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

Expression analysis of Dickeya dadantii 3937 infecting an aphid (Acyrthosiphon pisum clone LL01) host

ABSTRACT: Investigation of whole genome gene expression level changes in the phytopathogenic Dickeya dadantii wild-type strain 3937 during an acute per os infection of an aphid body, in comparison with a colony grown in standard LB medium. The pathosystem described in this study has been analysed and first published in Grenier et al. 2006, and further detailed in Costechareyre et al. 2011 A two chip study using total RNA recovered from three separate (aphid-, or in vitro-grown) samples

ORGANISM(S): Dickeya dadantii 3937

SUBMITTER: Yvan RahbM-CM-)

PROVIDER: E-GEOD-42585 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Phenotypic plasticity in the pea aphid Acyrthosiphon pisum: miRNA expression

Project description:We developed high throughput Solexa sequencing and bioinformatic analyses of the genome of the pea aphid Acyrthosiphon pisum in order to identify the first miRNAs from a hemipteran insect. By combining these methods we identified 155 miRNAs including 56 conserved and 99 new miRNAs. Moreover, we investigated the regulation of these miRNAs in different alternative morphs of the pea aphid by analysing the expression of miRNAs across the switch of reproduction mode. An array including the 155 aphid microRNAs was designed in order to follow the expression of aphid microRNAs during the modification of reproduction mode of the pea aphid

2010-05-06 | E-GEOD-20106 | biostudies-arrayexpress

Isolation of the Buchnera aphidicola flagellum basal body complexes from the Buchnera membrane

Project description:Buchnera aphidicola is an intracellular bacterial symbiont of aphids and maintains a small genome of only 600 kbps. Buchnera is thought to maintain only genes relevant to the symbiosis with its aphid host. Curiously, the Buchnera genome contains gene clusters coding for flagellum basal body structural proteins and for flagellum type III export machinery. These structures have been shown to be highly expressed and present in large numbers on Buchnera cells. No recognizable pathogenicity factors or secreted proteins have been identified in the Buchnera genome, and the relevance of this protein complex to the symbiosis is unknown. Here, we show isolation of Buchnera flagellum basal body proteins from the cellular membrane of Buchnera, confirming the enrichment of flagellum basal body proteins relative to other proteins in the Buchnera proteome. This will facilitate studies of the structure and function of the Buchnera flagellum structure, and its role in this model symbiosis.

2021-09-10 | PXD024664 | Pride

Influence of NaCl on gene expression in Dickeya dadantii

Project description:Growth in 0.3 M NaCl M63 minimal medium affects the transcriptome of Dickeya dadantii 3937.in comparison to that of cells grown in M63 medium. NimbleGen design name 2005-05-31_Ogg_Erwinia_24mer, NimbleGen design ID 2181 A 1:2 expression design for 4597 genes from Dickeya dadantii 3937 with 20 24-mer probe pairs (PM/MM) per gene. Each probe is replicated 2 times. The design includes random GC and other control probes. Protocol: High-density DNA array prepared with Maskless Array Synthesizer (MAS) technology. See manufacturer's website at http://www.nimblegen.com/.

2015-11-01 | E-GEOD-64739 | biostudies-arrayexpress

Response to nicotine in heads of the tobacco aphid Myzus persicae

Project description:This SuperSeries is composed of the following subset Series: GSE18657: Response to nicotine (100 ÂµM) in heads of the tobacco aphid Myzus persicae GSE18658: Response to nicotine (250 ÂµM) in heads of the tobacco aphid Myzus persicae Refer to individual Series

2010-10-08 | E-GEOD-18659 | biostudies-arrayexpress

Phenotypic plasticity in the pea aphid Acyrthosiphon pisum: miRNA sequencing

Project description:Bioinformatic prediction, deep sequencing of microRNA and expression analysis during phenotypic plasticity in the pea aphid acyrthosiphon pisum We developed high throughput Solexa sequencing and bioinformatic analyses of the genome of the pea aphid Acyrthosiphon pisum in order to identify the first miRNAs from a hemipteran insect. By combining these methods we identified 155 miRNAs including 56 conserved and 99 new miRNAs. Moreover, we investigated the regulation of these miRNAs in different alternative morphs of the pea aphid by analysing the expression of miRNAs across the switch of reproduction mode. deep sequencing of small RNAs from parthenogenetic Acyrthosiphon pisum

