BCO-DMO | ERDDAP - bcodmo_dataset_918860_v1

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\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 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.\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\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\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	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

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.918860.1

attribute

NC_GLOBAL

infoUrl

String

https://www.bco-dmo.org/dataset/918860 (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 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.\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\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\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

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

ERDDAP, Version 2.22
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