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Caulobacter vibrioides CB15N mRNA expression in M2-Glucose Vs. M2-Inositol

ABSTRACT: The purpose of this experiment was to examine the differential transcriptional profiles of Caulobacter CB15N grown in M2-Glucose versus M2-Inositol. mRNA expression was compared between Caulobacter CB15N cells grown in M2-Glucose vs. M2-Inositol. Four arrays were run, two of each dye combination.

ORGANISM(S): Caulobacter vibrioides

SUBMITTER: Sean Crosson

PROVIDER: E-GEOD-12414 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Genetic and computational identification of a conserved bacterial metabolic module.

Boutte Cara C CC Srinivasan Balaji S BS Flannick Jason A JA Novak Antal F AF Martens Andrew T AT Batzoglou Serafim S Viollier Patrick H PH Crosson Sean S

PLoS genetics 20081219 12

We have experimentally and computationally defined a set of genes that form a conserved metabolic module in the alpha-proteobacterium Caulobacter crescentus and used this module to illustrate a schema for the propagation of pathway-level annotation across bacterial genera. Applying comprehensive forward and reverse genetic methods and genome-wide transcriptional analysis, we (1) confirmed the presence of genes involved in catabolism of the abundant environmental sugar myo-inositol, (2) defined a ...[more]

PMID: 19096521

Similar Datasets

Caulobacter vibrioides CB15N mRNA expression in M2-Glucose Vs. M2-Inositol

Project description:The purpose of this experiment was to examine the differential transcriptional profiles of Caulobacter CB15N grown in M2-Glucose versus M2-Inositol.

2008-12-20 | GSE12414 | GEO

Caulobacter vibrioides

Project description:Caulobacter vibrioides CB15N mRNA expression in M2-Glucose Vs. M2-Inositol

| PRJNA113105 | ENA

Comparing the transcriptional profiles of a Caulobacter crescentus CB15N (NA1000) wild-type to a SpoT null in carbon starvation.

Project description:SpoT is an Rsh (Rel / Spo homolog) protein, which synthesizes the alarmone ppGpp in response to starvation. This experiment is quantifying transcription in two Caulobacter strains after 5 minutes of glucose starvation: one strain is wild-type CB15N (NA1000); the other strain is NA1000 which has a chromosomal in-frame deletion of the spoT gene. The wild-type strain can synthesize the alarmone ppGpp in response to starvation and the spoT null strain cannot. Both strains were cultured in M2 defined medium with glucose as the sole carbon source, and then washed and incubated in M2 medium lacking glucose for 5 minutes before RNA isolation. Triplicate cultures of: 1) C. crescentus strain CB15N , and 2) CB15N ?SpoT, cultured in M2-glucose media, then starved for glucose for 5 minutes.

2011-05-01 | E-GEOD-21206 | biostudies-arrayexpress

Caulobacter strains ET163 and ET166 vs. CB15N (wild-type)

Project description:The goal of this study was to compare the expression profiles of inversion strains ET163 and ET166 to that of wild-type. To this end we performed transcriptional profiling of Caulobacter crescentus swarmer cells from strains ET163, ET166, and CB15N (WT). Two strain experiment. ET163 vs. WT and ET166 vs. WT. Biological replicates: 2 ET163, 2 ET166, and 3 Wild-type

2011-12-01 | E-GEOD-31468 | biostudies-arrayexpress

Comparing the transcriptional profiles of a Caulobacter crescentus CB15N (NA1000) wild-type to a SpoT null in carbon starvation.

2011-05-01 | GSE21206 | GEO

Effects of SocB toxin on genome-wide expression in Caulobacter crescentus

Project description:Caulobacter cells were grown to exponential phase in rich PYE medium. At time zero, expression of socB-M2 was induced by the addition of 0.3% xylose. A reference sample was also collected at this time point. Atter 1.5 hours, the experimental sample was then collected. RNA was extracted from the reference and experimental samples, reverse transcribed into Cy3- or Cy5-labeled cDNA, and then hybridized to Agilent 4x44K Caulobacter arrays. <br><br>

2013-12-10 | E-MEXP-3990 | biostudies-arrayexpress

Caulobacter strains ET163 and ET166 vs. CB15N (wild-type)

2011-12-01 | GSE31468 | GEO

chpT depletion data

Project description:chpT depletion ML808 versus wild type CB15N three independent colonies were grown to mid-log phase in PYE + xylose and RNA harvested for analysis on microarrays

2010-07-01 | E-GEOD-4617 | biostudies-arrayexpress

Measuring transcriptional differences between Caulobacter crescentus cultured in nitrate versus ammonium as the sole nitrogen source

Project description:This study is measuring the steady-state levels of mRNA in wild-type Caulobacter crescentus grown in M2 defined medium containing either ammonium or nitrate as the sole nitrogen source. Four independent cultures of Caulobacter crecentus were grown in each of two medium conditions: M2(nitrate)glucose and M2(ammonium)glucose. Cultures in each medium type were grown to OD660=0.3 and RNA was isolated from each.

2010-06-20 | E-GEOD-21203 | biostudies-arrayexpress

UV (UVC, 10J/m2) light irradiation effect on Ewing Sarcoma cells

Project description:LAP-35 and SK-N_MC cells were treated with 10 J/m2 UV light versus untreated Alternative pre-mRNA processing plays a key role in the response to DNA damage as well as in neoplastic transformation. We found that two Ewing Sarcoma (ES) cell lines exhibit different sensitivity to UV light irradiation, with SK-N-MC cells being more sensitive than LAP-35 cells. RNA profiling during the response to low doses of UV light irradiation revealed genes differentially regulated between the two cell lines. In particular, UV light irradiation induced a novel isoform of the RNA helicase DHX9 which is targeted to nonsense-mediated decay (NMD) and therefore causes down-regulation of DHX9 in SK-N-MC cells, but not in LAP-35 cells. DHX9 protein forms a complex with RNA polymerase II (RNAPII) and EWS-FLI1 to enhance transcription, and we found that down-regulation of DHX9 by UV light irradiation in SK-N-MC cells impairs the recruitment of EWS-FLI1 to target genes and increases sensitivity to DNA damage. Notably, sensitivity of SK-N-MC cells to irradiation correlated with enhanced phosphorylation and decreased processivity of RNAPII upon irradiation, which in turn causes inclusion of the novel DHX9 exon in SK-N-MC cells exposed to UV light, an observation that could be recapitulated in LAP35 cells by pharmacological reduction of RNAPII processivity. Our data suggest that EWS-FLI1 oncogene activity could be targeted by modulation of DHX9 gene expression. Three biological replicates were labeled in direct and dye-swap microarray experiments and hybridized onto an Agilent custom splicing-sensitive microarray platform

2015-10-20 | E-GEOD-59889 | biostudies-arrayexpress

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