GEO DataSets

(Submitter supplied) The fate of the carbon stocked in permafrost soils following global warming and permafrost thaw is of major concern in view of the potential for increased CH4 and CO2 emissions from these soils. Complex carbon compound degradation and greenhouse gas emissions are due to soil microbial communities, but their composition and functional potential in permafrost soils are largely unknown. Here, a 2 m deep permafrost and its overlying active layer soil were subjected to metagenome sequencing, quantitative PCR, and microarray analyses. more...

Organism:

Archaea; environmental samples; environmental samples; environmental samples; Bacteria; environmental samples

Type:

Other

Platform:

GPL8953

10 Samples

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(Submitter supplied) The 16S rRNA gene probe design for the microarray was as follows: 1) database searches in Greengenes (http://greengenes.lbl.gov) for 16S rRNA gene sequences with keywords "Arctic," "Antarctic," "Polar," "Cold," "Psychro" (2891 sequences retrieved, performed on April 15th, 2008); 2) clustering of the database sequences together with 16S rRNA gene sequences from strains isolated in our lab in previous studies of polar environments using Blastclust (NCBI, Bethesda, MD); 3) design of five 25-mer probes for each of the 99%-similarity clusters having 3 or more representatives using OligoPicker (32); 4) elimination of probes having a ΔG >-3 kJ; 5) BLAST comparison of the central 17 nucleotides of each probe against all the original sequences; 6) selection, for each cluster, of the probe that showed less significant hits to sequences outside the cluster and most significant hits within the cluster. more...

Organism:

Bacteria; Archaea

5 Series

115 Samples

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