CeNGEN

Complete Gene Expression Map of an Entire Nervous System

openproblems_v1

Info

openproblems_v1/cengen
Hammarlund et al. (2018)
778.17 MiB
02-02-2024
100955 cells × 22469 genes

Used in

No related benchmarks found.

Description

100k FACS-isolated C. elegans neurons from 17 experiments sequenced on 10x Genomics.

Preview

dataset is an AnnData object with n_obs × n_vars = 100955 × 22469 with slots:

Reference

Name Description Type Data type Size
obs
batch A batch identifier. This label is very context-dependent and may be a combination of the tissue, assay, donor, etc. vector category 100955
cell_type Classification of the cell type based on its characteristics and function within the tissue or organism. vector category 100955
size_factors The size factors created by the normalisation method, if any. vector float32 100955
tissue Specific tissue from which the cells were derived, key for context and specificity in cell studies. vector category 100955
var
feature_name A human-readable name for the feature, usually a gene symbol. vector object 22469
hvg Whether or not the feature is considered to be a ‘highly variable gene’ vector bool 22469
hvg_score A ranking of the features by hvg. vector float64 22469
obsp
knn_connectivities K nearest neighbors connectivities matrix. sparsematrix float32 100955 × 100955
knn_distances K nearest neighbors distance matrix. sparsematrix float64 100955 × 100955
obsm
X_pca The resulting PCA embedding. densematrix float32 100955 × 50
varm
pca_loadings The PCA loadings matrix. densematrix float32 22469 × 50
layers
counts Raw counts sparsematrix float32 100955 × 22469
normalized Normalised expression values sparsematrix float32 100955 × 22469
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

Hammarlund, Marc, Oliver Hobert, David M. Miller, and Nenad Sestan. 2018. “The CeNGEN Project: The Complete Gene Expression Map of an Entire Nervous System.” Neuron 99 (3): 430–33. https://doi.org/10.1016/j.neuron.2018.07.042.