Mouse myeloid

Myeloid lineage differentiation from mouse blood

openproblems_v1

Info

openproblems_v1/mouse_blood_olsson_labelled
Olsson et al. (2016)
117.4 MiB
02-02-2024
660 cells × 116918 genes

Used in

Description

660 FACS-isolated myeloid cells from 9 experiments sequenced using C1 Fluidigm and SMARTseq in 2016 by Olsson et al.

Preview

dataset is an AnnData object with n_obs × n_vars = 660 × 116918 with slots:

Reference

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 660
size_factors The size factors created by the normalisation method, if any. vector float32 660
var
feature_name A human-readable name for the feature, usually a gene symbol. vector object 116918
hvg Whether or not the feature is considered to be a ‘highly variable gene’ vector bool 116918
hvg_score A ranking of the features by hvg. vector float64 116918
obsp
knn_connectivities K nearest neighbors connectivities matrix. sparsematrix float32 660 × 660
knn_distances K nearest neighbors distance matrix. sparsematrix float64 660 × 660
obsm
X_pca The resulting PCA embedding. densematrix float32 660 × 50
varm
pca_loadings The PCA loadings matrix. densematrix float64 116918 × 50
layers
counts Raw counts sparsematrix float32 660 × 116918
normalized Normalised expression values sparsematrix float32 660 × 116918
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

References

Olsson, Andre, Meenakshi Venkatasubramanian, Viren K. Chaudhri, Bruce J. Aronow, Nathan Salomonis, Harinder Singh, and H. Leighton Grimes. 2016. “Single-Cell Analysis of Mixed-Lineage States Leading to a Binary Cell Fate Choice.” Nature 537 (7622): 698–702. https://doi.org/10.1038/nature19348.