SummaryUnderstanding neural circuits requires deciphering the interactions of myriad cell types defined by anatomy, spatial organization, gene expression, and functional properties. Resolving these cell types requires both single neuron resolution and high-throughput, a combination that is challenging to achieve with conventional anatomical methods. Here we introduce BARseq, a method for mapping the projections of thousands of spatially resolved neurons by combining the high throughput of DNA sequencing with the high spatial resolution of microscopy. We used BARseq to determine the projections of 1309 neurons in mouse auditory cortex to 11 targets. We observed 264 distinct projection patterns. Hierarchical clustering confirmed the major classical classes of projection neurons, segregated across cortical laminae. Further analysis revealed 25 subclasses, largely intermingled across laminae. Unlike cell types defined by gene expression, projection subclasses beyond the major classes were rarely enriched in specific laminae, raising the possibility that the organization of projection patterns in mature neurons is orthogonal to that of gene expression. In this way, downstream brain areas could receive information from multiple cell types through parallel pathways. By sequencing in situ, BARseq has the potential to bridge anatomical, transcriptomic, functional, and other approaches at single neuron resolution with high throughput, and thereby offer unprecedented insight of the structure and function of a neural circuit.. CC-BY-NC 4.0 International license It is made available under a was not peer-reviewed) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.The copyright holder for this preprint (which . http://dx.doi.org/10.1101/294637 doi: bioRxiv preprint first posted online Apr. 3, 2018; 2 An important challenge in neuroscience is to relate diverse characteristics of single neurons, in a co-registered fashion, within single brains 1 . Even simultaneous co-registration of two characteristics can be challenging, and has led to insights about the functional organization of neural circuits 2,3 . A high-throughput method capable of such multimodal co-registration would yield a "Rosetta Brain"-an integrative dataset that could constrain theoretical efforts to bridge across levels of structure and function in the nervous system 1 .As a first step toward this goal we began with MAPseq 4,5 (Fig. 1A, left), a sequencing-based method capable of mapping long-range projections of thousands of single neurons in a single brain. MAPseq achieves multiplexing by uniquely labeling individual neurons with random RNA sequences, or "barcodes". Because MAPseq, like most other sequencing methods, relies on tissue homogenization, it cannot resolve the spatial organization of the neuronal somata. This spatial organization, however, potentially allows the registration of distinct neuronal characteristics. We therefore sought to develop a method that would preserve the spatial organization of barc...
