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A Derived Positional Mapping of Inhibitory Subtypes in the Somatosensory Cortex

Obtaining a catalog of cell types is a fundamental building block for understanding the brain. The ideal classification of cell-types is based on the profile of molecules expressed by a cell, in particular, the profile of genes expressed. One strategy is, therefore, to obtain as many single-cell tra...

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Autores principales: Keller, Daniel, Meystre, Julie, Veettil, Rahul V., Burri, Olivier, Guiet, Romain, Schürmann, Felix, Markram, Henry
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2019
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6691028/
https://www.ncbi.nlm.nih.gov/pubmed/31447655
http://dx.doi.org/10.3389/fnana.2019.00078
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author Keller, Daniel
Meystre, Julie
Veettil, Rahul V.
Burri, Olivier
Guiet, Romain
Schürmann, Felix
Markram, Henry
author_facet Keller, Daniel
Meystre, Julie
Veettil, Rahul V.
Burri, Olivier
Guiet, Romain
Schürmann, Felix
Markram, Henry
author_sort Keller, Daniel
collection PubMed
description Obtaining a catalog of cell types is a fundamental building block for understanding the brain. The ideal classification of cell-types is based on the profile of molecules expressed by a cell, in particular, the profile of genes expressed. One strategy is, therefore, to obtain as many single-cell transcriptomes as possible and isolate clusters of neurons with similar gene expression profiles. In this study, we explored an alternative strategy. We explored whether cell-types can be algorithmically derived by combining protein tissue stains with transcript expression profiles. We developed an algorithm that aims to distribute cell-types in the different layers of somatosensory cortex of the developing rat constrained by the tissue- and cellular level data. We found that the spatial distribution of major inhibitory cell types can be approximated using the available data. The result is a depth-wise atlas of inhibitory cell-types of the rat somatosensory cortex. In principle, any data that constrains what can occur in a particular part of the brain can also strongly constrain the derivation of cell-types. This draft inhibitory cell-type mapping is therefore dynamic and can iteratively converge towards the ground truth as further data is integrated.
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spelling pubmed-66910282019-08-23 A Derived Positional Mapping of Inhibitory Subtypes in the Somatosensory Cortex Keller, Daniel Meystre, Julie Veettil, Rahul V. Burri, Olivier Guiet, Romain Schürmann, Felix Markram, Henry Front Neuroanat Neuroscience Obtaining a catalog of cell types is a fundamental building block for understanding the brain. The ideal classification of cell-types is based on the profile of molecules expressed by a cell, in particular, the profile of genes expressed. One strategy is, therefore, to obtain as many single-cell transcriptomes as possible and isolate clusters of neurons with similar gene expression profiles. In this study, we explored an alternative strategy. We explored whether cell-types can be algorithmically derived by combining protein tissue stains with transcript expression profiles. We developed an algorithm that aims to distribute cell-types in the different layers of somatosensory cortex of the developing rat constrained by the tissue- and cellular level data. We found that the spatial distribution of major inhibitory cell types can be approximated using the available data. The result is a depth-wise atlas of inhibitory cell-types of the rat somatosensory cortex. In principle, any data that constrains what can occur in a particular part of the brain can also strongly constrain the derivation of cell-types. This draft inhibitory cell-type mapping is therefore dynamic and can iteratively converge towards the ground truth as further data is integrated. Frontiers Media S.A. 2019-08-06 /pmc/articles/PMC6691028/ /pubmed/31447655 http://dx.doi.org/10.3389/fnana.2019.00078 Text en Copyright © 2019 Keller, Meystre, Veettil, Burri, Guiet, Schürmann and Markram. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Neuroscience
Keller, Daniel
Meystre, Julie
Veettil, Rahul V.
Burri, Olivier
Guiet, Romain
Schürmann, Felix
Markram, Henry
A Derived Positional Mapping of Inhibitory Subtypes in the Somatosensory Cortex
title A Derived Positional Mapping of Inhibitory Subtypes in the Somatosensory Cortex
title_full A Derived Positional Mapping of Inhibitory Subtypes in the Somatosensory Cortex
title_fullStr A Derived Positional Mapping of Inhibitory Subtypes in the Somatosensory Cortex
title_full_unstemmed A Derived Positional Mapping of Inhibitory Subtypes in the Somatosensory Cortex
title_short A Derived Positional Mapping of Inhibitory Subtypes in the Somatosensory Cortex
title_sort derived positional mapping of inhibitory subtypes in the somatosensory cortex
topic Neuroscience
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6691028/
https://www.ncbi.nlm.nih.gov/pubmed/31447655
http://dx.doi.org/10.3389/fnana.2019.00078
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