Human Tumor Atlas Pilot Project (HTAPP) Webinar Series


Toolbox paper

Slyper et al Nature Medicine volume 26, pp 792–802(2020): A single-cell and single-nucleus RNA-Seq toolbox for fresh and frozen human tumors.


Single-cell genomics is essential to chart tumor ecosystems. Although single-cell RNA-Seq (scRNA-Seq) profiles RNA from cells dissociated from fresh tumors, single-nucleus RNA-Seq (snRNA-Seq) is needed to profile frozen or hard-to-dissociate tumors. Each requires customization to different tissue and tumor types, posing a barrier to adoption. Here, we have developed a systematic toolbox for profiling fresh and frozen clinical tumor samples using scRNA-Seq and snRNA-Seq, respectively. We analyzed 216,490 cells and nuclei from 40 samples across 23 specimens spanning eight tumor types of varying tissue and sample characteristics. We evaluated protocols by cell and nucleus quality, recovery rate and cellular composition. scRNA-Seq and snRNA-Seq from matched samples recovered the same cell types, but at different proportions. Our work provides guidance for studies in a broad range of tumors, including criteria for testing and selecting methods from the toolbox for other tumors, thus paving the way for charting tumor atlases.


WEBINAR 1: Tissue acquisition workflows and sc/snRNA-Seq processing protocols

December 3rd, 2020


  1. HTAPP overview
  2. Fresh tissue acquisition workflow
  3. Key components of a tissue acquisition and allocation workflow
  4. Key aspects to keep in mind for each component
  5. Fresh tissue processing for sc-RNAseq
  6. Description of the processing workflow
  7. Guidelines for testing and selecting protocols
  8. Frozen tissue processing for snRNA-Seq
  9. Description of the processing workflow
  10. Guidelines for testing and selecting protocols
  11. Single-cell vs single nucleus RNA-Seq processing
  12. Lessons learned & challenges
  13. Q&A


Judit Jané-Valbuena, Ph.D, Scientific Manager, Klarman Cell Observatory, Broad Institute

Sébastien Vigneau, Ph.D. Head of the Innovation Lab, Center for Cancer Genomics, Dana-Farber Cancer Institute

Michal Slyper, Ph.D. Research Scientist, Klarman Cell Observatory, Broad Institute