Dataset: MMETSP transcriptome sequences

Name: Eukaryote transcriptome assemblies and associated metadata available on iMicrobe (P-ExpEv project)
Published: 2016-05-20
Keywords: biota, oceans

Cite This Dataset

Spatial Extent: N:78.5922 E:166.75 S:-64.7667 W:-179.23

Project:

Impacts of Evolution on the Response of Phytoplankton Populations to Rising CO2 (P-ExpEv)

Program:

Science, Engineering and Education for Sustainability NSF-Wide Investment (SEES): Ocean Acidification (formerly CRI-OA) (SEES-OA)

Principal Investigator:

Sonya T. Dyhrman (Lamont-Doherty Earth Observatory, LDEO)

Co-Principal Investigator:

Michael J. Follows (Massachusetts Institute of Technology, MIT)

Richard E Lenski (Michigan State University, MSU)

James Jeffrey Morris (University of Alabama at Birmingham, UA/Birmingham)

BCO-DMO Data Manager:

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

Version Date:

2016-05-20

Restricted:

Validated:

Yes

Current State:

Final no updates expected

Eukaryote transcriptome assemblies and associated metadata available on iMicrobe (P-ExpEv project)

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Description

This dataset includes links to eukaryote transcriptome assemblies and associated metadata for species grown under replete nutrients and either modern or future CO2 concentrations. Further information on the overarching project and experiment details (e.g., nutrient concentrations, growth medium, GenBank BioSample IDs, etc) are available on iMicrobe MMETSP site: http://data.imicrobe.us/project/view/104 or by clicking on the accession numbers listed below.

Accession Species/condition
MMETSP0053 Prorocentrum minimum (Pmi): replete;modern CO2
MMETSP0057 Prorocentrum minimum (Pmi): replete; future CO2
MMETSP0088 Chaetoceros affinis (Caf): replete;modern CO2
MMETSP0092 Chaetoceros affinis (Caf): replete; future CO2
MMETSP0093 Alexandrium monilatum (Amo): replete;modern CO2
MMETSP0097 Alexandrium monilatum (Amo): replete; future CO2
MMETSP0143 Chyrsochromulina polylepis (Cpo): replete;modern CO2
MMETSP0147 Chrysochromulina polylepis (Cpo): replete; future CO2
MMETSP0292 Heterosigma akashiwo (Hak): replete;modern CO2
MMETSP0296 Heterosigma akashiwo (Hak): replete; future CO2
MMETSP1363 Gephyrocapsa oceanica (Goc): replete;modern CO2
MMETSP1364 Gephyrocapsa oceanica (Goc): replete; future CO2

Methods & Sampling

The workflow for transcriptome assembly is described on the MMETSP website and is available at: http://marinemicroeukaryotes.org/home/faq. Sequencing was done by the National Center for Genome Resources (NCGR).

Data Files

File
MMETSP_data.csv (Comma Separated Values (.csv), 1.72 KB) MD5:5e08b3166bd653228d79ef4be6275ea9 Primary data file for dataset ID 646128

More Information about this dataset

Funding Sources

Funding Source	Award Number
NSF Division of Ocean Sciences	OCE-1314336

Deployments

Deployment	Synonyms	Start Date	Platform	Investigator
Dyhrman_2013		2013-01-01	LDEO	Sonya T. Dyhrman (Principal Investigator)	data info

Instruments

Automated DNA Sequencer

Supplied Name:

Supplied Description:

Pacific Biosciences RS and Illumina HiSeq 2000 at NCGR

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

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

Supplied Name	Supplied description	Supplied Units	Standard Name
external_link	link to iMicrobe data repository	text	external_link
brief_desc	brief description of link	text	brief_desc

Status message

Database

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Dataset: MMETSP transcriptome sequences