2010-03-01 | E-GEOD-20107 | biostudies-arrayexpress

Comparison of saliva proteins signature of three aphid species

Project description:In this study we used a multidisciplinary proteomics approach combining LC-ESI-MS/MS and 2D-DIGE/MALDI-TOF/MS to compare the salivary proteins from three aphid species including Acyrthosiphon pisum, Megoura viciae, and Myzus persicae. Comparative analyses revealed variability among aphid salivary proteomes. Among the proteins that varied 22% were related to DNA-binding, 19% were related to GTP-binding, and 19% had oxidoreductase activity.

2017-08-17 | PXD000476 | Pride

Novel male-biased expression in paralogs of the aphid slilmfast nutrient amino acid transporter expansion

Project description:A major goal of molecular evolutionary biology is to understand the fate and consequences of duplicated genes. In this context, aphids are particularly intriguing because the newly sequenced pea aphid genome is characterized by extraordinarily high levels of lineage-specific gene duplication relative to other insect genomes. While analyzing the results of a microarray comparing gene expression between male, sexual female and asexual female Myzus persicae aphids, we unexpectedly found duplicated nutrient amino acid transporters highly upregulated in males. These transporters, homologous to the Drosophila slimfast, belong to an aphid-specific gene family expansion in which other paralogs are thought to have functionally diverged to fill a role in mediating interactions between aphids and their nutrititonally required bacterial symbiont. The lack of a known male role for slimfast in other insects suggests that aphid slimfast paralogs have been retained as a result of functional divergence to fill multiple novel functional roles in symbiosis and in males. Two biological replicates, four treatments (males, asexual females at long day, asexual females at short day, sexual females), dye flip

2011-09-13 | E-GEOD-31024 | biostudies-arrayexpress

Arabidopsis thaliana gene expression changes upon treatment with green peach aphid saliva

Project description:Myzus persicae (green peach aphid) feeding on Arabidopsis thaliana induces a defense response, quantified as reduced aphid progeny production, in infested leaves but not in other parts of the plant. Similarly, infiltration of aphid saliva into Arabidopsis leaves causes only a local increase in aphid resistance. Further characterization of the defense-eliciting salivary components indicates that Arabidopsis recognizes a proteinaceous elicitor with a size between 3 to 10 kD. Genetic analysis using well-characterized Arabidopsis mutant shows that saliva-induced resistance against M. persicae is independent of the known defense signaling pathways involving salicylic acid, jasmonate, and ethylene. Among 78 Arabidopsis genes that were induced by aphid saliva infiltration, 52 had been identified previously as aphid-induced, but few are responsive to the well-known plant defense signaling molecules salicylic acid and jasmonate. Quantitative PCR analysis confirms expression of saliva-induced genes. In particular, expression of a set of O-methyltransferases, which may be involved in the synthesis of aphid-repellent glucosinolates, was significantly up-regulated by both M. persicae feeding and treatment with aphid saliva. However, this did not correlate with increased production of 4-methoxyindol-3-ylmethylglucosinolate, suggesting that aphid salivary components trigger an Arabidopsis defense response that is independent of this aphid-deterrent glucosinolate. Experiment Overall Design: 3 biological replicates (control and treatment). Total number of samples: 6.

2009-06-23 | E-GEOD-16497 | biostudies-arrayexpress

Response to nicotine (250 ÂµM) in heads of the tobacco aphid Myzus persicae

Project description:Response of the aphid head transcriptome to nicotine in artificial diets (250 ÂµM nicotine, 24 hours feeding) Two condition experiment: heads of aphids feeding on control diet vs heads of aphids feeding on 250 ÂµM nicotine containing diet

2010-05-14 | E-GEOD-18658 | biostudies-arrayexpress

Response to nicotine (100 ÂµM) in heads of the tobacco aphid Myzus persicae

Project description:Response of the aphid head transcriptome to nicotine in artificial diets (100 ÂµM nicotine, 24 hours feeding) Two condition experiment: heads of aphids feeding on control diet vs heads of aphids feeding on 100 ÂµM nicotine containing diet

2010-05-14 | E-GEOD-18657 | biostudies-arrayexpress

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