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Thalassiosira oceanica CCMP1005
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Principle Investigator(s) | Bethany Jenkins |
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External sample ID | CCMP1005_Replete |
NCGR Sample ID | MMETSP0970 |
Sample accession number | CAM_SMPL_002690 |
Assembly accession number | CAM_ASM_000508 |
Combined Assembly Name | Thalassiosira-oceanica-CCMP1005 |
Genus | Thalassiosira |
Species | oceanica |
Strain | CCMP1005 |
Clonal | Yes |
Axenic | Yes |
Prelim. NCBI Taxon ID | 159749 |
18S rRNA | |
Importance of organism and transcriptomes | Previous 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of genes varies in response to fluctuations in nutrient regimes (Mock et al. 2008; Dhyrman, Jenkins, Ryearson, Saito, unpublished data).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of a species that is a coastal isolate within the same genus (Mock et al. 2008; Dhyrman, Jenkins, Ryearson, Saito, unpublished data), T. pseudonana 1335, that will be very useful for comparison with this oceanic isolate.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 references | Mock, 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 available | von 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). |
Latitude | 33.1833 |
Longitude | -65.25 |
Salinity (psu) | 36.32 |
Temperature (ºC) | 22.7 |
Collection date | 11-DEC-58 |
Sample collection site | Sargasso Sea |
Sample material (e.g. "seawater," "sediment," etc.) | seawater |
Habitat | marine habitat |
Experimental Data | |
Date of experiment | 19-JUN-11 |
Growth medium | f/2 amended seawater |
Modifications to growth medium | f/2 for all nutrients except iron, which was added at 400nM |
Temperature (ºC) | 25 |
Salinty (psu) | 35 |
pH | 8.2 |
Light (µmol photons / m2 / sec) | 120 |
Day portion of day:night cycle in hours | 14 |
Night portion of day:night cycle in hours | 10 |
Nitrate (μmol/L) | 882 |
Phosphate (μmol/L) | 36.2 |
Silicate (μmol/L) | 106 |
Total Fe (nmol/L) | 400 |
Trace elements (total) (nmol/L) | 1093.8 |
Investigation type | Eukaryotes |
Other experimental metadata available | Sampled 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 |