Zebrafish embryonic cells

Single-cell mRNA sequencing of zebrafish embryonic cells.



Wagner et al. (2018)
777.92 MiB
26022 × 25258

Used in


90k cells from zebrafish embryos throughout the first day of development, with and without a knockout of chordin, an important developmental gene.


dataset is an AnnData object with n_obs × n_vars = 26022 × 25258 with slots:


Name Description Type Data type Size
batch A batch identifier. This label is very context-dependent and may be a combination of the tissue, assay, donor, etc. vector category 26022
cell_type Classification of the cell type based on its characteristics and function within the tissue or organism. vector category 26022
size_factors The size factors created by the normalisation method, if any. vector float32 26022
feature_name A human-readable name for the feature, usually a gene symbol. vector object 25258
hvg Whether or not the feature is considered to be a ‘highly variable gene’ vector bool 25258
hvg_score A ranking of the features by hvg. vector float64 25258
knn_connectivities K nearest neighbors connectivities matrix. sparsematrix float32 26022 × 26022
knn_distances K nearest neighbors distance matrix. sparsematrix float64 26022 × 26022
X_pca The resulting PCA embedding. densematrix float32 26022 × 50
pca_loadings The PCA loadings matrix. densematrix float32 25258 × 50
counts Raw counts sparsematrix float32 26022 × 25258
normalized Normalised expression values sparsematrix float32 26022 × 25258
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


Wagner, Daniel E., Caleb Weinreb, Zach M. Collins, James A. Briggs, Sean G. Megason, and Allon M. Klein. 2018. “Single-Cell Mapping of Gene Expression Landscapes and Lineage in the Zebrafish Embryo.” Science 360 (6392): 981–87. https://doi.org/10.1126/science.aar4362.