Dataset: Gene expression
Deployment: lab_WHOI_sd_C-MORE

Gene expression data

Principal Investigator:

Sonya T. Dyhrman (Woods Hole Oceanographic Institution, WHOI)

Contact:

Sonya T. Dyhrman (Woods Hole Oceanographic Institution, WHOI)

Data Manager:

Jasmine Nahorniak (Oregon State University, OSU-CEOAS)

BCO-DMO Data Manager:

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

Project:

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

Version:

14 September 2009

Deployment Synonyms:

C-MORE lab WHOI

Version Date:

2009-09-14

Data URL:

https://www.bco-dmo.org/dataset-deployment/452790/data

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Description

C-MORE Gene Expression
Gene expression data from Trichodesmium culture experiments

Methods & Sampling

Dataset acquisition description

Reference:

Orchard et al. (2009)
Elizabeth D. Orchard, Eric A. Webb, Sonya T. Dyhrman. 2009. "Molecular analysis of the phosphorus starvation response in Trichodesmium spp.". Environmental Microbiology 11:2400-2411.
DOI: 10.1111/j.1462-2920.2009.01968.x
US: http://dx.doi.org/10.1111/j.1462-2920.2009.01968.x

This dataset includes some acronyms, defined as follows:

P		phosphorus
phoA		alkaline phosphatase
sphX		sphX gene
pstS		pstS gene
nifH		nitrogenase iron protein
APA		alkaline phosphatase activity

Experiments were conducted to study the expression of genes involved in Phosphorus (P) uptake and (Dissolved Organic Phosphorus) DOP hydrolysis. There were two different types of experimental design: (i) 'transfer experiment' wherein exponentially growing cells were transferred to replete (+P) and no P (-P) media, and (ii) 're-feed experiment' in which cells were starved for P and then P was added back in. Each of these experiments was replicated with similar results.

Data Processing Description

Dataset Processing Description

More information about this dataset deployment

Instruments

None available yet

Parameters

Supplied Name	Supplied description	Supplied Units	Standard Name
gene_name	gene name	text	no_bcodmo_term
experiment_type	experiment type	text	no_bcodmo_term
hours_from_start	hours from experiment start	hours	no_bcodmo_term
gene_expression_P_limited	gene expression ratio relative to time 0	phophorus limited	no_bcodmo_term
stderr_gene_expression_P_limited	standard error for the gene_expression_P_limited data	dimensionless	no_bcodmo_term
gene_expression_P_replete	gene expression ratio relative to time 0	phophorus replete	no_bcodmo_term
stderr_gene_expression_P_replete	standard error for the gene_expression_P_replete data	dimensionless	no_bcodmo_term
statistically_different	indicates statistical differences between the P_limited and P_replete gene expression data (y or n)	text	no_bcodmo_term

Database

Contribute Data

Dataset: Gene expression
Deployment: lab_WHOI_sd_C-MORE

Dataset acquisition description

Reference:

Dataset Processing Description

Database

Contribute Data

Dataset: Gene expressionDeployment: lab_WHOI_sd_C-MORE

Dataset acquisition description

Reference:

Dataset Processing Description

Dataset: Gene expression
Deployment: lab_WHOI_sd_C-MORE