Diatom (Thalassiosira pseudonana) physiological data from experiments designed to study single-cell transcriptional profiling of nutrient acquisition heterogeneity in diatoms conducted in December of 2022 (NCEI Accession 0291298)

This dataset contains biological, chemical, optical, and survey - biological data collectedat Laboratory study from 2022-12-04 to 2022-12-09. These data include Nitrate, fluorescence, pH, and species. The instruments used to collect these data include CO2 Analyzer and Fluorometer. These data were collected by Christopher Lausted and Sui Huang of Institute for Systems Biology and Monica V. Orellana of University of Washington as part of the "EAGER: Diatom Programmed Cell Death at Single-Cell Resolution (Diatom Death)" project and "Ocean Carbon and Biogeochemistry (OCB)" program. The Biological and Chemical Oceanography Data Management Office (BCO-DMO) submitted these data to NCEI on 2024-02-01.

The following is the text of the dataset description provided by BCO-DMO:

Methods and Sampling: Cultures: Axenic Thalassiosira pseudonana (CCMP 1335, National Center for Marine Algae and Microbiota, Maine, USA; LSID urn:lsid:marinespecies.org:taxname:148934 ) batch cultures were grown in enriched artificial seawater (ESAW) medium modified with reduced levels of nitrate (170 μM) to characterize starvation. Before the experiment, the diatoms were acclimated to a constant 20 °C temperature and under a 12: 12 h dark: light diurnal cycle at 300 μmol photons·m −2 ·s −1 using cool fluorescent lights. The cultures were continuously equilibrated at ambient (420 ppm CO 2 by bubbling mixed gasses (air and CO 2 at 0.4 L/min) regulated using mass-flow controllers (GFC17, Aalborg) and monitored with a CO 2 analyzer (model Q-S151; Qubit Systems) into a 1.5-L glass bioreactor system. The bioreactors were inoculated with 150,000 cells/ml of acclimated, axenic T. pseudonana and grown for 5 days on a 12: 12 h dark: light cycle. The pH was monitored spectrophotometrically (Dickson et al. 2007); the photochemical yield of photosystem II (variable fluorescence/maximum fluorescence Fv/Fm) was measured with an AquaPen AP100; and total dissolved nitrogen was measure using the Nitrite/Nitrate, Colorimetric Test Roche # 11746081001) kit after syringe-filtering (0.2μm) the samples. Samples were taken twice a day, in the middle of dark-time, and the middle of the light-time representing different growth conditions regulating the metabolism based on light and nitrogen on days one and two (Ashworth et al. 2013). On days three and four, samples were only taken during the light time for experiment b. This experiment was repeated to evaluate the recovery of the cells from starvation by amending NO 3 (170 uM+/- 5uM) on day 5, after 70 hrs of starvation for T. pseudonana and sampled at T1: 0h, T2: 1h and T3: 3 hr, and T4: 6 hr after adding the supplemental nitrogen. Samples T1, T2, T3, were set on ice in the dark before analysis at when T4 was sampled.

Experiment Metadata (physiology, gene and cell information):

Experiment

Start_Date 12-4

Light:Dark 12:12

Lights_On 1:00 PM

Lights_(umols/m.s) 1000 umoles m-2s-1

CO2_ppm ~420

scRNAseq_Timepoints 18 hours, 30 hours, 42 hours, 54 hours, 68 hours, 80 hours, 92 hours

scRNAseq_Timepoint_Labels

Notes scRNA, Full ESAW nitrate limited (170uM). Starting innoculate = 150k/m