Cell Type Mapping Evaluation on Allen Institute Taxonomies
Allen Institute Taxonomies are defined by clusters of cells that meet criteria establishing a level of distinctness in the cells' transcriptomic signature. Application of our taxonomies typically involves annotation of newly generated single cell RNA-seq against the cell type taxonomy, starting from clusters and moving up into broader cell categories. However, not all clusters can be robustly annotated onto new data for various reasons, such as cutting gradients or lacking distinct marker gene expression.
To provide transparency into mapping algorithm biases and accuracies when using Allen Institute taxonomies; we designed a cell type mapping evaluation procedure and shared the results for each taxonomy below:
Human and Mammalian Brain Atlas (HMBA): Basal Ganglia
Cell Type Mapping Evaluations:
This resource presents a cross-species consensus taxonomy of basal ganglia cell types across human, macaque, marmoset, and mouse. Supported by the NIH BRAIN Initiative Cell Atlas Network (BICAN) this resource provides standardized nomenclature based in-part on pre-existing literature supported by conserved marker gene expression.
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