@article{08135d1ab6c34b1aa853c35b1296f807,
title = "High-Throughput Mapping of Long-Range Neuronal Projection Using In Situ Sequencing",
abstract = "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 barcoded anatomy resolved by sequencing (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 3,579 neurons in mouse auditory cortex using BARseq confirmed the laminar organization of the three top classes (intratelencephalic [IT], pyramidal tract-like [PT-like], and corticothalamic [CT]) of projection neurons. In depth analysis uncovered a 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.",
keywords = "auditory cortex, cellular barcoding, high throughput, in situ sequencing, projection mapping",
author = "Xiaoyin Chen and Sun, {Yu Chi} and Huiqing Zhan and Kebschull, {Justus M.} and Stephan Fischer and Katherine Matho and Huang, {Z. Josh} and Jesse Gillis and Zador, {Anthony M.}",
note = "Funding Information: The authors would like to acknowledge Kay Tye, Gordon Shephard, and Jessica Tollkuhn for useful discussions, and Barry Burbach, Nour El-Amine, Stephen Hearn, Jon Preall, and Yan Li for technical support. This work was supported by the following funding sources: NIH ( 5RO1NS073129 and 5RO1DA036913 to A.M.Z.), Brain Research Foundation ( BRF-SIA-2014-03 to A.M.Z.), IARPA MICrONS ( D16PC0008 to A.M.Z.), Simons Foundation ( 382793/SIMONS to A.M.Z.), Paul Allen Distinguished Investigator Award (to A.M.Z.), and a postdoctoral fellowship from the Simons Foundation to X.C. This work was performed with assistance from CSHL Shared Resources, which are funded, in part, by the NIH ( Cancer Center support grant 5P30CA045508 ). Funding Information: The authors would like to acknowledge Kay Tye, Gordon Shephard, and Jessica Tollkuhn for useful discussions, and Barry Burbach, Nour El-Amine, Stephen Hearn, Jon Preall, and Yan Li for technical support. This work was supported by the following funding sources: NIH (5RO1NS073129 and 5RO1DA036913 to A.M.Z.), Brain Research Foundation (BRF-SIA-2014-03 to A.M.Z.), IARPA MICrONS (D16PC0008 to A.M.Z.), Simons Foundation (382793/SIMONS to A.M.Z.), Paul Allen Distinguished Investigator Award (to A.M.Z.), and a postdoctoral fellowship from the Simons Foundation to X.C. This work was performed with assistance from CSHL Shared Resources, which are funded, in part, by the NIH (Cancer Center support grant 5P30CA045508). X.C. and A.M.Z. conceived the study. X.C. H.Z. and Y.-C.S. optimized and performed BARseq. X.C. and Y.-C.S. performed BARseq in combination with FISH and in Cre-labeled mice. J.M.K. and H.Z. performed MAPseq. X.C. performed single-cell RNA-seq. K.M. and Z.J.H. generated Cre-labeled mice. X.C. and A.M.Z. analyzed the BARseq and MAPseq data. X.C. S.F. and J.G. analyzed the single-cell RNA-seq data. X.C. and A.M.Z. wrote the paper. A.M.Z. is a founder and equity owner of MapNeuro. Publisher Copyright: {\textcopyright} 2019 Elsevier Inc.",
year = "2019",
month = oct,
day = "17",
doi = "10.1016/j.cell.2019.09.023",
language = "English (US)",
volume = "179",
pages = "772--786.e19",
journal = "Cell",
issn = "0092-8674",
publisher = "Cell Press",
number = "3",
}