The Single-Cell Pediatric Cancer Atlas: Data portal and open-source tools for single-cell transcriptomics of pediatric tumors
TL;DR
The Single-Cell Pediatric Cancer Atlas (ScPCA) Portal provides uniformly processed single-cell and single-nucleus RNA sequencing data for over 700 pediatric tumor samples across 55 cancer types.
Problem / question
There is a need for a centralized, uniformly processed, and easily accessible repository of single-cell and single-nucleus RNA sequencing data specifically for pediatric tumors to facilitate research and analysis.
Methods
The portal aggregates scRNA-seq and snRNA-seq data from 10 ALSF-funded projects and community contributions, processing them uniformly using the open-source Nextflow workflow scpca-nf and alevin-fry for gene expression quantification.
Key findings
The ScPCA Portal currently hosts summarized gene expression data for over 700 samples spanning 55 pediatric cancer types. Downloads are provided as SingleCellExperiment or AnnData objects containing raw and normalized counts, PCA and UMAP coordinates, automated cell-type annotations, and copy-number variation estimates. Additionally, some samples include matched bulk RNA-seq, spatial transcriptomics, or CITE-seq feature barcoding data.
Why it matters
By providing uniformly processed, ready-to-use data objects and open-source processing tools, the portal lowers the barrier to analyzing pediatric cancer single-cell data and enables cross-study comparisons.
Limitations
The provided text does not explicitly mention limitations, caveats, or biases of the portal or data.
Takeaway
The ScPCA Portal is a comprehensive, uniformly processed resource offering ready-to-analyze single-cell transcriptomic data for over 700 pediatric tumor samples across 55 cancer types.