Project funded to develop a ‘Virtual microscope’ for single cell RNA-sequencing data

The California Institute for Regenerative Medicine (CIRM) has awarded $1,160,126 in funding for a major stem cell research project led by scientists at UC Santa Cruz, “An interactive data resource for hypothesis testing in stem cell single-cell gene expression and validation of the results with brain organoids.”

Max Haeussler, Associate Research Scientist at the UCSC Genomics Institute and his team will build a user-friendly database that brings together a wide range of single cell RNA-sequencing data, which reveals information about the gene expression levels of an individual cell, from the developing and diseased human cerebral cortex. The database is imagined as a “virtual microscope” which will improve the curation and visualization of this data and allow scientists to investigate the role of a specific gene in the development of the cerebral cortex without special computational training.

The database will support spatial transcriptomics data, an emerging technique for determining the relative location of a given cell within the tissue. Users will be able to compare single cell RNA-sequencing data with spatial transcriptomic information to those without spatial transcriptomic information, increasing the ability to compare previously produced data to newer data.

The database will be hosted on the Genomics Institute’s existing cell browser platform, a free, open-source tool used by researchers and pharmaceutical companies around the world.

Two Genomics Institute staff members will collect existing data on gene activity in the human brain from researchers across the world and make it accessible in the interactive map viewer that Haeussler has been developing for the last five years. Aparna Bhaduri, Haeussler’s collaborator at UCLA for this grant, will produce new spatial data to add to this collection.

“After years of searching, I’m excited to get funding for this software project,” Haeussler said. “Already several thousand researchers every week are consulting this interactive explorer of gene activity. The CIRM funding allows us to add several hundred datasets in the human brain, it will be the first brain-focussed gene activity explorer that hosts datasets from different labs across the world and as such from a broad diversity of patients”

SourceUC Santa Cruz

Leave a Reply

Your email address will not be published. Required fields are marked *


Time limit is exhausted. Please reload CAPTCHA.