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Items: 1 to 20 of 293

1.

Chip-SIP analysis of Monterey Bay surface waters incubated with organic carbon substrates

(Submitter supplied) October 2013 surface seawater collected from Monterey Bay was incubated with 1 micromolar 13C labeled glucose, starch, acetate, lipids, protein, or amino acids for 12 hours. Community RNA was extracted and hybridized to a Roche Nimblegen microarray and analyzed by NanoSIMS to obtain isotope ratio data for all probe spots.
Organism:
marine metagenome
Type:
Other
Platform:
GPL20727
17 Samples
Download data: PAIR, TXT
Series
Accession:
GSE71228
ID:
200071228
2.

Phylogenetic patterns in the microbial response to resource availability: amino acid incorporation in San Francisco Bay

(Submitter supplied) Aquatic microorganisms are typically identified as either oligotrophic or copiotrophic, representing trophic strategies adapted to low or high nutrient concentrations, respectively. Here, we sought to take steps towards identifying these and additional adaptations to nutrient availability with a quantitative analysis of microbial resource use in mixed communities. We incubated an estuarine microbial community with stable isotope labeled amino acids (AAs) at concentrations spanning three orders of magnitude, followed by taxon-specific quantitation of isotopic incorporation using NanoSIMS analysis of high-density microarrays. more...
Organism:
marine metagenome
Type:
Non-coding RNA profiling by array
Platform:
GPL18455
5 Samples
Download data: PAIR, TIFF, TXT
Series
Accession:
GSE56119
ID:
200056119
3.

Community composition of bacteria involved in fixed nitrogen loss in the water column of two major oxygen minimum zones in the ocean

(Submitter supplied) The community composition (in terms of abundance, distribution and contribution of diverse clades) of bacteria involved in nitrogen transformations in the oxygen minimum zones may be related to the rates of fixed N loss in these systems. The abundance of both denirifying and anammox bacteria, and the assemblage composition of denitrifying bacteria were investigated in the Eastern Tropical South Pacific and the Arabian Sea using assays based on molecular markers for the two groups of bacteria. more...
Organism:
uncultured bacterium; marine metagenome; synthetic construct
Type:
Other
Platform:
GPL17721
25 Samples
Download data: GPR, TXT, XLSX
Series
Accession:
GSE50787
ID:
200050787
4.

Community composition of ammonia-oxidizing archaea from surface and anoxic depths of oceanic oxygen minimum zones

(Submitter supplied) Ammonia-oxidizing archaea (AOA) have been reported at high abundance in much of the global ocean, even in environments such as pelagic oxygen minimum zones (OMZs), where conditions seem unlikely to support aerobic ammonium oxidation. Due to the lack of information on any potential alternative metabolism of AOA, the AOA community composition might be expected to differ between oxic and anoxic environments, indicating some difference in ecology and/or physiology of the AOA assemblage. more...
Organism:
synthetic construct; uncultured crenarchaeote; marine metagenome
Type:
Other
Platform:
GPL17151
23 Samples
Download data: GPR, TXT, XLSX
Series
Accession:
GSE46851
ID:
200046851
5.

Unveiling the transcriptional features associated with coccolithovirus infection of natural Emiliania huxleyi blooms.

(Submitter supplied) Lytic viruses have been implicated in the massive cellular lysis observed during algal blooms, through which they assume a prominent role in oceanic carbon and nutrient flows. Despite their impact on biogeochemical cycling, the transcriptional dynamics of these important oceanic events is still poorly understood. Here, we employ an oligonucleotide microarray to monitor host (Emiliania huxleyi) and virus (coccolithovirus) transcriptomic features during the course of E. more...
Organism:
Emiliania huxleyi; Emiliania huxleyi virus 86; Emiliania huxleyi virus 163; marine metagenome
Type:
Expression profiling by array
Platform:
GPL10968
85 Samples
Download data: TXT
Series
Accession:
GSE24341
ID:
200024341
6.

