UO Data

Permanent URI for this collection

https://hdl.handle.net/1794/12310

Browse

Browsing UO Data by Subject "Amazon rainforest"

Now showing 1 - 1 of 1
  • ItemOpen Access
    Amazon Rainforest Microbial Observatory Metagenomes
    (University of Oregon, 2010-04) Bohannan, Brendan J. M.; Meyer, Kyle M.; Klein, Ann M.; Rodrigues, Jorge L. M.; Nusslein, Klaus; Tringe, Susannah G.; Mirza, Babur S.; Tiedje, James M.
    This data archive contains 79 files of quality-filtered, shotgun metagenomic DNA sequence data generated as part of the Amazon Rainforest Microbial Observatory (ARMO) project. Ten soil cores were collected from Amazon Rainforest Microbial Observatory in April 2010 (5 soil cores from primary rainforest and 5 from a 38 year-old converted pasture). Soil was sampled to a depth of 10 cm (after removal of the litter layer) using standard coring methods and homogenized. Samples were frozen on the spot, transported on dry ice, and stored at -80° C until extraction. DNA was extracted from five soil subsamples per core (i.e. 50 extractions per 10 soil cores). Metagenomic libraries were constructed from the 10 samples using the Illumina TruSeq kit with ~270 bp insert sizes according to standard protocol. Sequencing of 150 bp paired-end reads was performed on the Illumina HiSeq platform at the Joint Genome Institute. In total, 21 lanes (2-3 lanes per sample) were sequenced to produce 6.4 billion paired-end reads, resulting in an average of 636 million (±12%) reads per sample. Raw sequences were uploaded to MG-RAST (http://metagenomics.anl.gov), and paired-end reads were joined using fastq-join as part of the MG-RAST pipeline. Single end reads that could not be joined were retained. After merging paired-end reads, a total of 6.3 billion sequences with an average length of 171 bp were processed through the MG-RAST pipeline. All other pipeline options were left as default (i.e. trimming of low quality bases, removal of artificial replicate sequences, and filtering of sequences with greater than 5 ambiguous bases). Also included are two OTU tables (community matrices).