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Links from GEO DataSets

Items: 20

1.

MMP101

(Submitter supplied) Methanococcus maripaludis is a methanogenic archaeon. Within its genome, there are two operons for membrane associated hydrogenases, eha and ehb. To investigate the regulation of ehb on the cell, an S40 mutant was constructed in such a way that a portion of the ehb operon was replaced by pac cassette in the wild type parental strain S2 (done by Whitman's group at the University of Georgia). Four samples of each strain were grown in batch culture. more...
Organism:
Methanococcus maripaludis
Type:
Expression profiling by array
Platform:
GPL2509
16 Samples
Download data
Series
Accession:
GSE2745
ID:
200002745
2.

MMP qualitative and quantitative mass spectrometry

(Submitter supplied) Methanococcus maripaludis is a methanogenic archaeon. Within its genome, there are two operons for membrane associated hydrogenases, eha and ehb. To investigate the regulation of ehb on the cell, an S40 mutant was constructed in such a way that a portion of the ehb operon was replaced by pac cassette in the wild type parental strain S2 (done by Whitman's group at the University of Georgia). The S40 and S2 strains were grown in 14N and 15N media with acetate separately. more...
Organism:
Methanococcus maripaludis S2; Methanococcus maripaludis
Type:
Other
Platforms:
GPL2102 GPL2103
2 Samples
Download data
Series
Accession:
GSE2744
ID:
200002744
3.

Genetic, Biochemical, and Molecular Characterization of Methanosarcina barkeri Mutants Lacking Three Distinct Classes of Hydrogenase

(Submitter supplied) Hydrogenases are a critical component of H2-dependent energy-conservation pathways in Methanosarcina barkeri. To allow phenotypic analysis of the hydrogenases, we constructed mutants lacking the frhADGB, freAEGB, vhtGACD, vhxGAC and echABCDEF operons, individually and in all possible combinations. In addition to measuring the effect of each deletion on growth, methane production, and hydrogenase activity, the effect on gene expression was measured by RNA sequencing to detect potential transcriptional regulation by the hydrogenases.
Organism:
Methanosarcina barkeri str. Fusaro
Type:
Expression profiling by high throughput sequencing
Platform:
GPL20638
27 Samples
Download data: XLSX
Series
Accession:
GSE98441
ID:
200098441
4.

Steady-state samples of Methanococcus maripaludis MM901 grown on formate under hydrogen limited conditions

(Submitter supplied) Hydrogenotrophic methanogenic Archaea are defined by a H2 requirement for growth. Despite this requirement, many hydrogenotrophs are also capable of growth with formate as an electron donor for methanogenesis. Hydrogenotrophs respond to H2 starvation both phenotypically and at the level of gene expression; however, the responses during growth on formate have not been characterized. Here we report that during continuous culture of Methanococcus maripaludis under defined nutrient conditions, growth yields relative to methane production decreased markedly with either H2 excess or formate excess, suggesting that energy spilling occurs. more...
Organism:
Methanococcus maripaludis S2
Type:
Expression profiling by genome tiling array
Platform:
GPL15063
8 Samples
Download data: TXT
Series
Accession:
GSE42111
ID:
200042111
5.

Methanococcus maripaludis response to hydrogen limitation

(Submitter supplied) Methanococcus maripaludis is a methanogenic Archaea that conserves energy from molecular hydrogen to reduce carbon dioxide to methane. Chemostat grown cultures limited for hydrogen, phosphate, or leucine were compared to determine the regulatory response to hydrogen limitation. This was done by comparing hydrogen limited cultures to both leucine limited and phosphate limited cultures. Slow and rapid growing samples limited for either hydrogen or phosphate were compared to determine the regulatory effects of growth rate. more...
Organism:
Methanococcus maripaludis
Type:
Expression profiling by array
Platform:
GPL2509
68 Samples
Download data
Series
Accession:
GSE6747
ID:
200006747
6.

Time series of Methanococcus maripaludis MM901, a shift from a H2-limited condition to a H2-excess condition

(Submitter supplied) Methanogens catalyze the critical, methane-producing step (called methanogenesis) in the anaerobic decomposition of organic matter and have applications in carbon-neutral fuel production. Here, we present the first predictive model of global gene regulation of methanogenesis in a hydrogenotrophic methanogen, Methanococcus maripaludis. We generated a comprehensive list of genes (protein-coding and non-coding) for M. more...
Organism:
Methanococcus maripaludis S2
Type:
Expression profiling by genome tiling array
Platform:
GPL15063
32 Samples
Download data: TXT
Series
Accession:
GSE42167
ID:
200042167
7.

Time series of Methanococcus maripaludis MM901:del_mtd (MMP0372), a shift from a H2-excess and P-limiting condition to a H2-limited and P-excess condition in chemostats (growth rate held constant)

(Submitter supplied) Methanogens catalyze the critical, methane-producing step (called methanogenesis) in the anaerobic decomposition of organic matter and have applications in carbon-neutral fuel production. Here, we present the first predictive model of global gene regulation of methanogenesis in a hydrogenotrophic methanogen, Methanococcus maripaludis. We generated a comprehensive list of genes (protein-coding and non-coding) for M. more...
Organism:
Methanococcus maripaludis S2
Type:
Expression profiling by genome tiling array
Platform:
GPL15063
22 Samples
Download data: TXT
Series
Accession:
GSE42166
ID:
200042166
8.