Linking phytoplankton community composition to seasonal changes in f ratio

(Submitter supplied) Seasonal changes in nitrogen assimilation have been studied in the western English Channel by sampling at approximately weekly intervals for 12 months. Nitrate concentrations showed strong seasonal variations. Available nitrogen in the winter was dominated by nitrate but this was close to limit of detection from May to September, after the spring phytoplankton bloom. 15N uptake experiments showed that nitrate was the nitrogen source for the spring phytoplankton bloom but regenerated nitrogen supported phytoplankton productivity throughout the summer. more...
Organism:
synthetic construct; marine metagenome
Type:
Other
Platform:
GPL13292
15 Samples
Download data: TXT
Series
Accession:
GSE27998
ID:
200027998
7.

Analysis of sulfur-related transcription by Roseobacter communities using a taxon-specific functional gene microarray

(Submitter supplied) The fraction of dissolved dimethylsulfoniopropionate (DMSPd) converted by marine bacterioplankton into the climate-active gas dimethylsulfide (DMS) varies widely in the ocean, with the factors that determine this value still largely unknown. One current hypothesis is that the ratio of DMS formation:DMSP demethylation is determined by DMSP availability, with 'availability' in both an absolute sense (i.e., concentration in seawater) and in a relative sense (i.e., proportionally to other labile organic S compounds) being proposed as the critical factor. more...
Organism:
Ruegeria pomeroyi DSS-3; Jannaschia sp. CCS1; Ruegeria sp. TM1040; Oceanicola granulosus HTCC2516; Sulfitobacter sp. NAS-14.1; Maritimibacter alkaliphilus; marine metagenome; Sulfitobacter sp. EE-36; Roseovarius nubinhibens ISM; Pseudooceanicola batsensis HTCC2597; Sagittula stellata E-37; Yoonia vestfoldensis SKA53; Roseobacter sp. MED193; Roseovarius sp. 217
Type:
Expression profiling by array
Platform:
GPL10323
20 Samples
Download data: GPR
Series
Accession:
GSE21325
ID:
200021325
8.

Time-series analyses of Monterey Bay coastal microbial picoplankton using a “genome proxy” microarray

(Submitter supplied) To gain improved temporal, spatial and phylogenetic resolution of marine microbial communities, in this study we expanded the original prototype genome proxy array (an oligonucleotide microarray targeting marine microbial genome fragments and genomes), evaluated it against metagenomic sequencing, and applied it to time series samples from the Monterey Bay long term ecological research site. The expanded array targeted 268 microbial genotypes (vs. more...
Organism:
uncultured marine bacterium 440; uncultured marine bacterium 583; marine metagenome; uncultured marine group II euryarchaeote EF100_57A08; uncultured marine alpha proteobacterium; uncultured Pseudomonadota bacterium; uncultured crenarchaeote 74A4; uncultured marine bacterium EB000_55B11; unidentified; uncultured marine bacterium 577; uncultured gamma proteobacterium eBACHOT4E07; uncultured proteobacterium 65D09; uncultured crenarchaeote 4B7; Prochlorococcus marinus subsp. pastoris str. CCMP1986; uncultured marine gamma proteobacterium EBAC31A08; uncultured marine group II euryarchaeote 37F11; uncultured marine bacterium EB0_41B09; uncultured proteobacterium 60D04
Type:
Other
Platform:
GPL10357
58 Samples
Download data: GPR
Series
Accession:
GSE21502
ID:
200021502
9.

Metatranscriptomes of phytoplankton blooms from an ocean acidification mesocosm experiment

(Submitter supplied) Sequencing the metatranscriptome can provide information about the response of organisms to varying environmental conditions. We present a methodology for obtaining random whole-community mRNA from a complex microbial assemblage using Pyrosequencing. The metatranscriptome had, with minimum contamination by ribosomal RNA, significant coverage of abundant transcripts, and included significantly more potentially novel proteins than in the metagenome. more...
Organism:
marine metagenome
Type:
Expression profiling by high throughput sequencing
Platform:
GPL26673
4 Samples
Download data: XLS
Series
Accession:
GSE10119
ID:
200010119
10.

