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Growth phase dependent gene expression and motility_3 time courses

ABSTRACT: The microarrays for the three time course experiments described in the publication titled "Gene expression profiling of Helicobacter pylori reveals a growth phase dependent switch in virulence gene expression". TC1 refers to the first time course investigating gene expression changes over the time course of growth while TC2 refers to the second time course. TC Motility_broth refers to the third time course described in the manuscript used to investigate the concurrent changes in motility and the expression of the genes in the flagellar regulon. Detailed description of the growth of H. pylori for these 3 time courses can be found in the Materials and Methods section of the manuscript along with the exact filtering criteria used to download the data from these arrays. Note that in all three time courses the data for each array were transformed after download such that the abundance of each gene's transcript represented by a given spot was relative to the level of that transcript at the 6 h time point. Also duplicate spots for each ORF on the microarray were averaged for analysis after transformation. Groups of assays that are related as part of a time series. Keywords: time_series_design

ORGANISM(S): Helicobacter pylori

PROVIDER: GSE3636 | GEO | 2005/11/22

SECONDARY ACCESSION(S): PRJNA93753

REPOSITORIES: GEO

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Growth phase dependent gene expression and motility_3 time courses

Project description:The microarrays for the three time course experiments described in the publication titled "Gene expression profiling of Helicobacter pylori reveals a growth phase dependent switch in virulence gene expression". TC1 refers to the first time course investigating gene expression changes over the time course of growth while TC2 refers to the second time course. TC Motility_broth refers to the third time course described in the manuscript used to investigate the concurrent changes in motility and the expression of the genes in the flagellar regulon. Detailed description of the growth of H. pylori for these 3 time courses can be found in the Materials and Methods section of the manuscript along with the exact filtering criteria used to download the data from these arrays. Note that in all three time courses the data for each array were transformed after download such that the abundance of each gene's transcript represented by a given spot was relative to the level of that transcript at the 6 h time point. Also duplicate spots for each ORF on the microarray were averaged for analysis after transformation. Groups of assays that are related as part of a time series. Computed

2005-11-21 | E-GEOD-3636 | biostudies-arrayexpress

Listeria infection of Caco-2 cells

Project description:This experiment set contains all of the arrays described in Baldwin et al., Genome Biology, 2002. All experiments are time courses, with the exception of multiple measurements for the zero time point in the parallel time course for the purpose of zero transformation. The parallel four hour time course was performed on a single day and three independent measurements were taken prior to infection. The eight hour time courses were each performed on different days, with single time zero measurements. Each array represents a measurement of human mRNA from cultured intestinal epithelial cells (red channel), relative to the control reference pool of mRNA (green channel), at different time points during the course of an infection by Listeria monocytogenes, or the mutants actA (defective in actin-based motility) and prfA (defective in virulence factor gene expression). Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc. Keywords: Logical Set

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Transcription profiling of human gastric epithelial (AGS) cells infected with wild type H. pylori (G27) and isogenic mutants in cagA and vacA for 0, 0.5, 3, 6, and 12 hours

Project description:TC1: gastric epithelial (AGS) cells infected with wild type H. pylori (G27) and isogenic mutants in cagA and vacA for 0, 0.5, 3, 6, and 12 hours. Total RNA was used to make single stranded Cy5 labelled probe and compared to Cy3 labelled probe from uninfected AGS cells. Hybridizations of G27 (trial 4) and cagA- (trial 3) timecourses were done in parallel. A technical replicate of the G27 time course (trial 5) and hybridization of vacA- (trial 3) time course were done in parallel. The cagA 6 and 12 hour time points were technically replicated (trial 4) (the cagA 6 hour sample of trial 3 was lost). TC2: Biological replication and expansion of TC1, using more isogenic mutants and timepoints. AGS cells were mock infected, infected with G27, and isogenic mutants in cagN, cagA, cagE, and a deletion of the cag PAI for 0. 1, 3, 6, 12, and 24 hours. Probe synthesis and hybridization was done as in TC1. Note: there may have been a sample mix-up with PAI 12, swapping it with G27 or cagN 12.

2005-09-30 | E-SMDB-1661 | biostudies-arrayexpress

Cag pathogenicity island-specific responses of gastric epithelial cells to Helicobacter pylori infection.

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Cag pathogenicity island-specific responses of gastric epithelial cells to Helicobacter pylori infection.

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Project description:For each strain two time courses for mRNA abundance: Oxidative and MMS and two time courses for decay: reference decay and following oxidative stress

2011-07-30 | GSE26829 | GEO

Transcription profiling of listeria infected human Caco-2 cells

2005-09-30 | E-SMDB-1527 | biostudies-arrayexpress

Profiling of plant miRNAs induced by drought stress in the rice plant

Project description:Expression profiles were analyzed between drought stress and normal watered control at the tillering and inflorescence stages. 1. We applied microarray analysis to detect drought-stress-regulated miRNAs from tillering to inflorescence-forming stages in rice. 2. Three time courses at the tillering stage and two time courses at the inflorescence-forming stage. Two replicates were carried out in each time course.

2011-10-25 | E-GEOD-14246 | biostudies-arrayexpress

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Project description:Growth phase dependent gene expression and motility_3 time courses

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Polarized T84 Cells Response to H. pylori infection

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