Integrative analysis of mouse and human single-cell gene expression data. What are conserved cell types in the brain and what are their characteristics?
Main idea: perform integrative analysis of mouse and human (and possibly other species, including macaques and marmosets) neocortical cell types according to transcriptomics and possibly intrinsic electrophysiology. These analyses will directly feed into cell and circuit models of mouse and human circuits, led by Etay’s group.
Key questions:
- Can we identify orthologous cell types between species?
- What genes / features distinguish cell types?
- Are there aspects of these features that seem relevant to computational processing of cells and circuits?
- What characteristics of these features can be modelled in the context of cell and circuit models?
What (dataset) resources are available to help answer this question? Allen Institute for Brain Sciences Cell Types database
Transcriptomics TAs: Sonny Chen, Mel Davie
Dataset information:
- Region mapping between species
- Includes number of cells available within each region for full human and mouse datasets
Seurat tutorials:
Getting started:
- Preprocessing completed using code here
- Finding homologous genes between species, downsampling large datasets, filtering out undetected genes
- Initial Seurat analysis
- Dataset integration, de novo clustering, visualization