriptional profiles assessed with Affymetrix GeneChip Human Genome U133 Plus 2.0

2011-04-01 | E-MTAB-220 | biostudies-arrayexpress

Analysis of prebiotic carbohydrate utilization by Bifidobacterium lactis Bl-04 using differential transcriptomics

Project description:The global transcriptome of the Bifidobacterium animalis subsp. lactis Bl-04 was analyzed during exponential growth on 11 prebiotic carbohydrates and glucose to identify the specific gene cluster differentially upregulated in response to each carbohydrate. Affymetrix hybridization experiments were performed to compare the differential transcriptional profiles of the B. lactis Bl-04 at the early-log (OD600nm 0.3-0.5) phase. 12 carbohydrates were tested with two technical replicates to each condition for a total of 24 hybridizations.

2013-10-23 | E-GEOD-41906 | biostudies-arrayexpress

SigX ECF sigma factor deletion mutant expression profile in Pseudomonas aeruginosa in M9 minimal medium (M9G)

Project description:Analysis of a SigX knockout mutant of Pseudomonas aeruginosa H103 strain in minimal medium with glucose as carbon source (M9G). SigX, one of the 19 extra-cytoplasmic function sigma factors of P. aeruginosa, was only known to be involved in transcription of the gene encoding the major outer membrane protein OprF in Pseudomonas aeruginosa. Deletion of the ECF sigma factor sigX gene provide insights into the SigX role in several virulence and biofilm- related phenotypes in Pseudomonas aeruginosa. To better understand the cellular function of SigX, a deletion mutant of the sigX gene (PAOSX) was generated and its expression profile was compared with parental strain Pseudomonas aeruginosa H103. To this end, H103 and a sigX mutant were cultured in M9G, in which their growth are similar. Three independant biological replicate were taken for the RNA extraction and hybridization on affymetrix array in the middle of the exponential growth phase.

2014-01-01 | E-GEOD-51076 | biostudies-arrayexpress

Transcription profiling of pigment cells in the tunicate Ciona intestinalis to study pigment cell specification within Central Nervous System

Project description:Its known that FGF signaling induces pigment cell precursors formation. We perturbed the endogenous FGF signaling cascade by using a dominant-negative form of the unique Ci-FGF receptor (FGFRDN) and a constitutively active form of Ci-Ets1/2 (Ets:Vp16), a transcriptional effector of FGF/MAP Kinase cascade. Targeted expression of dominant negative FGF receptor and Ets:VP16 fusion protein was achieved in PCPs using the Tyrosinase-related protein 1/2a (Tyrp1/2a) cis-regulatory region. The PCPs were isolated by Fluorescent Activated Cell Sorting (FACS) as GFP+ cells at two developmental stages: 8 hpf at ~16C (neurula stage) corresponding to early FGF-mediated induction and 12 hpf at ~18C (tailbud stage) where PCPs are already fate restricted as pigment cells. To avoid a contamination by mesenchyme cells where Ciona enhancers are often ectopically activated, we co-electroporated the MyoD905>YFP construct and counter-selected YFP+ cells. In summary the conditions used are: FGFRDN, Ets:VP16 and Control samples at 8 and 12 hpf (four samples for each condition).

2014-07-14 | E-MTAB-2759 | biostudies-arrayexpress

Analysis of gene expression regulated by Drosophila melanogaster Tis11

Project description:In mammalian cells, AU-rich elements (AREs) are well known regulatory sequences located in the 3' untranslated region (UTR) of many short-lived mRNAs that suppress gene expression at the posttranscriptional level. Tis11, a zinc finger RNA-binding protein homologous to mammalian tristetraprolin, targets ARE-containing reporter mRNAs for rapid degradation in SL2 cells. To identify Drosophila mRNA targets of Tis11, we performed genome-wide expression profiling after dsRNA-mediated depletion of endogenous Tis11 in SL2 cells. Furthermore, we studied the involvement of Tis11 in regulating the Drosophila immune response by profiling mRNA expression after LPS treatment, in the presence or absence of Tis11. SL2 cells were treated with either dsRNA against Tis11 or dsRNA against GFP (control). After 4 days of treatment with 12.5 microgram dsRNA / ml medium, total RNA was extracted and hybridized to Drosophila Genome 2.0 Arrays (Affymetrix, Cat. No. 900531). Where indicated, cells were treated with lipopolysaccharide (LPS, Sigma, O55:B5) at a concentration of 10 microgram / ml for 4 hours before lysis. All experiments were performed in 3 biological replicates.

2011-03-24 | E-GEOD-28147 | biostudies-arrayexpress

Expression data from MCF7 cells: control or tuberin-depleted

Project description:Analysis of the expression profiles of MCF7 cells transduced with a control shRNA and an TSC2-targeted shRNA (leading to tuberin depletion). MCF7 cells were cultured in standard conditions, transduced, selected with puromycin (pLKO.1 shRNA vectors) and processed for expression profiling.

2015-04-28 | E-GEOD-68324 | biostudies-arrayexpress

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