5k Peripheral blood mononuclear cells

5k Peripheral Blood Mononuclear Cells (PBMCs) from a healthy donor. Sequenced on 10X v3 chemistry in July 2019 by 10X Genomics. 5247 cells x 20822 features with no cell type labels

reference 10x Genomics, 2019

homo sapiens Organism

5,247 × 20,822 Dimensions

156.82 MiB Size

log_cp10k Normalization

Source

Description

5k Peripheral Blood Mononuclear Cells (PBMCs) from a healthy donor. Sequenced on 10X v3 chemistry in July 2019 by 10X Genomics. 5247 cells x 20822 features with no cell type labels

Preview

An AnnData object with n_obs × n_vars = 5,247 × 20,822 with slots:

obs: size_factors

var: feature_name , hvg , hvg_score

obsp: knn_connectivities , knn_distances

obsm: X_pca

varm: pca_loadings

layers: counts , normalized

uns: dataset_description , dataset_id , dataset_name , dataset_organism , dataset_reference , dataset_summary , dataset_url , knn , normalization_id , pca_variance

Data structure

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

Download & explore

The processed dataset lives on the OpenProblems public S3 bucket, which is world-readable. Download the file directly, or copy its S3 URI to fetch it with your tool of choice.

dataset.h5ad 156.82 MiB

Download

s3://openproblems-data/resources/datasets/openproblems_v1/tenx_5k_pbmc/log_cp10k/dataset.h5ad

Used in

Dimensionality Reduction for Visualisation

References

10x Genomics. (2019). 5k Peripheral Blood Mononuclear Cells (PBMCs) from a Healthy Donor with a Panel of TotalSeq-B Antibodies (v3 chemistry). link ↗