Cellxgene Human Aging Meta Summary

A curated summary of human single-cell RNA-seq datasets from cellxgene, focused on aging and development, with standardized metadata across experiments and assays.

Intended Use

This summary is intended as a scaffold for integrating other curated or custom single-cell datasets (e.g., aging or disease-focused studies) with Cellxgene metadata. Enables exploration, QC, and pre-integration filtering at the experiment level. The seafront package contains code to pull the gene matrices associated with this metadata.

Dataset Description

This dataset provides a summarized table where:

Each row corresponds to a unique dataset_id + simplified assay combination (experiment).
Numeric columns (e.g. n_measured_vars, raw_sum) are aggregated as medians per dataset.
Categorical metadata (e.g. cell_type, assay, tissue, disease) are reported as comma-separated unique values.
Ontology term IDs are also preserved and listed uniquely.
Ambiguous developmental stages are filtered out; valid stages are converted to integer ages (age_int).
Low-quality experiments (e.g. with median counts < 3000) are excluded.

Data Sources

Data pulled from the cellxgene_census API (version 2025-01) using cellxgene_census.open_soma().
All human single-cell datasets with interpretable metadata and sufficient quality metrics were included.

Processing Steps

Assay Simplification: Assay names are normalized into categories like 10x_3_prime, 10x_5_prime, BD_WTA, ScaleBio, etc.
Experiment Definition: An experiment is defined as a unique combination of dataset_id and assay_simple.
Age Filtering: Text-based developmental stages are mapped to integer age values using a rule-based filter.
Quality Filtering: Datasets with median raw counts < 3000 are excluded.
Metadata Summary: Output table generated using a per-experiment groupby summarization of all relevant columns.

Files

cellxgene_human_dataset_overview.parquet: Cleaned and summarized metadata per experiment.
All variable names used in the datasets are saved for future integration compatibility.

Example Columns

experiment, dataset_id, donor_id
unique_cell_types_present
unique_tissues_present
unique_assays_present, assay_simple
median_raw_sum, median_n_measured_vars
age_int (if available)

Citation

Please cite the original Cellxgene datasets as per their respective DOIs. This metadata summary is derived and standardized but does not modify raw gene expression data.