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SRX007369: HOT186_75m_gDNA
2 LS454 (454 GS FLX) runs: 673,674 spots, 164.1M bases, 406.1Mb downloads

Accession: SRX007369
Experiment design: n/a
Submitted by: Massachusetts Institute of Technology
Study summary: SRP000109 • Planktonic microbial communities from North Pacific Subtropical Gyre • PRJNA16339 • All experiments  • Run Selector (more...)(less...)
Abstract: <p> This project consists of analyses of of planktonic microbial communities in a region of the North Pacific Ocean. The Subtropical Gyre consists of a clockwise swirling vortex of ocean currents that make up most of the northern Pacific Ocean. Samples were taken at different depths (10 m to 4000 m) at the Hawaii open-ocean time-series station ALOHA (22<sup>o</sup>45' N, 158<sup>o</sup>W) and large DNA fragments were cloned (36 kbp fosmids) from the samples and shotgun sequenced. A comparison of protein sequences encoded by samples at various depths and clustering of functional categories revealed definite gradients. For example, proteins involved in photosynthesis were found in the photic zone, as expected, while proteins involved in surface attachment were more prevalent in deep samples, suggesting a greater tendency for surface colonization at those ocean depths. </p> There are a set of GenBank Accession Numbers associated with this study. <a href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?holding=&amp;amp;db=Nucleotide&amp;cmd=search&amp;term=DU731018:DU796676[accn]">DU731018-DU796676 </a>and <a href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?holding=&amp;db=Nucleotide&amp;cmd=search&amp;term=DU800850:DU800864[accn]">DU800850-DU800864 </a>correspond to fosmid end sequences while <a href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?holding=&amp;db=Nucleotide&amp;cmd=search&amp;term=DQ300508:DQ300926[accn]">DQ300508-DQ300926</a> are the small subunit ribosomal RNA sequences. <p> In addition <a href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?holding=&amp;db=Nucleotide&amp;cmd=search&amp;term=EF089401:EF089402[accn]">EF089401-EF089402 </a>, <a href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?holding=&amp;db=Nucleotide&amp;cmd=search&amp;term=EF100190:EF100191[accn]">EF100190-EF100191 </a>, <a href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?holding=&amp;db=Nucleotide&amp;cmd=search&amp;term=EF107101:EF107103[accn]">EF107101-EF107103 </a>, <a href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?holding=&amp;db=Nucleotide&amp;cmd=search&amp;term=EF107106[accn]">EF107106 </a>, <a href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?holding=&amp;db=Nucleotide&amp;cmd=search&amp;term=EU016559:EU016674[accn]">EU016559-EU016674 </a> and <a href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?holding=&amp;db=Nucleotide&amp;cmd=search&amp;term=GQ412706:GQ412710[accn]">GQ412706-GQ412710 </a> are genomic sequences derived from this study. </p> <p> 454 sequence data is available from the Short Read Archive (SRA): <a href="ftp://ftp.ncbi.nih.gov/pub/TraceDB/ShortRead/SRA000262 ">SRA000262</a> and <a href="ftp://ftp.ncbi.nih.gov/pub/TraceDB/ShortRead/SRA000263 ">SRA000263</a>.</p>
Center Project: North Pacific Subtropical Gyre Planktonic Microbial Community
Sample: SAMN00002903 • Generic sample from marine metagenome (more...)(less...)
Library: HOT186_75m_gDNA  (more...)(less...)
Strategy: WGS
Source: GENOMIC
Selection: RANDOM
Layout: SINGLE
Platform: LS454  (more...)(less...)
Instrument model: 454 GS FLX
Spot descriptor:
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Total: 2 runs, 673,674 spots, 164.1M bases, 406.1Mb 
#Run# of Spots# of BasesSizePublished
1. SRR020488462,768124M293.8Mb2009-10-01
2. SRR020489210,90640.2M112.3Mb2009-10-01

ID:
7635

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