Time series of Methanococcus maripaludis MM901:del_fruA (MMP1382)-del_frcA (MMP0820), a shift from a H2-excess and P-limiting condition to a H2-limited and P-excess condition in chemostats (growth rate held constant)

(Submitter supplied) Methanogens catalyze the critical, methane-producing step (called methanogenesis) in the anaerobic decomposition of organic matter and have applications in carbon-neutral fuel production. Here, we present the first predictive model of global gene regulation of methanogenesis in a hydrogenotrophic methanogen, Methanococcus maripaludis. We generated a comprehensive list of genes (protein-coding and non-coding) for M. more...
Organism:
Methanococcus maripaludis S2
Type:
Expression profiling by genome tiling array
Platform:
GPL15063
22 Samples
Download data: TXT
Series
Accession:
GSE42165
ID:
200042165
9.

Time series of Methanococcus maripaludis MM901:del_MMP1447, a shift from a H2-excess and P-limiting condition to a H2-limited and P-excess condition in chemostats (growth rate held constant)

(Submitter supplied) Methanogens catalyze the critical, methane-producing step (called methanogenesis) in the anaerobic decomposition of organic matter and have applications in carbon-neutral fuel production. Here, we present the first predictive model of global gene regulation of methanogenesis in a hydrogenotrophic methanogen, Methanococcus maripaludis. We generated a comprehensive list of genes (protein-coding and non-coding) for M. more...
Organism:
Methanococcus maripaludis S2
Type:
Expression profiling by genome tiling array
Platform:
GPL15063
20 Samples
Download data: TXT
Series
Accession:
GSE42164
ID:
200042164
10.

Time series of Methanococcus maripaludis MM901:del_MMP1100, a shift from a H2-excess and P-limiting condition to a H2-limited and P-excess condition in chemostats (growth rate held constant)

(Submitter supplied) Methanogens catalyze the critical, methane-producing step (called methanogenesis) in the anaerobic decomposition of organic matter and have applications in carbon-neutral fuel production. Here, we present the first predictive model of global gene regulation of methanogenesis in a hydrogenotrophic methanogen, Methanococcus maripaludis. We generated a comprehensive list of genes (protein-coding and non-coding) for M. more...
Organism:
Methanococcus maripaludis S2
Type:
Expression profiling by genome tiling array
Platform:
GPL15063
20 Samples
Download data: TXT
Series
Accession:
GSE42162
ID:
200042162
11.

Time series of Methanococcus maripaludis MM901:del_MMP0719, a shift from a H2-excess and P-limiting condition to a H2-limited and P-excess condition in chemostats (growth rate held constant)

(Submitter supplied) Methanogens catalyze the critical, methane-producing step (called methanogenesis) in the anaerobic decomposition of organic matter and have applications in carbon-neutral fuel production. Here, we present the first predictive model of global gene regulation of methanogenesis in a hydrogenotrophic methanogen, Methanococcus maripaludis. We generated a comprehensive list of genes (protein-coding and non-coding) for M. more...
Organism:
Methanococcus maripaludis S2
Type:
Expression profiling by genome tiling array
Platform:
GPL15063
20 Samples
Download data: TXT
Series
Accession:
GSE42159
ID:
200042159
12.

Time series of Methanococcus maripaludis MM901, a shift from a H2-excess condition to a H2-limiting condition

(Submitter supplied) Methanogens catalyze the critical, methane-producing step (called methanogenesis) in the anaerobic decomposition of organic matter and have applications in carbon-neutral fuel production. Here, we present the first predictive model of global gene regulation of methanogenesis in a hydrogenotrophic methanogen, Methanococcus maripaludis. We generated a comprehensive list of genes (protein-coding and non-coding) for M. more...
Organism:
Methanococcus maripaludis S2
Type:
Expression profiling by genome tiling array
Platform:
GPL15063
32 Samples
Download data: TXT
Series
Accession:
GSE42143
ID:
200042143
13.

Time series of Methanococcus maripaludis MM901, a shift from a H2-excess and P-limiting condition to a H2-limited and P-excess condition in chemostats (growth rate held constant)

(Submitter supplied) Methanogens catalyze the critical, methane-producing step (called methanogenesis) in the anaerobic decomposition of organic matter and have applications in carbon-neutral fuel production. Here, we present the first predictive model of global gene regulation of methanogenesis in a hydrogenotrophic methanogen, Methanococcus maripaludis. We generated a comprehensive list of genes (protein-coding and non-coding) for M. more...
Organism:
Methanococcus maripaludis S2
Type:
Expression profiling by genome tiling array
Platform:
GPL15063
32 Samples
Download data: TXT
Series
Accession:
GSE42130
ID:
200042130
14.

