Grant Award Details

An interactive data resource for hypothesis testing in stem cell single-cell gene expression and validation of the results with brain organoids
Grant Number: 
DISC0-14514
Project Objective: 
  • To create a web-based database of all single cell RNA-seq datasets relevant for the study of neurodevelopment of the cerebral cortex, complemented by an analytical tool that combines these data with a small selection of new spatial transcription assays that are much more labor intensive and expensive.
Investigator: 
Disease Focus: 
Neurological Disorders
Human Stem Cell Use: 
Embryonic Stem Cell
Award Value: 
$1,160,126
Status: 
Pre-Active

Grant Application Details

Application Title: 
  • An interactive data resource for hypothesis testing in stem cell single-cell gene expression and validation of the results with brain organoids
Public Abstract: 

Research Objective

We are building a "virtual molecular microscope" where anyone can quickly visualize a very recent, high-throughput molecular assay, single-cell RNA-seq and spatial gene
expression studies

Impact

Currently, a lot of data has been published, hundreds of datasets on the cerebral cortex alone, but it takes hours to convert the datasets and look at them. Our websites will reduce
this to seconds.

Major Proposed Activities

  • Find and convert existing single-cell gene activity datasets published over the last few years and add them to cells.ucsc.edu
  • Create the first "spatial" dataset of the cerebral cortex, one that shows gene activity in single cells but on sections of human brain tissue, not just the cells in isolation
  • Upgrade cells.ucsc.edu such that users can combine the data from Activity 1 (isolated cells) with Activity 2 (spatially arranged cells) and can compare the different datasets
Statement of Benefit to California: 

California is a hub for stem cell research, partially thanks to CIRM. Our new data repository and data analysis tool will allow stem cell researchers, many of which who are based
in California, to save a lot of time when looking at datasets. Our website will to share these datasets with the world. Finally, the project has a big potential to attract more research
funding from other sources to California. Hopefully, there will ultimately be health benefits to Californians thanks to this tool.