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Published October 19, 2016 | Supplemental Material + Accepted Version
Journal Article Open

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

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.

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.

Attached Files

Accepted Version - nihms820662.pdf

Supplemental Material - mmc1.pdf

Supplemental Material - mmc2.xlsx

Supplemental Material - mmc3.xlsx

Supplemental Material - mmc4.xlsx

Supplemental Material - mmc5.xlsx

Supplemental Material - mmc6.xlsx

Supplemental Material - mmc7.xlsx

Supplemental Material - mmc8.xlsx

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Created:
August 20, 2023
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