<div><p>Water samples were collected from Marsh Landing Dock on Sapelo Island GA, prefiltered through a 3 micron membrane filter to remove most eukaryotic microbes, and incubated in 10 L carboys in situ in the dark for 24 h. At the beginning and end of the incubation, three carboys were sacrificed for nucleic acid extraction on 0.2 micron membrane filters, and microbial transcripts were analyzed from two of the three replicates according to methods in Satinsky et al. 2013 and 2014 and protocols.io (<a href="https://www.protocols.io/g/moran-lab">https://www.protocols.io/g/moran-lab</a>).</p></div>
Taxonomic binning of transcripts from samples collected during the SIMCO1 and SIMCO2
<div><p>Incubation experiments examining concurrent changes in DOC composition and microbial transcription patterns were carried out in July 2014 (SIMCO1) and October 2014 (SIMCO2) at Sapelo Island, GA. This dataset contains the taxonomic assignments of transcripts to reference genome bins. Cells were collected by filtration at the time of initial surface water collection (Time 0) and after a 24 hr incubation (Time 24) for both high and low tide water collections on each of the two sample dates. Filters were processed for RNA extraction and mRNA-enriched material was sequenced on an Illumina HiSeq2500 run to produce single-end 250 bp reads.</p></div>
SIMCO 1 and 2: Taxonomic transcript bins
<div><p>Reads were put through a quality control pipeline that removed rRNAs and internal standards added for quantification (Satinsky et al. 2013). Putative protein encoding reads were analyzed by RAPSearch2 (<a href="http://omics.informatics.indiana.edu/mg/RAPSearch2/">http://omics.informatics.indiana.edu/mg/RAPSearch2/</a>) against a custom reference database of genomes and transcriptomes compiled from marine bacteria, archaea, and microbial eukaryotes; the database is available for download at: <a href="http://ssharma.marsci.uga.edu/Lab/MarineRef2/">http://ssharma.marsci.uga.edu/Lab/MarineRef2/</a>.</p>
<p><strong>References:</strong><br />
Brandon M. Satinsky, Scott M. Gifford, Byron C. Crump, Mary Ann Moran, 2013. Chapter 12: "Use of Internal Standards for Quantitative Metatranscriptome and Metagenome Analysis" in Methods in Enzymology, Vol. 531. ISSN 0076-6879, <a href="https://dx.doi.org/10.1016/B978-0-12-407863-5.00012-5">http://dx.doi.org/10.1016/B978-0-12-407863-5.00012-5</a>.</p>
<p>Brandon M. Satinskya, Byron C. Crumpb, Christa B. Smithc, Shalabh Sharmac, Brian L. Zielinskid, Mary Dohertye, Jun Mengc, Shulei Sunf, Patricia M. Medeirosc, John H. Pauld, Victoria J. Colese, Patricia L. Yagerc, and Mary Ann Moranc. 2014. Microspatial gene expression patterns in the Amazon River Plume. PNAS 111(30):11085-11090. <a href="/objectserver/f5c71d05af4addd7285f5b19869264a1/pnas.1402782111?url=http%3A%2F%2Fwww.pnas.org%2Fcgi%2Fdoi%2F10.1073%2Fpnas.1402782111&f=3939333030363636653964333937653636353933316366623265653764303431687474703a2f2f7777772e706e61732e6f72672f6367692f646f692f31302e313037332f706e61732e31343032373832313131">www.pnas.org/cgi/doi/10.1073/pnas.1402782111</a></p>
<p><strong>BCO-DMO Processing:</strong><br />
- added conventional header with dataset name, PI name, version date<br />
- column names reformatted to comply with BCO-DMO standards<br />
- replaced spaces with underscores<br />
- replaced commas with semi-colons<br />
- replaced str. and Strain with strain</p></div>
661835
SIMCO 1 and 2: Taxonomic transcript bins
2016-10-18T11:52:29-04:00
2016-10-18T11:52:29-04:00
2023-07-07T16:10:26-04:00
urn:bcodmo:dataset:661835
Taxonomic binning of transcripts from samples collected during the SIMCO1 (July 2014) and SIMCO2 (Oct 2014) incubation experiments on the linkage between DOM changes and microbial transcription patterns at Sapelo Island, GA.
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Moran, M. Ann (2016) Taxonomic binning of transcripts from samples collected during the SIMCO1 (July 2014) and SIMCO2 (Oct 2014) incubation experiments on the linkage between DOM changes and microbial transcription patterns at Sapelo Island, GA. Biological and Chemical Oceanography Data Management Office (BCO-DMO). Version Date 2016-10-26 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/661835 [access date]
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