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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Potyvirus effect-Transcriptionnal response to potyviruses infection in Arabidopsis

ABSTRACT: ra06-05_potyvirus-ecotypes - potyvirus effect - Common and specific genes deregulated in response to various potyviruses in different Arabidopsis genetic backgrounds. - Arabidopsis thaliana ecotype Ler was inoculated with three different Potyviruses. About 4 weeks after sowing, the 6 expanded leaves plants were inoculated with the different viruses or were mock-inoculated. Seven days after inoculation, inoculated leaves were collected, RNA was extracted and virus infection controlled. Three biological repeats have been done and two dye-swaps. Keywords: normal vs disease comparison 6 dye-swap - CATMA arrays

ORGANISM(S): Arabidopsis thaliana

SUBMITTER: Jean-Pierre Renou

PROVIDER: E-GEOD-10707 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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arabidopsis ecotypes-Transcriptionnal response to potyviruses infection in Arabidopsis

Project description:ra06-05_potyvirus-ecotypes - arabidopsis ecotypes - Common and specific genes deregulated in response to various potyviruses in different Arabidopsis genetic backgrounds. - Four different Arabidopsis ecotypes were inoculated with one Potyviruse. About 4 weeks after sowing, the 6 expanded leaves plants were inoculated with the different viruses or were mock-inoculated. Seven days after inoculation, inoculated leaves were collected, RNA was extracted and virus infection controlled. RNA fron infected plants was then used for microarrays hybridization. Three biological repeat have been done and two dye-swap. Keywords: normal vs disease comparison 6 dye-swap - CATMA arrays

2010-05-18 | E-GEOD-10711 | biostudies-arrayexpress

cDNA array expression in cotton fiber secondary cell wall development from two germplasm lines that differ in fiber strength

Project description:Comparison of gene expression profiles in cotton fiber development (from 10 to 23 DPA) of two lines. Line 1 was excellent fiber strength, denoted with H; Line 2 was poor fiber strength, denoted withL. Analysis used H20 RNA as control samples for comparison to the experimental samples taken at 5, 10, 15 and 23 DPA. Indirect comparisons were made across multiple arrays with raw data pulled from different channels for data analysis and comparison to the control data.Cy3 and Cy5 dyes were used as follows:Set 1:H10-Cy5 vs H20-Cy3, Set 1(dye swap):H10-Cy3 vs H20-Cy5; Set 2:H15-Cy5 vs H20-Cy3,Set 2 (dya swap):H15-Cy3 vs H20-Cy5; Set 3:H23-Cy5 vs H20-Cy3, Set 3 (dya swap):H23-Cy3 vs H20-Cy5; Set 4:L10-Cy5 vs H20-Cy3, Set 4 (dya swap):L10-Cy3 vs H20-Cy5; Set 5:L15-Cy5 vs H20-Cy3, Set 5 (dya swap):L15-Cy3 vs H20-Cy5; Set 6:L20-Cy5 vs H20-Cy3, Set 6 (dya swap):L20-Cy3 vs H20-Cy5; Set 7:L23-Cy5 vs H20-Cy3, Set 7 (dya swap):L23-Cy3 vs H20-Cy5; Set 8:H20-Cy5 vs H20-Cy3.

2015-07-22 | E-GEOD-30944 | biostudies-arrayexpress

Transcriptional profiling of Enterococcus faecalis cells exposed to sodium bicarbonate for 15 minutes in the ate exponential growth phase.

Project description:In an effort to begin to delineate the bicarbonate regulon, we used microarray analysis with cells grown to late exponential growth phase (3 hr) and then submitted to a 15 min exposure with 0.1 M NaHCO3. Our goal was to define the first set of genes affected by the presence of bicarbonate.

2010-01-06 | E-MEXP-2518 | biostudies-arrayexpress

dgpp-2 DGPP-regulated genes: Identification of diacylglycerol pyrophosphate-regulated genes in ABA signaling

Project description:rs05-06_dgpp - dgpp - 2. The specific plant phosphorylated form of phosphatidic acid (PA), diacyglycerol pyrophosphate (DGPP), was recently shown to be a second messenger in abscisic acid (ABA) signaling. The aim of the project is to identify among the set of ABA-regulated genes the ones also regulated by DGPP and/or PA. 4 dye-swap - CATMA arrays 5ml of 3 days-old suspension cells were incubated with ABA or DGPP 18:1 for 3hours under the conditions of culture. DGPP was emulsified by sonication for 1min 4 times at 4Â°C in 1ml of culture medium then added to 4ml of suspension cells. Cells were filtrated under vacuum, frozen in liquid nitrogen and RNA extracted. DGPP is from Avanti Polar Lipids.

2010-05-19 | E-GEOD-12938 | biostudies-arrayexpress

dgpp-DGPP regulated genes. Identification of diacylglycerol pyrophosphate regulated genes in ABA signaling.

