ERDDAP > info > bcodmo_dataset_918860_v1

Grid DAP Data	Sub- set	Table DAP Data	Make A Graph	W M S	Source Data Files	Acces- sible	Title	Sum- mary	FGDC, ISO, Metadata	Back- ground Info	RSS	E mail	Institution	Dataset ID
		data	graph		files	public	[T. pseudonana starve-recover experiments: Cell information] - Diatom (Thalassiosira pseudonana) cell information 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)		M	background			BCO-DMO	bcodmo_dataset_918860_v1

The Dataset's Variables and Attributes

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/
attribute	NC_GLOBAL	doi	String	10.26008/1912/bco-dmo.918860.1
attribute	NC_GLOBAL	infoUrl	String	https://www.bco-dmo.org/dataset/918860
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 for legal use, since it may contain inaccuracies. Neither the data Contributor, ERD, NOAA, nor the United States Government, nor any of their employees or contractors, makes any warranty, express or implied, including warranties of merchantability and fitness for a particular purpose, or assumes any legal liability for the accuracy, completeness, or usefulness, of this information.
attribute	NC_GLOBAL	sourceUrl	String	(local files)
attribute	NC_GLOBAL	summary	String	This dataset includes cell information 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 physiological data and gene information collected as part of the same study and experiments. Study description: Diatoms (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. Diatoms 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. In 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	title	String	[T. pseudonana starve-recover experiments: Cell information] - Diatom (Thalassiosira pseudonana) cell information 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	stage		String
attribute	stage	long_name	String	Stage
attribute	stage	units	String	unitless
variable	cell_barcode		String
attribute	cell_barcode	long_name	String	Cell_barcode
attribute	cell_barcode	units	String	unitless
variable	sample		String
attribute	sample	long_name	String	Sample
attribute	sample	units	String	unitless
variable	n_genes		int
attribute	n_genes	actual_range	int	55, 2333
attribute	n_genes	long_name	String	N_genes
attribute	n_genes	units	String	unitless
variable	n_counts		int
attribute	n_counts	actual_range	int	87, 6197
attribute	n_counts	long_name	String	N_counts
attribute	n_counts	units	String	unitless
variable	cluster		String
attribute	cluster	long_name	String	Cluster
attribute	cluster	units	String	unitless

The information in the table above is also available in other file formats (.csv, .htmlTable, .itx, .json, .jsonlCSV1, .jsonlCSV, .jsonlKVP, .mat, .nc, .nccsv, .tsv, .xhtml) via a RESTful web service.