Mouse hematopoietic stem cell differentiation

Name	Description	Type	Data type	Size
obs
`cell_type`	Classification of the cell type based on its characteristics and function within the tissue or organism.	vector	category	1920
`size_factors`	The size factors created by the normalisation method, if any.	vector	float32	1920
var
`feature_name`	A human-readable name for the feature, usually a gene symbol.	vector	object	43258
`hvg`	Whether or not the feature is considered to be a 'highly variable gene'	vector	bool	43258
`hvg_score`	A ranking of the features by hvg.	vector	float64	43258
obsp
`knn_connectivities`	K nearest neighbors connectivities matrix.	sparsematrix	float32	1920 × 1920
`knn_distances`	K nearest neighbors distance matrix.	sparsematrix	float64	1920 × 1920
obsm
`X_pca`	The resulting PCA embedding.	densematrix	float32	1920 × 50
varm
`pca_loadings`	The PCA loadings matrix.	densematrix	float64	43258 × 50
layers
`counts`	Raw counts	sparsematrix	float32	1920 × 43258
`normalized`	Normalised expression values	sparsematrix	float32	1920 × 43258
uns
`dataset_description`	Long description of the dataset.	atomic	str	1
`dataset_id`	A unique identifier for the dataset. This is different from the `obs.dataset_id` field, which is the identifier for the dataset from which the cell data is derived.	atomic	str	1
`dataset_name`	A human-readable name for the dataset.	atomic	str	1
`dataset_organism`	The organism of the sample in the dataset.	atomic	str	1
`dataset_reference`	Bibtex reference of the paper in which the dataset was published.	atomic	str	1
`dataset_summary`	Short description of the dataset.	atomic	str	1
`dataset_url`	Link to the original source of the dataset.	atomic	str	1
`knn`	Supplementary K nearest neighbors data.	dict		3
`normalization_id`	Which normalization was used	atomic	str	1
`pca_variance`	The PCA variance objects.	dict		2

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The processed dataset lives on the OpenProblems public S3 bucket, which is world-readable. Download the file directly, or copy its S3 URI to fetch it with your tool of choice.

dataset.h5ad 377.81 MiB

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s3://openproblems-data/resources/datasets/openproblems_v1/mouse_hspc_nestorowa2016/log_cp10k/dataset.h5ad

Used in

Dimensionality Reduction for Visualisation

References

Nestorowa, S., Hamey, F. K., Sala, B. P., Diamanti, E., Shepherd, M., Laurenti, E., Wilson, N. K., Kent, D. G., & Göttgens, B. (2016). A single-cell resolution map of mouse hematopoietic stem and progenitor cell differentiation. Blood, 128(8), e20–e31. 10.1182/blood-2016-05-716480 ↗