Project description:rs05-06_dgpp - dgpp - The specific plant phosphorylated form of phosphatidic acid (PA), diacyglycerol pyrophosphate (DGPP) was recently shown to be a second messenger in abscisic acid (ABA) signaling. The aim of the project is to identify among the set of ABA-regulated genes the ones also regulated by DGPP and/or PA. - Five ml of 3 days-old suspension cells was incubated with ABA or lipids for 3 h under the conditions of culture. Lipids were emulsified by sonication for 1 mi, four times, at 4Â°C, in one ml of culture medium then added to 4 ml suspension cells. Cells were filtrated under vacuum, frozen in liquid nitrogen and RNA extracted. Dioleoyl PA and dioctanoyl PA are from Sigma, dioleoyl DGPP and dioctanoyl DGPP are from Avanti Polar Lipids. Keywords: treated vs untreated comparison 5 dye-swap - CATMA arrays

2010-05-19 | E-GEOD-13019 | biostudies-arrayexpress

Influence of Nod Factors on early developmental stages of root development in Medicago truncatula

Project description:We would like to know how symbiotic molecules such as Nod Factors (NF) influence lateral root (LR) development in M. truncatula. We have preliminary evidence that this action is through early stages of root development. Auxin is the major phytohormone controlling LR development and we also have evidence that NF interfere with auxin for the control of LR development. This transcriptomic study aims at finding new molecular targets that would be responsive to auxin and NF treatment, even at a higher level by the combination of both auxin and NF. Such targets could be involved in the control or early development stages of LR that would be controlled both by auxin and NF treatment. - 2 day old M. truncatula (accession A17) plantlets grown on M medium were transferred for 2 days on M medium+ 10-5M NPA (1-N-Naphthylphthalamic acid, auxin transport inhibitor) then transferred for 10 h on M medium containing 10-6 M NAA (naphthalene-1-acetic acid, permeant auxin analog) or 10-7 M Nod factors (NF) or a combination of both (10-6 M NAA + 10-7 M NF). These are compared to mock treated (solvent only) plants. 12plex_med_2013_04 12 dye-swap - treated vs untreated comparison

2016-06-01 | E-GEOD-74099 | biostudies-arrayexpress

Response to acetic acid stress in Candida glabrata: effect of the CgHaa1 transcription factor

Project description:This transcriptomics analysis was undertaken to elucidate the effect of acetic acid stress in the reprogramming of C. glabrata KUE100 genomic expression. For this cells were cultivated in MM growth medium (at pH 4) either or not supplemented with a sub-lethal inhibitory concentration of acetic acid (30 mM). Furthermore it was also examined the response to the same concentration of acetic acid of a mutant devoid of the CgHaa1 transcription factor

2016-07-13 | E-MTAB-4875 | biostudies-arrayexpress

Tumor biopsies from 71 untreated patients with mantle cell lymphoma

Project description:The proliferation gene expression signature is a quantitative integrator of oncogenic events that predicts survival in mantle cell lymphoma Keywords: lymphochip; MCL; untreated Tumor biopsies from 71 untreated patients with mantle cell lymphoma

2010-05-23 | E-GEOD-10793 | biostudies-arrayexpress

Infection with Salmonella or Pseudomonas or E. coli - Interactions between plants and human pathogenic bacteria.

Project description:au07-07_salmonella - infection with Salmonella or Pseudomonas or E. coli. Identification of genes involved in early Arabidopsis response to pathogenic and non-pathogenic bacteria. Arabidopsis thaliana Col-0 seedlings were infected for 2 hours with a) Salmonella typhimurium strain 14028s, b) Pseudomonas syringae DC3000 or c) Escherichia coli DH5A Keywords: treated vs untreated comparison 6 dye-swap - CATMA arrays

2010-06-05 | E-GEOD-20996 | biostudies-arrayexpress

Chemical Probing Discovers New Insights into the Native Assembly State of a Bacterial Microcompartment

Project description:Microcompartments (BMCs) are widespread in bacteria and are used for a variety of metabolic purposes, including catabolism of host metabolites. A suite of proteins self-assembles into the shell and cargo layers of BMCs. However, the native assembly state of these large complexes remains to be elucidated. Herein, chemical probes were used to discover structural features of a native BMC. While the exterior could be demarcated with fluorophores, the interior was unexpectedly permeable, suggesting the shell layer may be more dynamic than thought. This allowed access to cross-linking chemical probes, which were analyzed for discovery of the protein interactome. These cross-links revealed a complex multivalent network among cargo proteins that contained encapsulation peptides and demonstrated that the shell layer follows discreet rules in its assembly. These results are consistent overall with a model where biomolecular condensation drives interactions of cargo proteins prior to envelopment by shell layer proteins.

2022-08-19 | PXD029675 | Pride

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