Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Transcriptomic response of Dickeya dadantii to topoisomerase I inhibition by seconeolitsine

ABSTRACT: We analyze the transcriptomic response of the phytopathogenic enterobacterium Dickeya dadantii to an increase of DNA supercoiling induced by seconeolitsine, a topoisomerase I inhibitor. The shock was applied to Dickeya cells grown in minimal medium supplemented with sucrose, in exponential or transition to stationary phase.

INSTRUMENT(S): Illumina HiSeq 2500

ORGANISM(S): Dickeya dadantii

SUBMITTER: Sam Meyer

PROVIDER: E-MTAB-10134 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Transcriptomic response of Dickeya dadantii to DNA relaxation by novobiocin

Project description:We analyze the transcriptomic response of the phytopathogenic enterobacterium Dickeya dadantii to a DNA supercoiling relaxation shock using the gyrase inhibitor novobiocin. The shock was applied to Dickeya cells grown in minimal medium supplemented with sucrose, in exponential or transition to stationary phase, and in minimal medium with sucrose + PGA (a pectin derivative) in transition to stationary phase.

2019-04-16 | E-MTAB-7650 | biostudies-arrayexpress

Transcriptomic response of Dickeya dadantii ihfA mutant to DNA relaxation by novobiocin

Project description:We analyze the transcriptomic response of the phytopathogenic enterobacterium Dickeya dadantii ihfA mutant to a DNA supercoiling relaxation shock using the gyrase inhibitor novobiocin. The shock was applied to Dickeya cells grown in minimal medium supplemented with sucrose, in exponential or transition to stationary phase, and in minimal medium with sucrose + PGA (a pectin derivative) in transition to stationary phase.

2021-02-10 | E-MTAB-9025 | biostudies-arrayexpress

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

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

Project description: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

2012-12-01 | E-GEOD-42585 | biostudies-arrayexpress

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.

2015-11-01 | GSE64739 | GEO

Analysis of DNA relaxation in Dickeya dadantii wild type, fis and hns strains

Project description:We have analyzed the transcriptomes of Dickeya dadantii wild type, fis and hns strains in condition of DNA relaxation induced by novobiocin, a DNA gyrase inhibitor. For DNA relaxation novobiocin was added for 15 min to 100µg/ml final concentration to exponentially growing wild type, hns and fis strains (OD600= 0.2) grown in M63 medium supplemented by sucrose 0.2% (w/v). At this concentration, novobiocin has no impact on D. dadantii growth The micro-arrays used in this study were custom designed and produced by Roche NimbleGen, Inc. (Madison, WI) based on the annotated sequence of D. dadantii, available at Genbank accession number n° CP002038, which comprises 4597 CDS. The 4plex expression micro-arrays consist of 60-mer oligonucleotides, triplicated in three blocks on the array (5 oligonucleotides per CDS). For micro-array analyses, cDNA was synthesized, labeled and hybridized by Roche NimbleGen Inc.

2015-04-16 | E-MTAB-2597 | biostudies-arrayexpress

Proteomics of the phytopathogen Dickeya dadantii

Project description:Here, we present the proteome characterization of Dickeya dadantii by shotgun proteomics (Data Dependent acquisition, DDA mode).

2017-01-02 | PXD004438 | Pride

Dickeya dadantii

Project description:Dickeya dadantii Genome sequencing

| PRJNA645728 | ENA

Genome-wide identification of transcriptional start sites in the phytopathogen Dickeya dadantii 3937 based on differential RNA-Seq (dRNA-Seq)

Project description:In this study transcriptional start sites (TSS) for the phytopathogen Dickeya dadantii 3937 were determined based on differential RNA-seq (dRNA-seq) as previously described (Sharma and Vogel, 2014). RNAs from E-MTAB-541 (Jiang et al. 2015) were pooled into four samples S1 to S4 reflecting a variety of environmental conditions. Each of them resulted in a combination of stress conditions (pH, NaCl, H2O2) and growth conditions: exponential phase with stress (S1), exponential phase without stress (S2), stationary phase with stress (S3), stationary phase without stress (S4). Those samples were then supplied to Vertis Biotechnologie AG for TEX treatment and Illumina sequencing. Briefly, ribosomal RNA molecules were depleted from the total RNA samples using the Ribo-Zero rRNA Removal Kit for bacteria (Epicentre). From the rRNA depleted RNA samples, the small RNA fractions <200 nt were separated from the large fractions using the RNeasy MinElute Cleanup Kit (Qiagen). TSS cDNA libraries were generated from the rRNA depleted large RNA fractions. First, the samples were fragmented using RNase III. Samples were then poly(A)-tailed using poly(A) polymerase, and split into two halves. One half was treated with Terminator exonuclease (+TEX, Epicentre), while the other one was left untreated (-TEX). 5'PPP structures were then converted into 5'P ends using RNA 5' Polyphosphatase (5'PP, Epicentre). Afterwards, an RNA adapter was ligated to the 5'P of the RNA. First-strand cDNA synthesis was performed using an oligo(dT)-adapter primer and the M-MLV reverse transcriptase. The resulting cDNAs were PCR-amplified using a high fidelity DNA polymerase, and purified using the Agencourt AMPure XP kit (Beckman Coulter Genomics). The cDNA pools were then sequenced on an Illumina NextSeq 500 system using 60 bp read length and a single-end, strand-specific protocol. Sequencing reads were trimmed, and both polyA and adapters removed.

2022-01-01 | E-MTAB-9075 | biostudies-arrayexpress

Dickeya dadantii

Project description:Dickeya dadantii Raw sequence reads

| PRJNA645731 | ENA