<div><p><strong>DNA extraction and purification</strong></p>
<p>DNA was extracted, in duplicate, from 8 to 20 g of of “Mobio” IODP sediment samples previously frozen at -80C using a Powersoil total RNA Isolation Kit with the DNA Elution Accessory Kit (MO-BIO Laboratories, Solana Beach, CA, USA) following the manufacturer protocol but without beads. Approximately 2 grams of sediments were utilized for each extraction, and DNA pellets from each depth were pooled together. DNA concentrations were measured using a Qubit 2.0 fluorometer with dsDNA High Sensitivity reagents (Invitrogen, Grand Island, NY, USA). The DNA from the extractions that yielded robust 16S rRNA and metagenomic sequences ranged from 3.75-15 ng of DNA per gram of sediments.</p>
<p><strong>Multiple Displacement Amplification (MDA)</strong></p>
<p>DNA was amplified using a REPLI-g Single Cell Kit (Qiagen, Germantown, MD, USA). Tubes, tube caps and reverse transcription-PCR grade water (Ambion, Grand Island, NY, USA) were UV-treated for 15 min in a PCR laminar flow hood. Quantitative PCR showed that the negative control began amplifying after 5 hr of incubation at 30°C, and therefore, the 30°C incubation step was shortened to 5 hr using a Bio-Rad C1000 Touch thermal cycler (Bio-Rad, Hercules, CA, USA). DNA concentrations were measured in duplicate on a Qubit 2.0 with dsDNA High Sensitivity reagents (Invitrogen, Grand Island, NY, USA).</p>
<p><strong>Illumina library preparation and sequencing</strong></p>
<p>Two micrograms of MDA DNA were used to generate genome libraries using a TruSeq DNA PCR-Free Kit following the manufacturer’s protocol (Illumina, San Diego, CA, USA). The resulting libraries were sequenced using a Rapid-Run on an Illumina HiSeq 2500 (Center for Integrative Genomics, Georgia Institute of Technology) to obtain 100 bp paired-end reads</p></div>
NCBI accession numbers for metagenomic sequences: IODP Site 1244, Hydrate Ridge, offshore Oregon
<div><p>This dataset was generated under a C-DEBI research grant.</p>
<p><strong>Related References:</strong></p>
<p>Tréhu, A.M, Bohrmann, G., Rack, F.R., Torres, M.E., et al., 2003. Proc. ODP, Init. Repts., 204: College Station, TX (Ocean Drilling Program).doi:10.2973/odp.proc.ir.204.2003</p>
<p>Shipboard Scientific Party, 2003. Site 1244. In Tréhu, A.M, Bohrmann, G., Rack, F.R., Torres, M.E., et al., Proc. ODP, Init. Repts., 204: College Station, TX (Ocean Drilling Program), 1–132. doi:10.2973/odp.proc.ir.204.103.2003</p>
<p>Tréhu, A.M., Bohrmann, G., Torres, M.E., and Colwell, F.S. (Eds.), 2006. Proc. ODP, Sci. Results, 204: College Station, TX (Ocean Drilling Program).doi:10.2973/odp.proc.sr.204.2006</p></div>
Metagenomic sequences: IODP Site 1244
<div><p><strong>BCO-DMO Processing</strong>:<br />
- Added cruise_id, lat and lon columns and created live links to NCBI pages.</p></div>
626776
Metagenomic sequences: IODP Site 1244
2015-11-20T11:29:55-05:00
2015-11-20T11:29:55-05:00
2023-07-07T16:10:26-04:00
urn:bcodmo:dataset:626776
NCBI accession numbers for metagenomic sequences collected from the R/V JOIDES Resolution (JRES-204) cruise in the Cascadia Continental Margin during 2002 (Methane-Hydrate Sediment Omics project)
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Glass, J. B. (2015) NCBI accession numbers for metagenomic sequences collected from the R/V JOIDES Resolution (JRES-204) cruise in the Cascadia Continental Margin during 2002 (Methane-Hydrate Sediment Omics project). Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 2015-12-02) Version Date 2015-12-02 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/626776 [access date]
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