Marine Microbial Eukaryote Transcriptome Sequencing Project
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Thalassiosira oceanica CCMP1005
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| Principle Investigator(s) | Bethany Jenkins |
|---|---|
| External sample ID | CCMP1005_Silicate Limitation |
| NCGR Sample ID | MMETSP0972 |
| Sample accession number | CAM_SMPL_002697 |
| Assembly accession number | CAM_ASM_000515 |
| 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of genes varies in response to fluctuations in nutrient regimes (Mock et al. 2008; Dhyrman, Jenkins, Ryearson, Saito, unpublished data).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of a species that is a coastal isolate within the same genus (Mock et al. 2008; Dhyrman, Jenkins, Ryearson, Saito, unpublished data), T. pseudonana 1335, that will be very useful for comparison with this oceanic isolate.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 | 24-JUL-11 |
| Growth medium | f/2 amended seawater |
| Modifications to growth medium | f/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 |
| 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) | 10.6 |
| 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 |