Imperial College London
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DrNathanSkene

Faculty of Medicine, Department of Brain Sciences

Lecturer in Dementia Research, UK DRI Group Leader
 
 
 
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Contact

 

n.skene Website

 
 
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Location

 

515Burlington DanesHammersmith Campus

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Summary

 

Publications

Citation

BibTex format

@article{Qian:2020:10.1038/s41592-019-0631-4,
author = {Qian, X and Harris, KD and Hauling, T and Nicoloutsopoulos, D and Muñoz-Manchado, AB and Skene, N and Hjerling-Leffler, J and Nilsson, M},
doi = {10.1038/s41592-019-0631-4},
journal = {Nature Methods},
pages = {101--106},
title = {Probabilistic cell typing enables fine mapping of closely related cell types in situ},
url = {http://dx.doi.org/10.1038/s41592-019-0631-4},
volume = {17},
year = {2020}
}
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RIS format (EndNote, RefMan)

TY  - JOUR
AB  - 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 neuronal types, but cannot reveal their spatial arrangement. Here we introduce probabilistic cell typing by in situ sequencing (pciSeq), an approach that leverages previous scRNA-seq classification to identify cell types using multiplexed in situ RNA detection. We applied this method by mapping the inhibitory neurons of mouse hippocampal area CA1, for which ground truth is available from extensive previous work identifying their laminar organization. Our method identified these neuronal classes in a spatial arrangement matching ground truth, and further identified multiple classes of isocortical pyramidal cell in a pattern matching their known organization. This method will allow identifying the spatial organization of closely related cell types across the brain and other tissues.
AU  - Qian,X
AU  - Harris,KD
AU  - Hauling,T
AU  - Nicoloutsopoulos,D
AU  - Muñoz-Manchado,AB
AU  - Skene,N
AU  - Hjerling-Leffler,J
AU  - Nilsson,M
DO  - 10.1038/s41592-019-0631-4
EP  - 106
PY  - 2020///
SN  - 1548-7091
SP  - 101
TI  - Probabilistic cell typing enables fine mapping of closely related cell types in situ
T2  - Nature Methods
UR  - http://dx.doi.org/10.1038/s41592-019-0631-4
UR  - https://www.ncbi.nlm.nih.gov/pubmed/31740815
UR  - https://www.nature.com/articles/s41592-019-0631-4
UR  - http://hdl.handle.net/10044/1/75467
VL  - 17
ER  -
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