Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Frequency of change determines effectiveness of microbial response strategies in sulfidic stream microbiomes

ABSTRACT: Chemostat incubations were established and inoculated with sediments collected from Canyon Creek, Calgary, Alberta, Canada. The chemostats experienced oxic-anoxic change of different frequency, High-frequency, Medium-frequency and Low-frequency. 18 samples were collected at the end of the final oxic phase and the final anoxic phase in the triplicated chemostats for metagenomic and metaproteomic analysis. 26 genomes were assembled from metagenomes. Proteomes were used to investigate translational regulation of each population associated with a genome.

INSTRUMENT(S): Q Exactive

ORGANISM(S): Arenimonas Sp. Acidovorax

SUBMITTER: Angela Kouris

LAB HEAD: Marc Strous

PROVIDER: PXD028583 | Pride | 2023-04-26

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	EXPA13_File_Sample_Description.txt	Txt
	EXPA13_Proteomics_DB_V1_CRAP_BH.fasta	Fasta
	Run1_EXPA13_A191_1500ng.raw	Raw
	Run1_EXPA13_A191_1500ng_acetyl.msf	Msf
	Run1_EXPA13_A191_1500ng_acetyl.pep.xml	Pepxml

Items per page:

1 - 5 of 94

Similar Datasets

Proteomics of groundwater microbiomes collected from five wells in Alberta, Canada

Project description:Groundwater samples were collected from five wells in Alberta, Canada. The sampling location and time are indicated in the table below. 13 to 29 genomes were assembled from each metagenome. Proteomic analyses were performed to investigate which genomes and genes were expressed in each well. Sample ID Location Latitude (NAD 83) Longitude (NAD 83) Sampling date 19GWC19026 218 Cluny 50.85 -112.84 30/07/2019 19GWC19028 114 Ross Creek 49.99 -110.46 31/07/2019 19GWC19045 265 Metiskow 52.42 -110.61 18/09/2019 19GWE00050 991 Cynthia 56.22 -117.81 04/09/2019 19GWE00515 33 Fort McMurray 56.98 -111.85 17/09/2019

2024-05-21 | PXD044305 | Pride

Diurnally synchronized transitions between oxic and anoxic physiologies in an archaeon

Project description:This SuperSeries is composed of the following subset Series: GSE15272: Diurnally synchronized transitions between oxic and anoxic physiologies in an archaeon, experiment "A" GSE15273: Diurnally synchronized transitions between oxic and anoxic physiologies in an archaeon, experiment "B" GSE15274: Diurnally synchronized transitions between oxic and anoxic physiologies in an archaeon, experiment "Control-1" GSE15275: Diurnally synchronized transitions between oxic and anoxic physiologies in an archaeon, experiment "C" GSE15276: Diurnally synchronized transitions between oxic and anoxic physiologies in an archaeon, experiment "Control-2" Refer to individual Series

2009-04-14 | E-GEOD-15282 | biostudies-arrayexpress

Dual oxic-anoxic co-culture enables direct study of host-anaerobe interactions at the airway epithelial interface

Project description:To understand the physiological response of Calu-3 cells to dual oxic-anoxic culture

2022-11-19 | GSE218124 | GEO

Comparison of microbial communities with different carbon source types

Project description:We reported the microbial communities in the biofilm anoxic-oxic-MBR system operated with different carbon source types.

2019-10-19 | GSE139113 | GEO

Salmonella under environmental stress

Project description:The aim of this study is to investigate the transcriptional response of S. Typhimurium to heat, osmotic, oxidative and acid stress under anoxic and oxic conditions and to non-stressed anoxic conditions.

2013-11-11 | E-MTAB-1804 | biostudies-arrayexpress

RNA expression data from Halobacterium NRC-1 in response to oxic/anoxic transitions, verification experiment

Project description:In order to ensure the reproducibility of the transcriptional response of Halobacterium NRC-1 to oxic/anoxic transitions, we repeated global mRNA measurements for the oxygen time series data in GSE5924, except that cultures were equilibrated to high oxygen for 12 hours prior to the start of the experiment rather than low oxygen. The results of these data suggest that there is good (~60%) reproducibility between datasets, and that Halobacterium responds robustly to oxic/anoxic transitions. Keywords: time series

2007-07-31 | GSE5925 | GEO

Project description:Oxic-anoxic-oxic estuary Metatranscriptome

| PRJNA940127 | ENA

aquatic metagenome

Project description:Oxic-anoxic-oxic estuary Metagenome

| PRJNA222777 | ENA

Halobacterium NRC-1_oxygen_response_timecourse_set3

Project description:In order to ensure the reproducibility of the transcriptional response of Halobacterium NRC-1 to oxic/anoxic transitions, we repeated global mRNA measurements for the oxygen time series data in GSE5924, except that cultures were equilibrated to low oxygen for 24 hours prior to the start of the experiment rather than 12 hours, and time course sampling continued to 12 hours post-shift to high oxygen rather than stopping at 6 hours. The results of these data suggest that there is good reproducibility between datasets, and that Halobacterium responds robustly to oxic/anoxic transitions. Keywords: time course

2007-07-31 | GSE7559 | GEO

Investigation on the anaerobic propionate degradation by Escherichia coli K12

Project description:Propionate is an abundant carboxylic acid in nature. Microorganisms metabolize propionate aerobically via the 2-methylcitrate pathway. This pathway depends on a series of three reactions in the citric acid cycle that leads to the conversion of succinate to oxaloacetate. Interestingly, the gamma-proteobacterium Escherichia coli can use propionate as a carbon and electron source under oxic but not under anoxic conditions. The typical downregulation of the citric acid cycle under anoxic conditions is only partially responsible for the inability to use propionate under anoxic conditions since an arcA mutant shows very limited growth on propionate. RT-PCR and transcriptomic analysis revealed a post-transcriptional regulation of the prp-genecluster encoding the necessary enzymes for propionate metabolism. The polycistronic mRNA was hydrolyzed in the 3`-5` direction under anoxic conditions. This regulatory strategy is highly constructive because the last gene of the operon encodes the first enzyme of the propionate metabolism. Further analysis revealed that RNase R catalyzes the hydrolysis of the prp transcripts. Consequently, an rnr-deletion strain could metabolize propionate under anoxic conditions. To the best of our knowledge, this is the first study describing the influence of RNase R on the anaerobic metabolism of E. coli.

2017-12-14 | GSE78814 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

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