GEO DataSets

(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:

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; uncultured marine alpha proteobacterium; uncultured proteobacterium; uncultured crenarchaeote 74A4; uncultured marine bacterium EB000_55B11; uncultured marine bacterium 440; uncultured marine bacterium 583; marine metagenome; uncultured marine group II euryarchaeote EF100_57A08

Type:

Other

Platform:

GPL10357

58 Samples

Download data: GPR

(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 crenarchaeote 74A4; uncultured proteobacterium 65D09; uncultured marine group II euryarchaeote EF100_57A08; uncultured marine bacterium EB000_55B11; Prochlorococcus marinus str. MIT 9313; uncultured proteobacterium; Prochlorococcus marinus str. MIT 9515; uncultured marine bacterium 577; uncultured gamma proteobacterium eBACHOT4E07; 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; uncultured marine group II euryarchaeote 37F11; uncultured marine bacterium 440; uncultured marine bacterium 583; marine metagenome

Type:

Other

Platform:

GPL6012

28 Samples

Download data: GPR

(Submitter supplied) update to platform GPL6012. DeLongLab_GenomeProxyArray_v2.0_268targets. Note supplementary platform for full array design and sequences of probes. Protocol: Glass slides with poly-lysine coating. The expanded genome proxy array was designed as in (Rich et al., 2008). Briefly, each genotype was targeted using suites of ~20 70-mer oligonucleotide probes designed using the program ArrayOligoSelector (Zhu et al., 2003). more...

Organism:

uncultured crenarchaeote 4B7; Prochlorococcus marinus subsp. pastoris str. CCMP1986; uncultured marine alpha proteobacterium; uncultured marine gamma proteobacterium EBAC31A08; uncultured marine group II euryarchaeote 37F11; uncultured proteobacterium; uncultured crenarchaeote 74A4; uncultured marine bacterium 440; uncultured marine bacterium 577; uncultured marine bacterium 583; uncultured gamma proteobacterium eBACHOT4E07; uncultured marine bacterium EB0_41B09; uncultured proteobacterium 60D04; uncultured proteobacterium 65D09; uncultured marine group II euryarchaeote EF100_57A08; uncultured marine bacterium EB000_55B11

1 Series

58 Samples

Download data: TXT

(Submitter supplied) ***Design Overview*** The prototype microarray targeted thirteen BAC or fosmid genome fragments (20-160kb) from both bacteria and archaea (Table 1), recovered from a variety of marine habitats (Table 2), as well as the cyanobacterium Prochlorococcus MED4. These clones were originally sequenced because of the presence of taxonomic marker or specific functional genes. This array consisted of sets of 70-bp oligonucleotides targeting each genome or genome fragment (Fig. more...

Organism:

uncultured crenarchaeote 4B7; Prochlorococcus marinus subsp. pastoris str. CCMP1986; uncultured marine alpha proteobacterium; uncultured marine gamma proteobacterium EBAC31A08; uncultured marine group II euryarchaeote 37F11; uncultured proteobacterium; uncultured crenarchaeote 74A4; uncultured marine bacterium 440; uncultured marine bacterium 577; uncultured marine bacterium 583; uncultured gamma proteobacterium eBACHOT4E07; uncultured marine bacterium EB0_41B09; uncultured proteobacterium 60D04; uncultured proteobacterium 65D09; uncultured marine group II euryarchaeote EF100_57A08; uncultured marine bacterium EB000_55B11

1 Series

28 Samples

Download data