Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

12 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

TAU - Ben-Jacob - P. vortex - Gene Prediction Validation - 105k

ABSTRACT: Validation of the de-novo sequenced Paenibacillus vortex annotation using microarray.

ORGANISM(S): Paenibacillus vortex

SUBMITTER: Eshel Ben-Jacob

PROVIDER: E-MEXP-3019 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Global transcriptional and phenotypic analyseis of Escherichia coli O157:H7 strain Xuzhou21 and its pO157_Sal cured mutant

Project description:Escherichia coli O157:H7 is an important food-borne pathogen that can cause hemorrhagic colitis (HC) and hemolytic-uremic syndrome (HUS) in humans. pO157_Sal, a novel conjugative plasmid is present in a Chinese O157:H7 outbreak strain Xuzhou21. Here we investigated the phenotypic and transcriptional differences between the wild type strain Xuzhou21 and the pO157_Sal cured mutant strain Xuzhou21m. RNA-seq analysis found that all 52 ORFs encoded on pO157_Sal were transcribed. 168 chromosomal and pO157 genes were differentially expressed (M-bM-^IM-%2 fold difference) between Xuzhou21 and Xuzhou21m. Sixty-seven and 101 genes were up-regulated and down-regulated respectively by pO157_Sal including genes related to stress response, adaption and virulence. The plasmid-cured mutant grew slower than wild type in M9 medium under the condition of high NaCl or presence of sodium deoxycholate (NaDC), corroborating with the RNA-seq data. Seven differentially expressed genes are associated with NaDC resistance, including the adenine-specific DNA-methyltransferase gene (dam), multidrug efflux system subunit gene mdtA, hyperosmotically inducible periplasmic protein gene osmY and oxidation-reduction related genes while two differentially expressed genes (osmY and pspD) are likely to be related to resistance to osmotic pressure. A number of differentially expressed genes were virulence associated including four genes encoding T3SS effectors from the chromosome and ehxD from pO157. These findings demonstrated that the plasmid pO157_Sal affects the chromosome and pO157 genes transcription and contributes to the enhanced ability to resist stress. We conclude that pO157_Sal plays an important role in regulating global gene expression and affects virulence and adaptation of E.coli O157:H7. The total mRNA extracted from Escherichia coli O157:H7 Xuzhou21 and its plasmid cured strain Xuzhou21m were sequenced using Illumina.

2013-03-05 | E-GEOD-44846 | biostudies-arrayexpress

Tiling path analysis of a library of transposon mutants generated in Salmonella enterica serovar Typhimurium strain SL1344 before and after infection in mice to identify mutants attenuated in vivo

Project description:A library of transposon mutants was generated in Salmonella enterica serovar Typhimurium strain SL1344 using custom Tn5 and Mu transposons with outward-facing T7 and SP6 promoters. The library was grown up in vitro, and used as the input pool for mouse infection experiments. An in vivo output pool was obtained from the mouse livers 2 days post-infection.<br><br>Genomic DNA was extracted from the input and output pools and digested with the restriction enzyme RsaI. Cy5-labelled RNA run-offs were produced seperately from the T7 and SP6 promoters and hybridised to a tiling microarray along with the Cy3-labelled in vitro transcription products from an untransposed SL1344 wild type control. Analysis of the microarray data allows the location of the transposon inserts to be determined. Mutants that are present in the input pool but that are absent or less prevalent in the output pools are inferred to be attenuated in vivo.

2009-08-25 | E-MEXP-2076 | biostudies-arrayexpress

Transcription profiling by array of Burkholderia cenocepacia J2315 from the beginning of the stationary phase compared to mid-log phase

Project description:Burkholderia cenocepacia J2315 was grown in LB broth to the beginning of stationary phase. The expression profile was compared to cultures harvested in mid-log phase.

2012-01-01 | E-MEXP-2754 | biostudies-arrayexpress

Transcription profiling by array of Burkholderia cenocepacia J2315 at the beginning of the stationary phase compared to mid-log phase

Project description:Burkholderia cenocepacia J2315 was grown at 37 degrees centigrade in LB broth to the beginning of stationary phase (18 hours incubation time). <br>The expression profile was compared to cultures harvested in mid-log phase (7 hours incubation time).<br>

2012-01-01 | E-MEXP-2790 | biostudies-arrayexpress

Transcription profiling of brain, liver and spleen from rats infected with Escherichia coli K1 and treated with capsule-selective endosialidase E

Project description:Transcription profiling of infected and treated (Capsule-Selective Endosialidase E Minimizes) of RNA isolated from brain/spleen/liver of rats with E.coli K1

2010-01-10 | E-MEXP-2406 | biostudies-arrayexpress

Nucleoside Analogues are Potent Inducers of Bacterial Mutagenesis

Project description:Drugs targeting DNA and RNA in mammalian cells or viruses can also affect bacteria present in the host and thereby induce the bacterial SOS system. This has the potential to increase mutagenesis and the development of antimicrobial resistance (AMR). Here we have examined nucleoside analogues (NAs) commonly used in anti-viral and anti-cancer therapies for potential effects on mutagenesis in Escherichia coli using the Rifampicin mutagenicity assay. To further explore the mode of action of the NAs, we appliedanalyzed metabolome and proteome of E.coli deletion mutants., and metabolome and proteome analyses. Five out of the thirteen NAs examined, including three nucleoside reverse transcriptase inhibitors (NRTIs) and two anti-cancer drugs, increased the mutation frequency in E. coli more than 25-fold at doses that were within reported plasma concentration range (Pl.CR), but that did not affect bacterial growth. We show that the SOS response is induced and that the increase in mutation frequency is mediated by the TLS polymerase Pol V. Quantitative mass spectrometry based metabolite profiling did not reveal large changes in nucleoside phosphate or other central carbon metabolite pools, which suggests that the SOS induction is an effect of increased replicative stress. Our results suggest that NAs/NRTIs can contribute to the development of AMR.

2021-07-15 | PXD025370 | Pride

RNAseq analyses of pathogenic Burkholderia glumae under in vitro and in vivo conditions

Project description:We analyzed B. glumae transcriptome from infected rice tissue using an RNAseq technique. To identify unique expression of B. glumae genes within rice tissues, we compared in vivo transcriptome data of B. glumae to in vitro data. To accomplish this, we analyzed differentially expressed genes (DEGs) and identified 2,906 transcripts that were significantly altered. Three in vitro (culture) and three in vivo (in plant) RNAseqs in B. glumae

2014-08-21 | E-GEOD-56958 | biostudies-arrayexpress

Transcription profiling by array of Burkholderia cenocepacia J2315 grown at 20C or 37C

Project description:B. cenocepacia J2315 was grown on LB medium to mid-stationary phase at O.D. 0.5 at 150 rpm in a shaking incubator at two different temperatures: 37 degrees and 20 degrees centigrade.

2012-01-01 | E-MEXP-2789 | biostudies-arrayexpress

Burkholderia multivorans reference dataset-Experiment 2

Project description:The gene expression of the opportunictic cystic fibrosis lung pathogen Burkholderia multivorans ATCC 17616 was investigated under different growth conditions relevant for growth in the cystic fibrosis lung.

2012-05-11 | E-MEXP-3209 | biostudies-arrayexpress

Molecular strategy for survival at a critical high temperature in Eschierichia coli

Project description:To investigate the effect for organisms by the treatment of the critical high remperature (CHT), we use Escherichia coli as a model organism and performed the transcriptome analysis to compare the genome wide transcriptional profiles between under the treatment of normal temperature, 37 degree C and 47 degree C.

2011-04-30 | E-MEXP-3191 | 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