The Single-Cell Pediatric Cancer Atlas - Data portal and open-source tools for single-cell transcriptomics of pediatric tumors

Sep 23, 2026

Uploaded by Mary Man

Hawkins and colleagues introduce the Single-Cell Pediatric Cancer Atlas (ScPCA) Portal, a centralized resource providing uniformly processed single-cell and single-nucleus RNA sequencing data and de-identified metadata from pediatric tumor samples. The Portal currently summarizes gene expression for more than 700 samples across 55 pediatric cancer types, drawing from ALSF-funded projects and community contributions. Data downloads include standardized SingleCellExperiment and AnnData objects with raw and normalized counts, PCA/UMAP coordinates, automated cell-type annotations, copy-number variation estimates, and optional bulk RNA-seq, spatial transcriptomics, or feature barcoding. Uniform processing is performed via an open-source Nextflow workflow (scpca-nf).

LanguageEnglish

CategoryHealthcare

FormatPDF

Pages24

Reading Time1 h 0 min

AccessFree to download

Summary

Introduction

Resource The Single-Cell Pediatric Cancer Atlas: Data portal and open-source tools for single-cell transcriptomics of pediatric tumors Authors Allegra G. Hawkins, Joshua A. Shapiro, Stephanie J. Spielman, ..., Jennifer O’Malley, Casey S. Greene, Jaclyn N. Taroni Correspondence [jaclyn.taroni@ccdatalab.org](jaclyn.taroni@ccdatalab.org) In brief Hawkins et al. introduce the Single-Cell Pediatric Cancer Atlas: a uniformly processed collection of sc/snRNA-seq data from pediatric cancer samples and models. 700 samples from 55 pediatric cancer types can be downloaded in standardized formats for R and Python ecosystems. • Data are uniformly processed via an open-source Nextflow pipeline (scpca-nf) • Downloads are available in standard formats for R and Python users • Over 50 pediatric cancer types are represented Hawkins et al., 2026, Cell Genomics 6, 101283 July 8, 2026 © 2026 The Author(s) . Published by Elsevier Inc. [https://doi.org/10.1016/j.xgen.2026.101283](https://doi.org/10.1016/j.xgen.2026.101283) ll ll OPEN ACCESS Resource The Single-Cell Pediatric Cancer Atlas: Data portal and open-source tools for single-cell transcriptomics of pediatric tumors Allegra G. Hawkins,1 Joshua A. Shapiro,1 Stephanie J. Spielman,1 David S. Mejia,1 Deepashree Venkatesh Prasad,1 Nozomi Ichihara,1 Arkadii Yakovets,1 Avrohom M. Gottlieb,1 Kurt G. Wheeler,1 Chante J. Bethell,1,2 Steven M. Foltz,1,3 Jennifer O’Malley,1 Casey S. Greene,1,4,5 and Jaclyn N. Taroni1,6,* 1Childhood Cancer Data Lab, Alex’s Lemonade Stand Foundation, Bala Cynwyd, PA 19004, USA 2The University of Texas MD Anderson Cancer Center, UTHealth Houston Graduate School of Biomedical Sciences, Houston, TX 77030, USA 3Translational Research, Multiple Myeloma Research Foundation, Norwalk, CT 06851, USA 4Center for Health AI, University of Colorado School of Medicine, Aurora, CO 80045, USA 5Department of Biomedical Informatics, University of Colorado School of Medicine, Aurora, CO 80045, USA 6Lead contact *Correspondence: [jaclyn.taroni@ccdatalab.org](jaclyn.taroni@ccdatalab.org) [https://doi.org/10.1016/j.xgen.2026.101283](https://doi.org/10.1016/j.xgen.2026.101283) SUMMARY The Single-Cell Pediatric Cancer Atlas (ScPCA) Portal is a resource for uniformly processed single-cell and single-nucleus RNA sequencing (RNA-seq) data and de-identified metadata from pediatric tumor samples. Originally comprising data from 10 projects funded by Alex’s Lemonade Stand Foundation (ALSF), the Portal currently contains summarized gene expression data for over 700 samples across 55 cancer types from ALSF-funded and community-contributed datasets. Downloads include expression data as SingleCellExperiment or AnnData objects containing raw and normalized counts, principal-component analysis (PCA) and uniform manifold approximation and projection (UMAP) coordinates, automated cell-type annotations, and copy-number variation estimates, along with summary reports. Some samples have additional data from bulk RNA-seq, spatial transcriptomics, and/or feature barcoding (e.g., CITE-seq) included in the download. All data on the Portal were uniformly processed using scpca-nf, an efficient and open-source Nextflow workflow that uses alevin-fry to quantify gene expression. Comprehensive documentation, including file descriptions and a getting-started guide, are available online. INTRODUCTION The number of studies employing single-cell and single-nucleus RNA sequencing (sc/snRNA-seq) has grown rapidly since their introduction.1 Unlike its predecessor, bulk RNA-seq, which averages expression profiles of all cells within a sample, single-cell technology quantifies gene expression in individual cells. Tumors are transcriptionally heterogeneous, highlighting the importance of using sc/snRNA-seq to study tumor samples.2 Researchers can use sc/snRNA-seq data from patient tumor samples to analyze and identify individual cell populations that may influence tum

FAQs

What does the Single-Cell Pediatric Cancer Atlas (ScPCA) Portal provide to researchers?

It provides uniformly processed single-cell and single-nucleus RNA sequencing data and de-identified metadata from pediatric tumor samples, including standardized summarized gene expression and supporting analyses.

How many samples and cancer types are currently represented in the Portal?

The Portal summarizes over 700 samples across 55 pediatric cancer types.

How is the data on the Portal processed and what tools are used for downloads?

All data are uniformly processed using the open-source Nextflow workflow scpca-nf, and downloads are available as SingleCellExperiment or AnnData objects with raw/normalized counts and coordinates.

Sep 23, 2026

Uploaded by Mary Man