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A spatial atlas of inhibitory cell types in mouse hippocampus

Authors :
Mats Nilsson
Kenneth D. Harris
Nathan G. Skene
Xiaoyan Qian
Jens Hjerling-Leffler
Ana B. Muñoz Manchado
Dimitris Nicoloutsopoulos
Thomas Hauling
Publication Year :
2018
Publisher :
Cold Spring Harbor Laboratory, 2018.

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.

Details

Language :
English
Database :
OpenAIRE
Accession number :
edsair.doi.dedup.....67e0f745a65c0272b5c7538957fc372d
Full Text :
https://doi.org/10.1101/431957