Dataset: Diel_Metatrans

Name: Diel metatranscriptome study in Monterey Bay, California, USA from August to September 2012 (C-MORE project, CANON project)
Published: 2015-04-16
Keywords: biota, oceans

Cite This Dataset

Spatial Extent: N:36.5 E:-122.2 S:35.7 W:-122.7

Project:

Center for Microbial Oceanography: Research and Education (C-MORE)

Controlled, Agile, and Novel Observing Network (CANON)

Principal Investigator:

Edward DeLong (Massachusetts Institute of Technology, MIT-Dept CEE)

Contact:

Edward DeLong (Massachusetts Institute of Technology, MIT-Dept CEE)

Data Manager:

Jasmine Nahorniak (Oregon State University, OSU-CEOAS)

BCO-DMO Data Manager:

Stephen R. Gegg (Woods Hole Oceanographic Institution, WHOI BCO-DMO)

Version:

16 April 2015

Version Date:

2015-04-16

Restricted:

Current State:

Final no updates expected

Diel metatranscriptome study in Monterey Bay, California, USA from August to September 2012 (C-MORE project, CANON project)

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Description

Diel metatranscriptome study in Monterey Bay, 2012.

Data from the accession numbers listed below can be accessed from NCBI (http://www.ncbi.nlm.nih.gov/).

GenBank accession numbers
BioProject: PRJNA268385 (http://www.ncbi.nlm.nih.gov/bioproject/PRJNA268385)
SRP: SRP050269 (http://www.ncbi.nlm.nih.gov/sra/?term=SRP050269)

Data Processing Description

# C-MORE Monterey Bay diel metatranscriptome study
# DeLong Lab - Massachusetts Institute of Technology
# Ed DeLong
# CMORE/MontereyBay
# Date ingested into BCO-DMO: April 16 2015

Data Files

File
diel_metatrans.csv (Comma Separated Values (.csv), 9.30 KB) MD5:6c22dce891af73ad13b43a67260abd59 Primary data file for dataset ID 555991

More Information about this dataset

Funding Sources

Funding Source	Award Number
NSF Division of Biological Infrastructure	DBI-0424599
Gordon and Betty Moore Foundation	unknown C-MORE Moore
US Department of Energy	unknown C-MORE DOE

Deployments

Deployment	Synonyms	Start Date	Platform	Investigator
CANON_2012_ESP		2012-08-31	Environmental Sample Processor	Dr Chris Scholin (Chief Scientist) Francisco Chavez (Co-Chief Scientist)	data info

Instruments

Environmental Sample Processor

Supplied Name: Environmental Sample Processor (ESP)

Supplied Description:

Environmental Sample Processor (ESP)

Instrument Type

Generic Name: Environmental Sample Processor

Acronym: ESP

Generic Description:

The MBARI Environmental Sample Processor—the ESP—provides on-site (in situ) collection and analysis of water samples from the subsurface ocean. The instrument is an electromechanical/fluidic system designed to collect discrete water samples, concentrate microorganisms or particles, and automate application of molecular probes and qPCR which identify microorganisms and their gene products. The ESP also archives samples so that further analyses may be done after the instrument is recovered.

Environmental Sample Processor

See references below for methodology used on the ESP:
Greenfield, D.I., R. Marin III, S. Jensen, E. Massion, B. Roman, J. Feldman, C. Scholin (2006). Application of the Environmental Sample Processor (ESP) methodology for quantifying Pseudo-nitzschia australis using ribosomal RNA-targeted probes in sandwich and fluorescent in situ hybridization. Limnology and Oceanography: Methods 4: 426-435.

Greenfield, D., R. Marin III, G.J. Doucette, C. Mikulski, S. Jensen, B. Roman, N. Alvarado, and C.A. Scholin (2008). Field applications of the second-generation Environmental Sample Processor (ESP) for remote detection of harmful algae: 2006-2007. Limnology and Oceanography: Methods 6: 667-679.

Marin III, R., and C. Scholin (2010). Sandwich Hybridization. In: Microscopic and molecular methods for quantitative phytoplankton analysis (Chapter 12), edited by B. Karlson, C. Cusack, and E. Bresnan, E.. IOC Manuals and Guides, no. 55. (IOC/2010/MG/55) Paris, UNESCO. 110 pp.

