Mouse HSPC

Haematopoeitic stem and progenitor cells from mouse bone marrow



Nestorowa et al. (2016)
377.81 MiB
1920 × 43258

Used in


1656 hematopoietic stem and progenitor cells from mouse bone marrow. Sequenced by Smart-seq2.


dataset is an AnnData object with n_obs × n_vars = 1920 × 43258 with slots:


Name Description Type Data type Size
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
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
knn_connectivities K nearest neighbors connectivities matrix. sparsematrix float32 1920 × 1920
knn_distances K nearest neighbors distance matrix. sparsematrix float64 1920 × 1920
X_pca The resulting PCA embedding. densematrix float32 1920 × 50
pca_loadings The PCA loadings matrix. densematrix float64 43258 × 50
counts Raw counts sparsematrix float32 1920 × 43258
normalized Normalised expression values sparsematrix float32 1920 × 43258
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


Nestorowa, Sonia, Fiona K. Hamey, Blanca Pijuan Sala, Evangelia Diamanti, Mairi Shepherd, Elisa Laurenti, Nicola K. Wilson, David G. Kent, and Berthold Göttgens. 2016. “A Single-Cell Resolution Map of Mouse Hematopoietic Stem and Progenitor Cell Differentiation.” Blood 128 (8): e20–31.