Dataset: SIMCO 1 and 2: Taxonomic transcript bins
Deployment: Moran_Sapelo_2012-14

Taxonomic binning of transcripts from samples collected during the SIMCO1 and SIMCO2

Principal Investigator:

Mary Ann Moran (University of Georgia, UGA)

BCO-DMO Data Manager:

Nancy Copley (Woods Hole Oceanographic Institution, WHOI BCO-DMO)

Project:

High Resolution Linkages Between DOC Turnover and Bacterioplankton in a Coastal Ocean (SIMCO)

Current State:

Final no updates expected

Version Date:

2016-10-18

Data URL:

https://osprey.bco-dmo.org/dataset-deployment/661865/data

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Description

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.

Methods & Sampling

Dataset acquisition description

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 (https://www.protocols.io/g/moran-lab).

Data Processing Description

Dataset Processing Description

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 (http://omics.informatics.indiana.edu/mg/RAPSearch2/) against a custom reference database of genomes and transcriptomes compiled from marine bacteria, archaea, and microbial eukaryotes; the database is available for download at: http://ssharma.marsci.uga.edu/Lab/MarineRef2/.

References:
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, http://dx.doi.org/10.1016/B978-0-12-407863-5.00012-5.

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. www.pnas.org/cgi/doi/10.1073/pnas.1402782111

BCO-DMO Processing:
- added conventional header with dataset name, PI name, version date
- column names reformatted to comply with BCO-DMO standards
- replaced spaces with underscores
- replaced commas with semi-colons
- replaced str. and Strain with strain

More information about this dataset deployment

Funding

Award Number	Funding Source
OCE-1356010	NSF Division of Ocean Sciences

Instruments

Automated DNA Sequencer

Supplied Name: Illumina HiSeq2500

Supplied Description:

mRNA-enriched material was sequenced

Instrument Type

Generic Name: Automated DNA Sequencer

Acronym: Automated Sequencer

Generic Description:

General term for a laboratory instrument used for deciphering the order of bases in a strand of DNA. Sanger sequencers detect fluorescence from different dyes that are used to identify the A, C, G, and T extension reactions. Contemporary or Pyrosequencer methods are based on detecting the activity of DNA polymerase (a DNA synthesizing enzyme) with another chemoluminescent enzyme. Essentially, the method allows sequencing of a single strand of DNA by synthesizing the complementary strand along it, one base pair at a time, and detecting which base was actually added at each step.

Parameters

Supplied Name	Supplied description	Supplied Units	Standard Name
sample	sample identification: S1 or S2 = SIMCO experiment 1 or 2; L = low tide; H = high tide; 0 = 0 hour incubation; 24 = 24 hour incubation	unitless	sample
organism_strain	description of organism and strain	unitless	sample_descrip
transcripts_per_L	number of transcripts per liter	transcripts/liter	count

Database

Contribute Data

Dataset: SIMCO 1 and 2: Taxonomic transcript bins
Deployment: Moran_Sapelo_2012-14

Dataset acquisition description

Dataset Processing Description

Database

Contribute Data

Dataset: SIMCO 1 and 2: Taxonomic transcript binsDeployment: Moran_Sapelo_2012-14

Dataset acquisition description

Dataset Processing Description

Dataset: SIMCO 1 and 2: Taxonomic transcript bins
Deployment: Moran_Sapelo_2012-14