Ottesen, E.A., R. Marin III, C.M. Preston, C.R. Young, J.P. Ryan, C.A. Scholin, and E.F. DeLong (2011). Metatranscriptomic analysis of autonomously collected and preserved marine bacterioplankton. The ISME Journal, 5: 1881-1895, doi: 10.1038/ismej.2011.70.

Ottesen, E.A., C.R. Young, J.M. Eppley, J.P. Ryan, F.P. Chavez, C.A. Scholin, and E.F. DeLong (2013). Pattern and synchrony of gene expression among sympatric marine microbial populations. Proceedings of the National Academy of Sciences, 110: E488-E497, doi: 10.1073/pnas.1222099110.

Ottesen, E.A., C.M. Young, S.M. Gifford, J.M. Eppley, R. Marin III, S.C. Schuster, C.A. Scholin, and E.F. DeLong (2014). Multispecies diel transcriptional oscillations in open ocean heterotrophic bacterial assemblages. Science, 345: 207-212, 10.1126/science.1252476.

Preston, C.M., A. Harris, J.P. Ryan, B. Roman, R. Marin III, S. Jensen, C. Everlove, J. Birch, J.M. Dzenitis, D. Pargett, M. Adachi, K. Turk, J.P. Zehr, and C.A. Scholin (2011). Underwater application of quantitative PCR on an ocean mooring. PLoS ONE, 6:e22522, doi: 10.1371/journal.pone.0022522.

Robidart, J.C., C.M. Preston, R.W. Paerl, K.A. Turk, A.C. Mosier, C.A. Francis, C.A. Scholin, and J.P. Zehr (2011). Seasonal Synechococcus and Thaumarchaeal population dynamics examined with high resolution with remote in situ instrumentation. The ISME Journal, 6: 513-523, doi: 10.1038/ismej.2011.127.

Robidart, J., M.J. Church, J.P. Ryan, F. Ascani, S.T. Wilson, D. Bombar, R. Marin III, K.J. Richards, D.M. Karl, C.A. Scholin, and J.P Zehr (2014). Ecogenomic sensor reveals controls on N2-fixing microorganisms in the North Pacific Ocean. The ISME Journal, 8: 1175-1185, 10.1038/ismej.2013.244.

Saito, M.A., V.V. Bulygin, D.M. Moran, C. Taylor, and C. Scholin (2011). Examination of microbial proteome preservation techniques applicable to autonomous environmental sample collection. Frontiers in Aquatic Microbiology, 2: doi: 10.3389/fmicb.2011.00215.

Scholin, C.. (2010). What are “ecogenomic sensors?” A review and thoughts for the future. Ocean Science 6: 51-60.

Ussler III, W., C.M. Preston, P. Tavormina, D. Pargett, S. Jensen, B. Roman, R. Marin III, S.R. Shah, P.R. Girguis, J.M. Birch, V.J. Orphan, and C. Scholin (2013). Autonomous application of quantitative PCR in the deep sea: In situ surveys of aerobic methanotrophs using the deep-sea Environmental Sample Processor. Environmental Science and Technology, 47: 9339–9346, doi: 10.1021/es4023199.

Varaljay, V.A, J. Robidart, C.M. Preston, S.M. Gifford, B. Durham, A.S. Burns, J.P. Ryan, R. Marin III, R.P. Kiene, J.P Zehr, C.A. Scholin, M. Moran. 2015. Single-taxon field measurements of bacterial gene regulation controlling DMSP fate. ISME Journal, doi:10.1038/ismej.2015.23|

Parameters

Date and time formats are described in python strftime() syntax.

Supplied Name	Supplied description	Supplied Units	Standard Name
lat	latitude (positive north)	decimal degrees	lat
lon	longitude (positive east)	decimal degrees	lon
sample	sample ID	dimensionless	sample
depth	depth	meters	depth
date	date	YYYYMMDD	date
BioProject	NCBI BioProject accession number	dimensionless	accession_number
SRX	NCBI SRX accession number	dimensionless	accession_number
BioSample	NCBI BioSample accession number	dimensionless	accession_number

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Database

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Dataset: Diel_Metatrans