Project
Developing Tools and Standards for Integration of Multidimensional Human Cell Atlas Data
Focus
Methods Focus, Urinary
Method
Epigenetic Sequencing, Single Cell Transcriptomics, Spatial Genomics
Project Summary
This network proposes a benchmarking framework to generate guidelines, technologies, quality metrics, and new computational tools that will serve as a compass for the Human Cell Atlas’s generation of reproducible and high-quality tissue atlases.
Results & Resources
This group developed tools to integrate single-cell data for multidimensional analysis, starting with mouse kidney samples. They improved zUMIs and powsimR — data processing pipelines designed to reduce ambient RNA in single-cell RNA sequencing data, a crucial problem in single-cell data analysis. This group published SPOTlight, a tool to deconvolute cell types and proportions from tissue sections at the single-cell resolution.
Investigators
Co-Principal Investigators

Piero Carninci, PhD

Wolfgang Enard, PhD

Samouil Farhi, PhD

Ernest Fraenkel, PhD

Holger Heyn, PhD

Matthias Kretzler, MD

Joshua Levin, PhD

Thierry Voet, PhD
Collaborators

Menna Clatworthy, MBBCh, PhD, FRCP

Anna Greka, MD, PhD

Aviv Regev, PhD

Orit Rozenblatt-Rosen, PhD, MSc

Sarah Teichmann, PhD