Design and testing of genome-proxy microarrays to profile marine microbial communities

(Submitter supplied) Microarrays are useful tools for detecting and quantifying specific functional and phylogenetic genes in natural microbial communities. In order to track uncultivated microbial genotypes and their close relatives in an environmental context, we designed and implemented a “genome proxy” microarray that targets microbial genome fragments recovered directly from the environment. Fragments consisted of sequenced clones from large-insert genomic libraries from microbial communities in Monterey Bay, the Hawaii Ocean Time-series station ALOHA, and Antarctic coastal waters. more...
Organism:
uncultured marine alpha proteobacterium; uncultured Pseudomonadota bacterium; uncultured crenarchaeote 74A4; uncultured proteobacterium 65D09; uncultured marine group II euryarchaeote EF100_57A08; uncultured marine bacterium EB000_55B11; Prochlorococcus marinus str. MIT 9313; Prochlorococcus marinus str. MIT 9515; uncultured marine bacterium 577; uncultured gamma proteobacterium eBACHOT4E07; uncultured marine group II euryarchaeote 37F11; uncultured marine bacterium 440; uncultured marine bacterium 583; marine metagenome; uncultured crenarchaeote 4B7; Prochlorococcus marinus subsp. pastoris str. CCMP1986; Prochlorococcus marinus str. MIT 9312; uncultured marine gamma proteobacterium EBAC31A08; uncultured marine bacterium EB0_41B09; uncultured proteobacterium 60D04
Type:
Other
Platform:
GPL6012
28 Samples
Download data: GPR
Series
Accession:
GSE9384
ID:
200009384
11.

(marine metagenome)

Organism:
marine metagenome
1 Series
4 Samples
Download data
Platform
Accession:
GPL26673
ID:
100026673
12.

NimbleGen marine metagenome array [XM_Nov2012_RMB]

(Submitter supplied) 25 bp probes targeting the 16S rRNA of uncultivated microbes of mixed microbial communities Protocol: ITO coated glass slides
Organism:
marine metagenome
1 Series
17 Samples
Download data: NDF
Platform
Accession:
GPL20727
ID:
100020727
13.

NimbleGen Estuarine Microbial Community Array [Berkeley Pier; Od_Ps_Bpier_V3C]

(Submitter supplied) mixed community B_pier Protocol: on ITO glass slides functionalized with superepoxy2 by Arrayit
Organism:
marine metagenome
1 Series
5 Samples
Download data: NDF
Platform
Accession:
GPL18455
ID:
100018455
14.

Plymouth Marine Laboratory 454 sequences, 439K

Organism:
marine metagenome
Download data
Platform
Accession:
GPL6355
ID:
100006355
15.

C8 13C

Organism:
marine metagenome
Source name:
stable isotope incubations of Monterey Bay surface water
Platform:
GPL20727
Series:
GSE71228
Download data: TXT
Sample
Accession:
GSM1831013
ID:
301831013
16.

C7 13C

Organism:
marine metagenome
Source name:
stable isotope incubations of Monterey Bay surface water
Platform:
GPL20727
Series:
GSE71228
Download data: TXT
Sample
Accession:
GSM1831012
ID:
301831012
17.

C1 13C

Organism:
marine metagenome
Source name:
stable isotope incubations of Monterey Bay surface water
Platform:
GPL20727
Series:
GSE71228
Download data: TXT
Sample
Accession:
GSM1831011
ID:
301831011
18.

B8 13C

Organism:
marine metagenome
Source name:
stable isotope incubations of Monterey Bay surface water
Platform:
GPL20727
Series:
GSE71228
Download data: TXT
Sample
Accession:
GSM1831010
ID:
301831010
19.

B7 13C

Organism:
marine metagenome
Source name:
stable isotope incubations of Monterey Bay surface water
Platform:
GPL20727
Series:
GSE71228
Download data: TXT
Sample
Accession:
GSM1831009
ID:
301831009
20.

B1 13C

Organism:
marine metagenome
Source name:
stable isotope incubations of Monterey Bay surface water
Platform:
GPL20727
Series:
GSE71228
Download data: TXT
Sample
Accession:
GSM1831008
ID:
301831008
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