BCO-DMO ERDDAP
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Row Type Variable Name Attribute Name Data Type Value
attribute NC_GLOBAL cdm_data_type String Other
attribute NC_GLOBAL Conventions String COARDS, CF-1.6, ACDD-1.3
attribute NC_GLOBAL creator_email String info at bco-dmo.org
attribute NC_GLOBAL creator_name String BCO-DMO
attribute NC_GLOBAL creator_url String https://www.bco-dmo.org/ (external link)
attribute NC_GLOBAL doi String 10.26008/1912/bco-dmo.918841.1
attribute NC_GLOBAL infoUrl String https://www.bco-dmo.org/dataset/918841 (external link)
attribute NC_GLOBAL institution String BCO-DMO
attribute NC_GLOBAL license String The data may be used and redistributed for free but is not intended\nfor legal use, since it may contain inaccuracies. Neither the data\nContributor, ERD, NOAA, nor the United States Government, nor any\nof their employees or contractors, makes any warranty, express or\nimplied, including warranties of merchantability and fitness for a\nparticular purpose, or assumes any legal liability for the accuracy,\ncompleteness, or usefulness, of this information.
attribute NC_GLOBAL sourceUrl String (local files)
attribute NC_GLOBAL summary String This dataset includes physiological data for diatom Thalassiosira pseudonana grown during experiments conducted as part of a study of \"Single-Cell transcriptional profiling of nutrient acquisition heterogeneity in diatoms.\"  See \"Related Datasets\" section for T. pseudonana gene and cell information collected as part of the same study and experiments.\n\n\nStudy description: \n\nDiatoms (Bacillariophyceae) are unicellular photosynthetic algae, accounting for about 40% of total marine primary production (equivalent to terrestrial rainforests) and critical ecological players in the contemporary ocean. Diatoms can form enormous blooms in the ocean that can be seen from space and are the base of food webs in coastal and upwelling systems, support essential fisheries, and are central to the biogeochemical cycling of important nutrients such as carbon and silicon. Over geological time, diatoms have influenced the world's climate by changing the carbon flux into the oceans. \n\nDiatoms have traditionally been studied on a population level. Growth is often measured by the total increase in biomass, and gene expression is analyzed by isolating mRNA from thousands or millions of cells. These methods generate a valuable analysis on the population's average functioning; however, they fail to show how each individual diatom cell contributes to the population phenotype. Bulk transcriptomes confound different stages and variability of cell states in heterogeneous populations. By contrast, single-cell transcriptomics measures gene expression in thousands of individual diatoms providing a quantitative and ultrahigh-resolution picture of transient cell states in population fractions enabling the reconstruction of the various phenotypic trajectories. Thus, the single-cell physiological and molecular parameters analysis allows an unsupervised assessment of cell heterogeneity within a population—a new dimension in diatoms and phytoplankton in general. \n\nIn this dataset, we examine the model diatom Thalassiosira pseudonana clonal cells grown in different nitrogen conditions, at the single cell level when grown in a light: dark cycle (12:12 h). Nitrogen is the major limiting nutrient for primary production and growth in the ocean's surface, specifically for diatoms and the food webs they support. We investigate nutrient limitation, starvation and recovery. We used droplet-based, single-cell transcriptomics to analyze ten samples in two stages.  In the first stage (\"starvation\"), six samples were collected over four days of culture as nutrient levels decreased.  In the second stage (\"recovery\"), four samples were collected over twelve hours after nutrients were replenished.
