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| Status |
Public on Apr 18, 2013 |
| Title |
Diel growth of Thalassiosira pseudonana |
| Platform organism |
Thalassiosira pseudonana |
| Sample organism |
Thalassiosira pseudonana CCMP1335 |
| Experiment type |
Expression profiling by array
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| Summary |
Transcript levels of all T. pseudonana genes was measured every twelve hours throughout the batch (non-chemostatic) growth of axenic cells grown in large glass bioreactors on a 12hr:12hr dark:light cycle for five days. The data were analyzed to reveal the physiological and regulatory changes that recurred in this diatom when transitioning between dark and light conditions, as well as from exponential phase to stationary, nutrient limited conditions. The longitudinal experiment was performed with two replicates, at 400 and 800ppm CO2.
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| Overall design |
Two growth experiments were conducted, with 10 and 9 longitudinal samples collected from each experiment, respectively. Two-color arrays were used with dye flips for labeling. A common internal reference sample was used for one channel on each array. Expression changes for longitudinal analysis were calculated as the difference from the mean log2 expression ratio for each to the common reference sample, for each gene, over all samples within an experiment. For the analysis of diel states in T. pseudonana, samples from the two series were matched according to the time from innoculation, and divided into four classes: dawn samples (taken at the end of each dark phase), dusk samples (taken at the end of each light phase), exponential samples (the first five samples in each series prior to a drop in growth rate on Day 3), and stationary samples (all samples including following the drop in growth rate on Day 3).
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| Contributor(s) |
Ashworth J, Orellana MV, Baliga NS |
| Citation(s) |
23596211 |
| Submission date |
Mar 18, 2013 |
| Last update date |
May 02, 2013 |
| Contact name |
Justin Ashworth |
| E-mail(s) |
justin.ashworth.research@gmail.com
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| Organization name |
Institute for Systems Biology
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| Street address |
401 Terry Ave N
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| City |
Seattle |
| ZIP/Postal code |
98109 |
| Country |
USA |
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| Platforms (1) |
| GPL16806 |
Agilent-029854 T. pseudonana gene-specific microarray |
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| Samples (19)
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| Relations |
| BioProject |
PRJNA193321 |
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