Dataset: Thaps microarrays - ISB

Name: Experimental results: microarrays for Thalassiosira pseudonana diatoms grown in the laboratory under different conditions; 2013 (OA Diatom Response project)
Published: 2015-01-30
Keywords: biota, oceans

Cite This Dataset

Project:

A Systems Biology Approach to Characterize Diatom Response to Ocean Acidification and Climate Change (OA Diatom Response)

Program:

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

Principal Investigator:

Monica V. Orellana (Institute for Systems Biology, ISB)

Co-Principal Investigator:

Nitin Baliga (Institute for Systems Biology, ISB)

Contact:

Dr Justin Ashworth (Institute for Systems Biology, ISB)

BCO-DMO Data Manager:

Shannon Rauch (Woods Hole Oceanographic Institution, WHOI BCO-DMO)

Version:

30 Jan 2015

Version Date:

2015-01-30

Validated:

Yes

Current State:

Final with updates expected

Experimental results: microarrays for Thalassiosira pseudonana diatoms grown in the laboratory under different conditions; 2013 (OA Diatom Response project)

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Description

Microarrays for Thalassiosira pseudonana diatoms grown in the laboratory under different conditions including
diel cycles and elevated CO2 levels.

Data from Ashworth et al. (2013) Proc. Natl. Acad. Sci. USA 110(18):7518-23 are publicly available on the NCBI GEO database under the accession code: GSE45252.

Data were submitted to the NCBI GEO database on May 16, 2014 under the accession code: GSE57737 and will be made publicly available upon publication of an accompanying manuscript in preparation.

References:
Ashworth J, Coesel S, Lee A, Armbrust EV, Orellana MO*, Baliga NS*. (2013) Genome-wide diel growth state transitions in the diatom Thalassiosira pseudonana. Proc. Natl. Acad. Sci. 110(18):7518-23. doi:10.1073/pnas.1300962110

Methods & Sampling

Transcriptomic profiling of the diatom Thalassiosira pseudonana at normal and elevlated CO2 levels and at normal and elevated light levels. Common reference total RNA (Agilent Quick-Amp Cy3-labeled) was used in all arrays as an internal standard. Triplicate batch cultures grown at normal (~400 ppm) and elevated (~800 ppm) CO2 levels, both at i) normal or ii) elevated light levels. Samples were taken during a) exponential and b) stationary growth during all growth experiments.

Result: 48 total transcriptomic measurements: [3 parallel replicates] x [400 ppm, 800 ppm] x [normal light, high
light] x [exponential, stationary] x [2 serial replicates].

Data Processing Description

Array slides were scanned using an Agilent slide scanner. Data were processed from Agilent files using the limma package in R, including background correction, loess (within-array) and 'Aquantile' (between-array) normalization.

Data Files

File
Thaps_microarrays.csv (Comma Separated Values (.csv), 406 bytes) MD5:af4f83e8407394ca48fd0449c525f9d7 Primary data file for dataset ID 546404

More Information about this dataset

Funding Sources

Funding Source	Award Number
NSF Emerging Frontiers Division	EF-1316206

Deployments

Deployment	Synonyms	Start Date	Platform	Investigator
ISB_Orellana		2013-07-01	Institute for Systems Biology	Monica V. Orellana (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

taxon

Taxon/species of study.

text

taxon

publication

Publication where the details of the study can be found.

Ashworth_et_al_2013 = Ashworth J, Coesel S, Lee A, Armbrust EV, Orellana MO*, Baliga NS*. (2013) Genome-wide diel growth state transitions in the diatom Thalassiosira pseudonana. Proc. Natl. Acad. Sci. 110(18):7518-23. doi:10.1073/pnas.1300962110

text

reference_paper

GEO_accession

Accession number and hyperlink to the NCBI GEO database.

alphanumeric

accession_number

Status message

Database

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Dataset: Thaps microarrays - ISB