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Thalassiosira oceanica CCMP1005


Principle Investigator(s) Bethany Jenkins
External sample IDCCMP1005_Silicate Limitation
Sample accession numberCAM_SMPL_002697
Assembly accession numberCAM_ASM_000515
Combined Assembly NameThalassiosira-oceanica-CCMP1005
Prelim. NCBI Taxon ID159749
18S rRNA
Importance of organism and transcriptomesPrevious transcriptome work with T. pseudonana has shown that the expression of different suites of genes varies in response to fluctuations in nutrient regimes (Mock et al. 2008; Dhyrman, Jenkins, Ryearson, Saito, unpublished data). We feel that the suite of variables we are proposing will give the most complete transcriptome display from this organism by covering not only a response to limitations of major nutrients (nitrogen and silica) but also an important micronutrient (iron). There is already a fully sequenced genome with a significant amount of transcriptome data from similar physiological conditions of a species that is a coastal isolate within the same genus (Mock et al. 2008; Dhyrman, Jenkins, Ryearson, Saito, unpublished data), T. pseudonana 1335, that will be very useful for comparison with this oceanic isolate.
Additional citations and referencesMock, T. et al. Whole-genome expression profiling of the marine diatom Thalassiosira pseudonana identifies genes involved in silicon bioprocesses. P Natl Acad Sci Usa 105, 1579-1584 (2008).
Environmental Data
Primary citation for organism's characterization, if availablevon Dassow, P., Petersen, T. W., Chepurnov, V. A. & Armbrust, E. V. Inter- and intraspecific relationships between nuclear DNA content and cell size in selected members of the centric diatom genus Thalassiosira (Bacillariophyceae). J Phycol 44, 335-349 (2008).
Salinity (psu)36.32
Temperature (ºC)22.7
Collection date11-DEC-58
Sample collection siteSargasso Sea
Sample material (e.g. "seawater," "sediment," etc.)seawater
Habitatmarine habitat
Experimental Data
Date of experiment24-JUL-11
Growth mediumf/2 amended seawater
Modifications to growth mediumf/2 for all nutrients except iron, which was added at 400nM and silica, which was added at f/20 (10.6 uM)
Temperature (ºC)25
Salinty (psu)35
Light (µmol photons / m2 / sec)120
Day portion of day:night cycle in hours14
Night portion of day:night cycle in hours10
Nitrate (μmol/L)882
Phosphate (μmol/L)36.2
Silicate (μmol/L)10.6
Total Fe (nmol/L)400
Trace elements (total) (nmol/L)1093.8
Investigation typeEukaryotes
Other experimental metadata availableSampled at midpoint of light cycle. Trace elements: 39.3 nM Cu; 26 nM Mo; 76.5 nM Zn; 42 nM Co; 910 nM Mn; EDTA = 11.7 uM