Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

13 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Genomic Array Footprinting of Shewanella oneidensis grown under aerobic conditions

ABSTRACT: We undertook a genomic array footprinting to identify genes important for aerobic growth of S. oneidensis. The data revealed that removal of 96 genes resulted in significant impacts on aerobic growth. Experimental cells collected 5 days after competition started; Control cells collected 1 day after competition started. In total, 6 samples were studied (3 for 5 days and 3 for 1 day, 3 replicates).

ORGANISM(S): Shewanella oneidensis

SUBMITTER: haichun gao

PROVIDER: E-GEOD-42479 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Response of Shewanella oneidensis wild type and arcA mutant strains to H2O2

Project description:We undertook a transcriptional profiling to identify genes coping with H2O2-induced oxidative stress in S. oneidensis. The data revealed that the well conserved scavenging genes such as as ahpCF, katB, and katG formed the first line of defense while iron-sulfur protecting proteins may not play a significant role. Experimental cells collected 5 min after H2O2 treatment; Control cells collected just before H2O2 treatment. In total, 8 samples were studied (4 for wild type and 4 for arcA mutant, 4 replicates).

2012-07-31 | E-GEOD-31053 | biostudies-arrayexpress

MR-1 nitrate sample to fumarate sample

Project description:One of the most striking observations in the S. oneidensis genome regarding nitrate respiration is that napC is missing and nrfBCD is degenerated. To gain insights into candidate genes encoding the protein(s) in place of NapC and NrfBCD function, i.e., delivering electrons to NapA and NrfA, transcriptional profiling was carried out using the S. oneidensis whole-genome cDNA microarray. Cells of MR-1 grown on nitrate or fumarate under anaerobic conditions were sampled at the exponential phase for the analysis. The quality of the array data was statistically assessed using the method reported previously. Keywords: Compararive microarray study Compare transcriptional profiles of MR-1 grown on nitrate and Fumarate aiming at finding the electron transfer proteins to NapA and NrfA.

2010-05-19 | E-GEOD-11198 | biostudies-arrayexpress

Comparative genomic hybridization of 137 Bordetella pertussis strains

Project description:Comparative genome hybridization (CGH) of sample of 137 Bordetella pertussis strains

2006-04-30 | E-TABM-54 | biostudies-arrayexpress

Comparative genomic hybridization of 12 Bordetella holmesii strains compared to Bordetella pertussis

Project description:Comparative genome hybridization (CGH) of a sample of 12 Bordetella holmesii strains compared to Bordetella pertussis Tohama I

2006-06-30 | E-TABM-55 | biostudies-arrayexpress

Comparative genomic hybridization of Bordetella bronchiseptica, B. pertussis, and B. parapertussis strains

Project description:Comparative genome hybridization (CGH) of sample of 58 Bordetella bronchiseptica, B. pertussis, and B. parapertussis strains selected to span four clusters as defined by MLST.

2005-12-31 | E-TABM-32 | biostudies-arrayexpress

Comparative genomic hybridization of 71 Bordetella parapertussis strains isolated from humans and sheep

Project description:Comparative genomic hybridization (CGH) of 71 Bordetella parapertussis strains isolated from either humans or sheep, and 1 B. bronchiseptica strain isolated from a rabbit

2006-09-04 | E-TABM-94 | biostudies-arrayexpress

Comparative genomic hybridization of genomic DNA from two B. bronchiseptica strains and one B. pertussis strain and sequenced reference genomes by comparative genome hybridization (CGH)

Project description:Genomic DNA from two B. bronchiseptica strains and one B. pertussis strain were compared to the sequenced reference genomes by comparative genome hybridization (CGH).

2006-03-31 | E-MEXP-399 | biostudies-arrayexpress

Comparative genomic hybridization of B. pertussis chromosomal fragments separated by PFGE

Project description:The genomes of Bordetella pertussis strains with different passage histories were digested with a restriction endonuclease and separated by pulsed-field gel electrophoresis (PFGE). Each PFGE fragment was labeled and hybridized to a microarray to assess the genome content of the fragment.

2006-04-30 | E-TABM-58 | biostudies-arrayexpress

Absolute quantification of selected photosynthetic electron transfer proteins in Chlamydomonas reinhardtii in the presence and absence of oxygen

Project description:The absolute amount of plastocyanin (PC), ferredoxin-NADP+-oxidoreductase (FNR), hydrogenase (HYDA1) and ferredoxin 5 (FDX5) were quantified in aerobic and anaerobic Chlamydomonas reinhardtii whole cells using purified (recombinant) proteins as internal standard in a mass spectrometric approach. Quantified protein amounts were related to the estimated amount of PSI. The ratios of PC to FNR to HYDA1 to FDX5 in aerobic cells were determined to be 2.1 : 1.8 : 0.005 : 0. In anaerobic cells, the ratios changed to 1.6 : 1.8 : 0.026 : 0.04 (PC : FNR : HYDA1 : Fdx5). Employing sodium dithionite and methyl viologen as electron donors the specific activity of hydrogenase in whole cells was calculated to be 382 ±96.5 μmolH2/min/mg. Importantly, these data demonstrate for competition of electrons from FDX1, HYDA1 is about 70-fold less abundant than its competitor FNR. Effective in vivo hydrogen production points to a channeling mechanism for FDX to HYDA1 electron transfer.

2022-02-23 | PXD008313 | Pride

Measuring transcriptional differences between Caulobacter crescentus cultured in nitrate versus ammonium as the sole nitrogen source

Project description:This study is measuring the steady-state levels of mRNA in wild-type Caulobacter crescentus grown in M2 defined medium containing either ammonium or nitrate as the sole nitrogen source. Four independent cultures of Caulobacter crecentus were grown in each of two medium conditions: M2(nitrate)glucose and M2(ammonium)glucose. Cultures in each medium type were grown to OD660=0.3 and RNA was isolated from each.

2010-06-20 | E-GEOD-21203 | 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