Immune Cell Atlas

Cross-tissue immune cell analysis reveals tissue-specific features in humans

cellxgene_census

Info

cellxgene_census/immune_cell_atlas
Domínguez Conde et al. (2022)
9.7 GiB
02-02-2024
329762 cells × 29335 genes

Used in

No related benchmarks found.

Description

Despite their crucial role in health and disease, our knowledge of immune cells within human tissues remains limited. We surveyed the immune compartment of 16 tissues from 12 adult donors by single-cell RNA sequencing and VDJ sequencing generating a dataset of ~360,000 cells. To systematically resolve immune cell heterogeneity across tissues, we developed CellTypist, a machine learning tool for rapid and precise cell type annotation. Using this approach, combined with detailed curation, we determined the tissue distribution of finely phenotyped immune cell types, revealing hitherto unappreciated tissue-specific features and clonal architecture of T and B cells. Our multitissue approach lays the foundation for identifying highly resolved immune cell types by leveraging a common reference dataset, tissue-integrated expression analysis, and antigen receptor sequencing.

Preview

dataset is an AnnData object with n_obs × n_vars = 329762 × 29335 with slots:

Reference

Name Description Type Data type Size
obs
assay Type of assay used to generate the cell data, indicating the methodology or technique employed. vector category 329762
assay_ontology_term_id Experimental Factor Ontology (EFO:) term identifier for the assay, providing a standardized reference to the assay type. vector category 329762
batch A batch identifier. This label is very context-dependent and may be a combination of the tissue, assay, donor, etc. vector category 329762
cell_type Classification of the cell type based on its characteristics and function within the tissue or organism. vector category 329762
cell_type_ontology_term_id Cell Ontology (CL:) term identifier for the cell type, offering a standardized reference to the specific cell classification. vector category 329762
dataset_id Identifier for the dataset from which the cell data is derived, useful for tracking and referencing purposes. vector category 329762
development_stage Stage of development of the organism or tissue from which the cell is derived, indicating its maturity or developmental phase. vector category 329762
development_stage_ontology_term_id Ontology term identifier for the developmental stage, providing a standardized reference to the organism’s developmental phase. If the organism is human (organism_ontology_term_id == 'NCBITaxon:9606'), then the Human Developmental Stages (HsapDv:) ontology is used. If the organism is mouse (organism_ontology_term_id == 'NCBITaxon:10090'), then the Mouse Developmental Stages (MmusDv:) ontology is used. Otherwise, the Uberon (UBERON:) ontology is used. vector category 329762
disease Information on any disease or pathological condition associated with the cell or donor. vector category 329762
disease_ontology_term_id Ontology term identifier for the disease, enabling standardized disease classification and referencing. Must be a term from the Mondo Disease Ontology (MONDO:) ontology term, or PATO:0000461 from the Phenotype And Trait Ontology (PATO:). vector category 329762
donor_id Identifier for the donor from whom the cell sample is obtained. vector category 329762
is_primary_data Indicates whether the data is primary (directly obtained from experiments) or has been computationally derived from other primary data. vector bool 329762
self_reported_ethnicity Ethnicity of the donor as self-reported, relevant for studies considering genetic diversity and population-specific traits. vector category 329762
self_reported_ethnicity_ontology_term_id Ontology term identifier for the self-reported ethnicity, providing a standardized reference for ethnic classifications. If the organism is human (organism_ontology_term_id == 'NCBITaxon:9606'), then the Human Ancestry Ontology (HANCESTRO:) is used. vector category 329762
sex Biological sex of the donor or source organism, crucial for studies involving sex-specific traits or conditions. vector category 329762
sex_ontology_term_id Ontology term identifier for the biological sex, ensuring standardized classification of sex. Only PATO:0000383, PATO:0000384 and PATO:0001340 are allowed. vector category 329762
size_factors The size factors created by the normalisation method, if any. vector float32 329762
soma_joinid If the dataset was retrieved from CELLxGENE census, this is a unique identifier for the cell. vector int64 329762
suspension_type Type of suspension or medium in which the cells were stored or processed, important for understanding cell handling and conditions. vector category 329762
tissue Specific tissue from which the cells were derived, key for context and specificity in cell studies. vector category 329762
tissue_general General category or classification of the tissue, useful for broader grouping and comparison of cell data. vector category 329762
tissue_general_ontology_term_id Ontology term identifier for the general tissue category, aiding in standardizing and grouping tissue types. For organoid or tissue samples, the Uber-anatomy ontology (UBERON:) is used. The term ids must be a child term of UBERON:0001062 (anatomical entity). For cell cultures, the Cell Ontology (CL:) is used. The term ids cannot be CL:0000255, CL:0000257 or CL:0000548. vector category 329762
tissue_ontology_term_id Ontology term identifier for the tissue, providing a standardized reference for the tissue type. For organoid or tissue samples, the Uber-anatomy ontology (UBERON:) is used. The term ids must be a child term of UBERON:0001062 (anatomical entity). For cell cultures, the Cell Ontology (CL:) is used. The term ids cannot be CL:0000255, CL:0000257 or CL:0000548. vector category 329762
var
feature_id Unique identifier for the feature, usually a ENSEMBL gene id. vector object 29335
feature_name A human-readable name for the feature, usually a gene symbol. vector object 29335
hvg Whether or not the feature is considered to be a ‘highly variable gene’ vector bool 29335
hvg_score A ranking of the features by hvg. vector float64 29335
soma_joinid If the dataset was retrieved from CELLxGENE census, this is a unique identifier for the feature. vector int64 29335
obsp
knn_connectivities K nearest neighbors connectivities matrix. sparsematrix float32 329762 × 329762
knn_distances K nearest neighbors distance matrix. sparsematrix float64 329762 × 329762
obsm
X_pca The resulting PCA embedding. densematrix float32 329762 × 50
varm
pca_loadings The PCA loadings matrix. densematrix float32 29335 × 50
layers
counts Raw counts sparsematrix float32 329762 × 29335
normalized Normalised expression values sparsematrix float32 329762 × 29335
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

Domínguez Conde, C., C. Xu, L. B. Jarvis, D. B. Rainbow, S. B. Wells, T. Gomes, S. K. Howlett, et al. 2022. “Cross-Tissue Immune Cell Analysis Reveals Tissue-Specific Features in Humans.” Science 376 (6594). https://doi.org/10.1126/science.abl5197.