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Cell Type Purification by Single-Cell Transcriptome-Trained Sorting

Much of current molecular and cell biology research relies on the ability to purify cell types by fluorescence-activated cell sorting (FACS). FACS typically relies on the ability to label cell types of interest with antibodies or fluorescent transgenic constructs. However, antibody availability is o...

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Autores principales: Baron, Chloé S., Barve, Aditya, Muraro, Mauro J., van der Linden, Reinier, Dharmadhikari, Gitanjali, Lyubimova, Anna, de Koning, Eelco J.P., van Oudenaarden, Alexander
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Cell Press 2019
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6863042/
https://www.ncbi.nlm.nih.gov/pubmed/31585086
http://dx.doi.org/10.1016/j.cell.2019.08.006
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author Baron, Chloé S.
Barve, Aditya
Muraro, Mauro J.
van der Linden, Reinier
Dharmadhikari, Gitanjali
Lyubimova, Anna
de Koning, Eelco J.P.
van Oudenaarden, Alexander
author_facet Baron, Chloé S.
Barve, Aditya
Muraro, Mauro J.
van der Linden, Reinier
Dharmadhikari, Gitanjali
Lyubimova, Anna
de Koning, Eelco J.P.
van Oudenaarden, Alexander
author_sort Baron, Chloé S.
collection PubMed
description Much of current molecular and cell biology research relies on the ability to purify cell types by fluorescence-activated cell sorting (FACS). FACS typically relies on the ability to label cell types of interest with antibodies or fluorescent transgenic constructs. However, antibody availability is often limited, and genetic manipulation is labor intensive or impossible in the case of primary human tissue. To date, no systematic method exists to enrich for cell types without a priori knowledge of cell-type markers. Here, we propose GateID, a computational method that combines single-cell transcriptomics with FACS index sorting to purify cell types of choice using only native cellular properties such as cell size, granularity, and mitochondrial content. We validate GateID by purifying various cell types from zebrafish kidney marrow and the human pancreas to high purity without resorting to specific antibodies or transgenes.
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spelling pubmed-68630422019-11-22 Cell Type Purification by Single-Cell Transcriptome-Trained Sorting Baron, Chloé S. Barve, Aditya Muraro, Mauro J. van der Linden, Reinier Dharmadhikari, Gitanjali Lyubimova, Anna de Koning, Eelco J.P. van Oudenaarden, Alexander Cell Article Much of current molecular and cell biology research relies on the ability to purify cell types by fluorescence-activated cell sorting (FACS). FACS typically relies on the ability to label cell types of interest with antibodies or fluorescent transgenic constructs. However, antibody availability is often limited, and genetic manipulation is labor intensive or impossible in the case of primary human tissue. To date, no systematic method exists to enrich for cell types without a priori knowledge of cell-type markers. Here, we propose GateID, a computational method that combines single-cell transcriptomics with FACS index sorting to purify cell types of choice using only native cellular properties such as cell size, granularity, and mitochondrial content. We validate GateID by purifying various cell types from zebrafish kidney marrow and the human pancreas to high purity without resorting to specific antibodies or transgenes. Cell Press 2019-10-03 /pmc/articles/PMC6863042/ /pubmed/31585086 http://dx.doi.org/10.1016/j.cell.2019.08.006 Text en © 2019 The Author(s) http://creativecommons.org/licenses/by-nc-nd/4.0/ This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).
spellingShingle Article
Baron, Chloé S.
Barve, Aditya
Muraro, Mauro J.
van der Linden, Reinier
Dharmadhikari, Gitanjali
Lyubimova, Anna
de Koning, Eelco J.P.
van Oudenaarden, Alexander
Cell Type Purification by Single-Cell Transcriptome-Trained Sorting
title Cell Type Purification by Single-Cell Transcriptome-Trained Sorting
title_full Cell Type Purification by Single-Cell Transcriptome-Trained Sorting
title_fullStr Cell Type Purification by Single-Cell Transcriptome-Trained Sorting
title_full_unstemmed Cell Type Purification by Single-Cell Transcriptome-Trained Sorting
title_short Cell Type Purification by Single-Cell Transcriptome-Trained Sorting
title_sort cell type purification by single-cell transcriptome-trained sorting
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6863042/
https://www.ncbi.nlm.nih.gov/pubmed/31585086
http://dx.doi.org/10.1016/j.cell.2019.08.006
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