Single-Cell Pediatric Cancer Atlas (ScPCA)

Growing database of uniformly processed single-cell data from pediatric cancer tumors and model systems.

Single-cell profiling is an exciting technology that can provide insight into how certain cells influence cancer progression and treatment response.

ALSF funds cutting-edge pediatric cancer research

Alex’s Lemonade Stand Foundation (ALSF) funded 10 awards for childhood cancer investigators from 8 different institutions working on single-cell profiling to create a publicly available atlas of single-cell pediatric cancer data.

The Data Lab processes the generated data

The Data Lab processes the single-cell, single-nuclei, and bulk RNA sequencing data generated by the ALSF-funded researchers. The data from these patient tumors is made widely and easily available in one location through the ScPCA Portal.

ScPCA Portal currently has

Cancer Types
Total Samples

You can view the number of tumor types and samples being processed here.

Features and Enhancements

Open Source Pipeline

The open-source pipeline used to process the data is fast, reusable, and cost-efficient. Others can utilize the pipeline for their own data, and the pipeline can be easily extended.

Community Contributions

More researchers can share their single-cell data on the Portal! We now accept dataset contributions from pediatric cancer researchers outside of the initial ScPCA grant. Learn more about contributing data.

More Choices for Users

Researchers can choose which file format to receive when downloading data. Downloads can be immediately used with two major software ecosystems for working with single-cell data. This means more users can avoid the time-consuming process of converting their ScPCA data to their preferred format and start working with it faster.


Open Source
and Free

The portal makes research faster and more cost-effective by uniformly processing the data with an open source, freely available, and well documented pipeline.

Trustworthy and Reproducible

The open source pipeline cultivates trust in the data and allows researchers to immediately utilize it for their own analyses and ensures reproducible results.

Making cutting-edge technology more accessible

Single-cell RNA sequencing is a cutting-edge technology and may not be available to all childhood cancer experts. The portal makes the outputs of this project widely accessible.