Dataset: DNA Time Series

Name: DNA metagenomic library statistics from HOT cruises from 2007-2009 (C-MORE project, HOT project)
Published: 2015-04-01
Keywords: biota, oceans

Cite This Dataset

Spatial Extent: N:22.75 E:-158 S:22.75 W:-158

Project:

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

[Current] Hawaii Ocean Time-series (HOT): 2023-2028; [Previous] Hawaii Ocean Time-series (HOT): Sustaining ocean ecosystem and climate observations in the North Pacific Subtropical Gyre (HOT)

Program:

Ocean Carbon and Biogeochemistry (OCB)

U.S. Joint Global Ocean Flux Study (U.S. JGOFS)

Ocean Time-series Sites (Ocean Time-series)

Principal Investigator:

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:

01 April 2015

Version Date:

2015-04-01

Restricted:

Current State:

Final no updates expected

DNA metagenomic library statistics from HOT cruises from 2007-2009 (C-MORE project, HOT project)

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Description

HOT DNA metagenomic library statistics

Location: The vicinity of Station ALOHA (22.75 N, 158.0 W) just north of Hawaii.

CMORE RNA and DNA Archive

Goal: The goal of this effort is to provide a time series collection of planktonic microbial DNA and RNA depth profiles from the HOT station, for CMORE research. DNA and RNA samples will be available for researchers to conduct and coordinate taxonomic and functional gene studies, for example using PCR and RT-PCR methods. Sequencing files are available as an NCBI BioProject (PRJNA16339)

Activity: Collect microbial cell fraction (1.6um prefiltered, >0.22um) from HOT hydrocasts, and extract nucleic acids, for RNA and DNA for downstream analyses by CMORE investigators. Collection depths are 25m, 45m, 75m, 125m, 200m, 500m, 770m and 1000m. Extracted DNA samples will be available for distribution.

Methods & Sampling

DeLong_CMORE_DNA_Sampling_protocol

Data Processing Description

DeLong_CMORE_DNA_Sampling_protocol

# C-MORE HOT metagenomic library statistics
# DeLong Lab - Massachusetts Institute of Technology
# Ed DeLong
# Original file : HOT_DNATime_Series_25m_500m_sequences.xls
# Ingested into BCO-DMO: April 1 2015

BCO-DMO Processing (2018.04.30): Parameter "16S_reads" was edited to "reads_16S" to conform to internal software conventions.

Data Files

File
dna_timeseries.csv (Comma Separated Values (.csv), 6.53 KB) MD5:dea31328d71fdfe5352896894c9730f5 Primary data file for dataset ID 555520

More Information about this dataset

Funding Sources

Funding Source	Award Number
NSF Division of Ocean Sciences	OCE-0926766
NSF Division of Biological Infrastructure	DBI-0424599

Deployments

Deployment	Synonyms	Start Date	Platform	Investigator
HOT_cruises	Hawaii Ocean Time-series cruises	1988-10-31	Multiple Vessels	Angelicque E. White (Principal Investigator) David M. Karl (Co-Principal Investigator) James Potemra (Co-Principal Investigator)	data info

Instruments

None available yet

Parameters

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

Supplied Name	Supplied description	Supplied Units	Standard Name
cruise_id	cruise ID	dimensionless	cruise_id
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
time	time (GMT)	HHMM	time
sequencing_chemistry	sequencing chemistry	dimensionless	no_bcodmo_term
non_dup_reads	number of non duplicated reads	dimensionless	no_bcodmo_term
reads_16S	number of 16S reads	dimensionless	no_bcodmo_term
read_length	average read length	dimensionless	no_bcodmo_term
SRX	NCBI SRX accession number	dimensionless	no_bcodmo_term

Status message

Database

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Dataset: DNA Time Series