attribute NC_GLOBAL time_coverage_end String 2022-12-10T03:00:00Z
attribute NC_GLOBAL time_coverage_start String 2022-12-04T21:00:00Z
attribute NC_GLOBAL title String [T. pseudonana starve-recover experiments: Physiological data] - 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 (EAGER: Diatom Programmed Cell Death at Single-Cell Resolution)
variable Species String
attribute Species long_name String Species
attribute Species units String unitless
variable Identification int
attribute Identification actual_range int 1, 1
attribute Identification long_name String Identification
attribute Identification units String unitless
variable Date String
attribute Date long_name String Date
attribute Date units String unitless
variable Time String
attribute Time long_name String Time
attribute Time units String unitless
variable time double
attribute time _CoordinateAxisType String Time
attribute time actual_range double 1.6701876E9, 1.6706412E9
attribute time axis String T
attribute time ioos_category String Time
attribute time long_name String Iso_datetime_utc
attribute time standard_name String time
attribute time time_origin String 01-JAN-1970 00:00:00
attribute time units String seconds since 1970-01-01T00:00:00Z
variable Hours int
attribute Hours actual_range int 0, 128
attribute Hours long_name String Hours
attribute Hours units String unitless
variable Diel String
attribute Diel long_name String Diel
attribute Diel units String unitless
variable PPM_CO2_analyzer int
attribute PPM_CO2_analyzer actual_range int 404, 442
attribute PPM_CO2_analyzer long_name String Ppm_co2_analyzer
attribute PPM_CO2_analyzer units String parts per million (ppm)
variable cell_counts_q1 int
attribute cell_counts_q1 actual_range int 23, 281
attribute cell_counts_q1 long_name String Cell_counts_q1
attribute cell_counts_q1 units String cells
variable cell_counts_q2 int
attribute cell_counts_q2 actual_range int 18, 241
attribute cell_counts_q2 long_name String Cell_counts_q2
attribute cell_counts_q2 units String cells
variable cell_counts_q3 int
attribute cell_counts_q3 actual_range int 16, 286
attribute cell_counts_q3 long_name String Cell_counts_q3
attribute cell_counts_q3 units String cells
variable cell_counts_q4 int
attribute cell_counts_q4 actual_range int 23, 264
attribute cell_counts_q4 long_name String Cell_counts_q4
attribute cell_counts_q4 units String cells
variable dF int
attribute dF actual_range int 1, 1
attribute dF long_name String Df
attribute dF units String unitless
variable cells_mL_avgerage int
attribute cells_mL_avgerage actual_range int 200000, 2560000
attribute cells_mL_avgerage long_name String Cells_ml_avgerage
attribute cells_mL_avgerage units String cells per ml (cells/ml)
variable Quantum_yield_1 float
attribute Quantum_yield_1 actual_range float 0.13, 0.51
attribute Quantum_yield_1 long_name String Quantum_yield_1
attribute Quantum_yield_1 units String unitless
variable Quantum_yield_2 float
attribute Quantum_yield_2 actual_range float 0.13, 0.51
attribute Quantum_yield_2 long_name String Quantum_yield_2
attribute Quantum_yield_2 units String unitless
variable Quantum_Yield_3 float
attribute Quantum_Yield_3 actual_range float 0.08, 0.5
attribute Quantum_Yield_3 long_name String Quantum_yield_3
attribute Quantum_Yield_3 units String unitless
variable QY_AVG float
attribute QY_AVG actual_range float 0.1166667, 0.5066667
attribute QY_AVG long_name String Qy_avg
attribute QY_AVG units String unitless
variable FT1 int
attribute FT1 actual_range int 664, 1852
attribute FT1 long_name String Ft1
attribute FT1 units String unitless
variable FT2 int
attribute FT2 actual_range int 648, 1875
attribute FT2 long_name String Ft2
attribute FT2 units String unitless
variable FT3 int
attribute FT3 actual_range int 649, 1877
attribute FT3 long_name String Ft3
attribute FT3 units String unitless
variable FT_AVG float
attribute FT_AVG actual_range float 654.3333, 1868.0
attribute FT_AVG long_name String Ft_avg
attribute FT_AVG units String unknown
variable pH float
attribute pH actual_range float 7.965, 8.729
attribute pH long_name String Ph
attribute pH units String unitless
variable Sample_for_RNA String
attribute Sample_for_RNA long_name String Sample_for_rna
attribute Sample_for_RNA units String unitless
variable Cell_Pellet String
attribute Cell_Pellet long_name String Cell_pellet
attribute Cell_Pellet units String unitless
variable CF_Media String
attribute CF_Media long_name String Cf_media
attribute CF_Media units String unitless
variable uM_Nitrate1 float
attribute uM_Nitrate1 actual_range float -4.268657, 158.8852
attribute uM_Nitrate1 long_name String Um_nitrate1
attribute uM_Nitrate1 units String micromolar (uM)
variable uM_Nitrate2 float
attribute uM_Nitrate2 actual_range float -3.522388, 146.4262
attribute uM_Nitrate2 long_name String Um_nitrate2
attribute uM_Nitrate2 units String micromolar (uM)
variable uM_Nitrate3 float
attribute uM_Nitrate3 actual_range float -3.074627, 142.4918
attribute uM_Nitrate3 long_name String Um_nitrate3
attribute uM_Nitrate3 units String micromolar (uM)
variable uM_Nitrate_AVG float
attribute uM_Nitrate_AVG actual_range float -3.621891, 148.612
attribute uM_Nitrate_AVG long_name String Um_nitrate_avg
attribute uM_Nitrate_AVG units String micromolar (uM)

 
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