U01 - Feng 1U01MH114819-01

A Molecular and Cellular Atlas of the Marmoset Brain

To help fill the evolutionary gap in knowledge between rodents and humans, Feng will lead a team to classify cells across the marmoset brain. They will use high-throughput single-cell RNA sequencing to identify cell types across 16 regions of the adult marmoset brain and will then spatially map the cell types they find in the brain using multiplexed error-robust in situ hybridization (MERFISH). By combining MERFISH with viral expression of marker proteins in subsets of neurons, the team will also correlate cell morphology with genetic information. Altogether these efforts will produce a census of cell types in the marmoset brain, which will be valuable information for future work into the genetics and circuits of the primate brain.  In the image above the highlighted areas are the first four brain regions of focus, eventually we have 16 brain regions of focus in the adult marmoset brain.  

Project Leadership

Guoping Feng, Ph.D. (Principal Investigator) 
Investigator, McGovern Institute 
Particia T. Poitras Professor, 
Brain and Cognitive Sciences, MIT 


Edward Boyden, Ph.D. (Co-Principal Investigator)
Associate Professor of Biological Engineering and Brain and Cognitive Sciences, MIT 
Media Lab and McGovern Institute 
Y. Eva Tan Professor in Neurotechnology 


Steven McCarroll, Ph. D. (Co-Principal Investigator)
Dorothy and Milton Flier Professor of Biomedical Science and Genetics 
Department of Genetics 
Harvard Medical School 

Project Data Types

  • 1.6 million RNAseq libraries across 16 different brain regions from the marmoset brain 
  • We will collect one experiment from each region and collect whole-cell-soma data using commercially available 10x platform (10x Genomics); the bulk of the data collection will come from single nuclei RNAseq (sn-RNAseq) 
  • Multiplexed FISH (MERFISH) will be used to define the morphology of at least 700 cell types based on single cell RNAseq data and we plan to integrate the cell morphology data with the digital mRNA expression data to have a complete view of the cell types. 

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