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In Situ Transcription Profiling of Single Cells Reveals Spatial Organization of Cells in the Mouse Hippocampus

Shah, Sheel and Lubeck, Eric and Zhou, Wen and Cai, Long (2016) In Situ Transcription Profiling of Single Cells Reveals Spatial Organization of Cells in the Mouse Hippocampus. Neuron, 92 (2). pp. 342-357. ISSN 0896-6273. PMCID PMC5087994. https://resolver.caltech.edu/CaltechAUTHORS:20161021-132836401

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Abstract

Identifying the spatial organization of tissues at cellular resolution from single-cell gene expression profiles is essential to understanding biological systems. Using an in situ 3D multiplexed imaging method, seqFISH, we identify unique transcriptional states by quantifying and clustering up to 249 genes in 16,958 cells to examine whether the hippocampus is organized into transcriptionally distinct subregions. We identified distinct layers in the dentate gyrus corresponding to the granule cell layer and the subgranular zone and, contrary to previous reports, discovered that distinct subregions within the CA1 and CA3 are composed of unique combinations of cells in different transcriptional states. In addition, we found that the dorsal CA1 is relatively homogeneous at the single cell level, while ventral CA1 is highly heterogeneous. These structures and patterns are observed using different mice and different sets of genes. Together, these results demonstrate the power of seqFISH in transcriptional profiling of complex tissues.


Item Type:Article
Related URLs:
URLURL TypeDescription
https://doi.org/10.1016/j.neuron.2016.10.001DOIArticle
https://doi.org/10.1016/j.neuron.2017.05.009DOIEditorial Note
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5087994PubMed CentralArticle
ORCID:
AuthorORCID
Lubeck, Eric0000-0002-5457-0258
Zhou, Wen0000-0003-0357-2744
Cai, Long0000-0002-7154-5361
Additional Information:© 2016 Elsevier Inc. Published: October 19, 2016. We thank Michael Elowitz, Henry Lester, Hongwei Dong, and Bosiljka Tasic for advice on the manuscript. We also would like to thank Niles Pierce, Viviana Gradinaru, Thanos Siapas, Mary Kennedy, and Carlos Lois for productive discussions. Raw data can be found in the Supplemental Information. The National Institute of Health (R01-HD075605, DP2OD008530), the McKnight Foundation, and the Allen Foundation supported this work. Author Contributions: L.C., S.S., and E.L. designed the experiments. W.Z., S.S., and E.L. performed the experiments. L.C., S.S., and E.L. analyzed the data and wrote the manuscript.
Funders:
Funding AgencyGrant Number
NIHR01-HD075605
NIHDP2OD008530
McKnight FoundationUNSPECIFIED
Paul G. Allen Family FoundationUNSPECIFIED
Issue or Number:2
PubMed Central ID:PMC5087994
Record Number:CaltechAUTHORS:20161021-132836401
Persistent URL:https://resolver.caltech.edu/CaltechAUTHORS:20161021-132836401
Official Citation:Sheel Shah, Eric Lubeck, Wen Zhou, Long Cai, In Situ Transcription Profiling of Single Cells Reveals Spatial Organization of Cells in the Mouse Hippocampus, Neuron, Volume 92, Issue 2, 19 October 2016, Pages 342-357, ISSN 0896-6273, http://dx.doi.org/10.1016/j.neuron.2016.10.001. (http://www.sciencedirect.com/science/article/pii/S0896627316307024)
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:71349
Collection:CaltechAUTHORS
Deposited By: Tony Diaz
Deposited On:21 Oct 2016 20:44
Last Modified:22 Apr 2020 21:07

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