PRJNA241382, RNA-seq, HC vs VLC, PRJNA241382

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Global transcriptomic changes following carbon limitation and elevated carbon dioxide in Nannochloropsis oceanica IMET1

This dataset was downloaded from NCBI bioproject : PRJNA241382 (GEO: GSE55861).

Below detailed description was retreived from Reference: Wei L et al., "Transcriptomic and proteomic responses to very low CO₂ suggest multiple carbon concentrating mechanisms in Nannochloropsis oceanica.", Biotechnol Biofuels, 2019;12:168.

Limited systems-level understanding of CO2 concentrating mechanism (CCM) and metabolic adaption in response to different CO2-level in wild oleaginous algae has hindered the development of microalgal feedstock and the knowledge of its role in global warming and oceanic acidification. Nannochloropsis are a group of small unicellular microalgae widely distributed in oceans and fresh water, which implies that it plays a crucial role in biogeochemical cycles impinged on global climate change. In addition, Nannochloropsis has been used for flue gas fixation in many large-scale and pilot-scale outdoor cultivation facilities for photosynthetic production of fuels and chemicals. To untangle the intricate genome-wide networks underlying CCM and metabolic adjustment under different CO2 concentrations in Nannochloropsis, we applied high-throughput mRNA-sequencing and reconstructed the structure and dynamics of the genome-wide functional network underlying robust microalgal CCM and in Nannochloropsis oceanica, by tracking the genome-wide, single-base-resolution transcript change for the complete time-courses of different CO2 concentrations. Overall design: Nannochloropsis oceanica IMET1 cells were grown in liquid cultures under continuous light (approximately 80±5 µmol photons m-2 s-1) at 25℃ and aerated by bubbling with a mixture of 5% CO2 in air. Mid-logarithmic phase algal cells were collected and washed three times with axenic seawater. Equal numbers of cells were re-inoculated in fresh medium and cultured under 5% CO2 for preadaption for one hour, and then two samples (from biological replicates) were collected as 0h samples. After the preadaption for one hour, half of them were sequentially grown under 5% in air (High carbon or HC) and other half of them were grown under 0.01% CO2 (Very low carbon or VLC) with 80±5 µmol m-2 s-1 light intensity, respectively. Cell aliquots were collected for RNA isolation after being transferred to the designated conditions for 3h, 6h, 12h and 24h. Three biological replicates of algal cultures were established under each of the above “VLC” and “HC” conditions, respectively. Two biological replicates were randomly selected to prepare mRNA-Seq library. In total, 18 samples collected at 5 time points (0h, 3h, 6h, 12h, and 24h) were used for mRNA-Seq library preparation and then submitted to Illumina HiSeq 2000 for sequencing.