Summary
Understanding neural circuits requires deciphering interactions among myriad cell types defined by spatial organization, connectivity, gene expression, and other properties. Resolving these cell types requires both single neuron resolution and high throughput, a challenging combination with conventional methods. Here we introduce BARseq, a multiplexed method based on RNA barcoding for mapping projections of thousands of spatially resolved neurons in a single brain, and relating those projections to other properties such as gene or Cre expression. Mapping the projections to 11 areas of 3579 neurons in mouse auditory cortex using BARseq confirmed the laminar organization of the three top classes (IT, PT-like and CT) of projection neurons. In depth analysis uncovered a novel projection type restricted almost exclusively to transcriptionally-defined subtypes of IT neurons. By bridging anatomical and transcriptomic approaches at cellular resolution with high throughput, BARseq can potentially uncover the organizing principles underlying the structure and formation of neural circuits.
Footnotes
Added new results using BARseq + FISH to reveal the organization of projections across transcriptionally defined subtypes of IT neurons. Added new results demonstrating the use of BARseq in Cre-labeled neurons. Added single-cell RNAseq experiments showing (1) IT subtypes in the auditory cortex correspond to those in the visual cortex, and (2) gene expression is preserved after barcoding.