Time series of Methanococcus maripaludis MM901, a shift from a H2-excess and N-limiting condition to a H2-limited and N-excess condition in chemostats (growth rate held constant)

(Submitter supplied) Methanogens catalyze the critical, methane-producing step (called methanogenesis) in the anaerobic decomposition of organic matter and have applications in carbon-neutral fuel production. Here, we present the first predictive model of global gene regulation of methanogenesis in a hydrogenotrophic methanogen, Methanococcus maripaludis. We generated a comprehensive list of genes (protein-coding and non-coding) for M. more...
Organism:
Methanococcus maripaludis S2
Type:
Expression profiling by genome tiling array
Platform:
GPL15063
32 Samples
Download data: TXT
Series
Accession:
GSE42126
ID:
200042126
15.

Steady-state samples of Methanococcus maripaludis MM901 grown on formate-excess medium

(Submitter supplied) Methanogens catalyze the critical, methane-producing step (called methanogenesis) in the anaerobic decomposition of organic matter and have applications in carbon-neutral fuel production. Here, we present the first predictive model of global gene regulation of methanogenesis in a hydrogenotrophic methanogen, Methanococcus maripaludis. We generated a comprehensive list of genes (protein-coding and non-coding) for M. more...
Organism:
Methanococcus maripaludis S2
Type:
Expression profiling by genome tiling array
Platform:
GPL15063
4 Samples
Download data: TXT
Series
Accession:
GSE42115
ID:
200042115
16.

Expression analysis of Thermococcus onnurineus NA1 KCTC10859 and an Frh-deficient mutant, Frh overexpression mutant and TON_0282 deletion mutant in a T. onnurineus NA1 strain.

(Submitter supplied) Investigation of whole genome gene expression level changes in an Frh-deficient mutant, Frh overexpression mutant and TON_0282 deletion mutant, compared to the wild-type strain. In this study, as a first step to assess the role of the frhAGB-encoding hydrogenases and TON_0282 gene, we constructed three mutants by deleting each gene in a T. onnurineus NA1.
Organism:
Thermococcus onnurineus NA1
Type:
Expression profiling by array
Platform:
GPL22562
8 Samples
Download data: CALLS, PAIR
Series
Accession:
GSE88718
ID:
200088718
17.

Screening of a novel strong promoter by RNA sequencing and its application to H2 production in a hyperthermophilic archaeon

(Submitter supplied) A strong promoter increases transcription of the genes of interest and enhances the production of various valuable substances. For a hyperthermophilic archaeon Thermococcus onnurineus NA1, which can produce H2 by carbon monoxide oxidation, we searched for a novel endogenous strong promoter by transcriptome analysis using high-throughput RNA sequencing. Based on the relative transcript abundance, we selected one promoter to encode a hypothetical gene, of which homologs were found only in several Thermococcales strains. more...
Organism:
Thermococcus onnurineus NA1
Type:
Expression profiling by high throughput sequencing
Platform:
GPL19533
2 Samples
Download data: TXT
Series
Accession:
GSE64036
ID:
200064036
18.

PROTEOFORMER: deep proteome coverage through ribosome profiling and MS integration

(Submitter supplied) An increasing amount of studies integrate mRNA sequencing data into MS-based proteomics to complement the translation product search space. We present the generation of a protein synthesis-based database from deep sequencing of ribosome-protected mRNA fragments. This approach increases the overall protein identification rates with 3% and 11% (improved and new identifications) for human and mouse respectively and enables proteome-wide detection of 5’-extended proteoforms, uORF translation and near-cognate translation start sites.
Organism:
Homo sapiens
Type:
Expression profiling by high throughput sequencing
Platform:
GPL11154
2 Samples
Download data: BEDGRAPH
Series
Accession:
GSE58207
ID:
200058207
19.

Transcriptome analysis of the archaeon Thermoplasma acidophilum cultured under aerobic and anaerobic conditions

(Submitter supplied) Investigation of whole genome gene expression level changes in Thermoplasma acidophilum cultured under aerobic and anaerobic conditions. The analysis are further described in Na Sun, Cuiping Pan, Stephan Nickell, Matthias Mann, Wolfgang Baumeister, and István Nagy, Quantitative proteome and transcriptome analysis of the archaeon Thermoplasma acidophilum cultured under aerobic and anaerobic conditions (submitted).
Organism:
Thermoplasma acidophilum DSM 1728
Type:
Expression profiling by array
Platform:
GPL10453
6 Samples
Download data: TXT
Series
Accession:
GSE21956
ID:
200021956
20.

MMP103

(Submitter supplied) Methanococcus maripaludis is a methanogenic Archaea that conserves energy from molecular hydrogen to reduce carbon dioxide to methane. Chemostat grown cultures limited for phosphate or leucine were compared to determine the regulatory response to leucine limitation. Keywords: archaea, hydrogen, leucine, phosphate, nutrient limitation, growth rate, methanogen
Organism:
Methanococcus maripaludis
Type:
Expression profiling by array
Platform:
GPL2509
16 Samples
Download data: SPT
Series
Accession:
GSE8728
ID:
200008728
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