5k PBMCs

5k peripheral blood mononuclear cells from a healthy donor

openproblems_v1

Info

openproblems_v1/tenx_5k_pbmc
10x Genomics (2019)
156.82 MiB
02-02-2024
5247 cells × 20822 genes

Used in

Description

5k Peripheral Blood Mononuclear Cells (PBMCs) from a healthy donor. Sequenced on 10X v3 chemistry in July 2019 by 10X Genomics.

Preview

dataset is an AnnData object with n_obs × n_vars = 5247 × 20822 with slots:

Reference

Name Description Type Data type Size
obs
size_factors The size factors created by the normalisation method, if any. vector float32 5247
var
feature_name A human-readable name for the feature, usually a gene symbol. vector object 20822
hvg Whether or not the feature is considered to be a ‘highly variable gene’ vector bool 20822
hvg_score A ranking of the features by hvg. vector float64 20822
obsp
knn_connectivities K nearest neighbors connectivities matrix. sparsematrix float32 5247 × 5247
knn_distances K nearest neighbors distance matrix. sparsematrix float64 5247 × 5247
obsm
X_pca The resulting PCA embedding. densematrix float32 5247 × 50
varm
pca_loadings The PCA loadings matrix. densematrix float64 20822 × 50
layers
counts Raw counts sparsematrix float32 5247 × 20822
normalized Normalised expression values sparsematrix float32 5247 × 20822
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

10x Genomics. 2019. “5k Peripheral Blood Mononuclear Cells (PBMCs) from a Healthy Donor with a Panel of TotalSeq-b Antibodies (V3 Chemistry).” https://www.10xgenomics.com/resources/datasets/5-k-peripheral-blood-mononuclear-cells-pbm-cs-from-a-healthy-donor-with-cell-surface-proteins-v-3-chemistry-3-1-standard-3-1-0.