Dataset: CO2 Chemostat Transcriptomes

For a full description of chemostat culturing methods see Hennon et al. (2014). Briefly, cells in chemostats were acclimated to 10 uM nitratelimitation at 70% of max growth rate for >10 days (equivalent to >15 generations) at 300, 475 or 800 uatm CO2, verified by pH and DIC measurements. After steady-state acclimation, ~1 x 10^8 cells were harvested on 0.2 micron polycarbonate filters by gentle vacuum filtration and flash frozen. Transition samples were collected daily as CO2 levels were increased from 300-800 ppm over four consecutive days (equivalent to 6 generations) after pre-acclimation to 300 ppm CO2 and nitrate limitation. ~1.5x10^7 cells were harvested from each day of the transition experiment on 0.2 micron polycarbonate filters by gentle vacuum filtration and flash frozen. Each sample condition was reproduced with four biological replicates. A total of 28 barcoded transcriptome libraries were prepared; 12 libraries (three treatments x four biological replicates) from steady-state culture experiments and 16 libraries (four days x four biological replicates) from transition experiments. RNA was extracted from filtered cells using the ToTALLY RNA kit. Messenger RNA was selectively amplified using MessageAmp II aRNA Amplification kit creating the antisense aRNA complement to mRNA from the sample. SOLiD barcoded libraries were prepared from aRNA as described in SOLiD Total RNA-seq kit and sequenced on a SOLiD 5500XL sequencer in two runs: one containing steady-state barcoded libraries and one containing transition barcoded libraries.

Reference:
Hennon, G. M. M., Quay, P., Morales, R. L., Swanson, L. M., & Armbrust, E. V. 2014. Acclimation conditions modify physiological response of the diatom Thalassiosira pseudonana to elevated CO2 concentrations in a nitrate-limited chemostat. Journal of Phycology, 253, 243–253. doi:10.1111/jpy.12156.