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A spatial atlas of inhibitory cell types in mouse hippocampus

Xiaoyan Qian, Kenneth D. Harris, Thomas Hauling, Dimitris Nicoloutsopoulos, Ana B. Muñoz-Manchado, Nathan Skene, Jens Hjerling-Leffler, Mats Nilsson
doi: https://doi.org/10.1101/431957
Xiaoyan Qian
1Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Sweden
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Kenneth D. Harris
2Institute of Neurology, University College London, UK
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  • For correspondence: kenneth.harris@ucl.ac.uk mats.nilsson@scilifelab.se
Thomas Hauling
1Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Sweden
2Institute of Neurology, University College London, UK
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Dimitris Nicoloutsopoulos
2Institute of Neurology, University College London, UK
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Ana B. Muñoz-Manchado
3Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
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Nathan Skene
2Institute of Neurology, University College London, UK
3Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
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Jens Hjerling-Leffler
3Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
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Mats Nilsson
1Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Sweden
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  • For correspondence: kenneth.harris@ucl.ac.uk mats.nilsson@scilifelab.se
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Abstract

Understanding the function of a tissue requires knowing the spatial organization of its constituent cell types. In the cerebral cortex, single-cell RNA sequencing (scRNA-seq) has revealed the genome-wide expression patterns that define its many, closely related cell types, but cannot reveal their spatial arrangement. Here we introduce probabilistic cell typing by in situ sequencing (pciSeq), an approach that leverages prior scRNA-seq classification to identify cell types using multiplexed in situ RNA detection. We applied this method to map the inhibitory neurons of hippocampal area CA1, a cell system critical for memory function, for which ground truth is available from extensive prior work identifying the laminar organization of subtly differing cell types. Our method confidently identified 16 interneuron classes, in a spatial arrangement closely matching ground truth. This method will allow identifying the spatial organization of fine cell types across the brain and other tissues.

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Posted October 01, 2018.
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A spatial atlas of inhibitory cell types in mouse hippocampus
Xiaoyan Qian, Kenneth D. Harris, Thomas Hauling, Dimitris Nicoloutsopoulos, Ana B. Muñoz-Manchado, Nathan Skene, Jens Hjerling-Leffler, Mats Nilsson
bioRxiv 431957; doi: https://doi.org/10.1101/431957
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A spatial atlas of inhibitory cell types in mouse hippocampus
Xiaoyan Qian, Kenneth D. Harris, Thomas Hauling, Dimitris Nicoloutsopoulos, Ana B. Muñoz-Manchado, Nathan Skene, Jens Hjerling-Leffler, Mats Nilsson
bioRxiv 431957; doi: https://doi.org/10.1101/431957

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