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Cell Type Purification by Single-Cell Transcriptome-Trained Sorting

45 Pages Posted: 16 May 2019 Sneak Peek Status: Published

See all articles by Chloé S. Baron

Chloé S. Baron

Royal Netherlands Academy of Arts and Sciences - Hubrecht Institute‐KNAW; Utrecht University, University Medical Center (Utrecht), Division Biomedical Genetics, Cancer Genomics Netherlands; The Netherlands Cancer Institute - Oncode Institute

Aditya Barve

Royal Netherlands Academy of Arts and Sciences - Hubrecht Institute‐KNAW; Utrecht University, University Medical Center (Utrecht), Division Biomedical Genetics, Cancer Genomics Netherlands; The Netherlands Cancer Institute - Oncode Institute

Mauro Muraro

Royal Netherlands Academy of Arts and Sciences - Hubrecht Institute‐KNAW; Utrecht University, University Medical Center (Utrecht), Division Biomedical Genetics, Cancer Genomics Netherlands; The Netherlands Cancer Institute - Oncode Institute; Single Cell Discoveries

Gitanjali Dharmadhikari

Royal Netherlands Academy of Arts and Sciences - Hubrecht Institute‐KNAW; Utrecht University, University Medical Center (Utrecht), Division Biomedical Genetics, Cancer Genomics Netherlands

Reinier van der Linden

Royal Netherlands Academy of Arts and Sciences - Hubrecht Institute‐KNAW; Utrecht University, University Medical Center (Utrecht), Division Biomedical Genetics, Cancer Genomics Netherlands

Anna Lyubimova

Royal Netherlands Academy of Arts and Sciences - Hubrecht Institute‐KNAW; Utrecht University, University Medical Center (Utrecht), Division Biomedical Genetics, Cancer Genomics Netherlands; The Netherlands Cancer Institute - Oncode Institute

Eelco JP de Koning

Royal Netherlands Academy of Arts and Sciences - Hubrecht Institute‐KNAW; Utrecht University, University Medical Center (Utrecht), Division Biomedical Genetics, Cancer Genomics Netherlands; Leiden University, Medical Center (LUMC), Department of Medicine, Section of Nephrology and Section of Endocrinology

Alexander van Oudenaarden

Royal Netherlands Academy of Arts and Sciences - Hubrecht Institute‐KNAW; Utrecht University, University Medical Center (Utrecht), Division Biomedical Genetics, Cancer Genomics Netherlands; The Netherlands Cancer Institute - Oncode Institute

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Abstract

Much of modern 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 the zebrafish kidney marrow and the human pancreas to high purity without resorting to specific antibodies or transgenes.

Keywords: Fluorescence activated cell sorting, single-cell RNA-Sequencing, transcriptome-trained sorting, cell type purification, zebrafish hematopoiesis, human pancreatic islets

Suggested Citation

Baron, Chloé S. and Barve, Aditya and Muraro, Mauro and Dharmadhikari, Gitanjali and van der Linden, Reinier and Lyubimova, Anna and de Koning, Eelco JP and van Oudenaarden, Alexander, Cell Type Purification by Single-Cell Transcriptome-Trained Sorting (May 14, 2019). CELL-D-19-01293. Available at SSRN: https://ssrn.com/abstract=3387654 or http://dx.doi.org/10.2139/ssrn.3387654
This is a paper under consideration at Cell Press and has not been peer-reviewed.

Chloé S. Baron

Royal Netherlands Academy of Arts and Sciences - Hubrecht Institute‐KNAW ( email )

Amsterdam, 1000 GC
Netherlands

Utrecht University, University Medical Center (Utrecht), Division Biomedical Genetics, Cancer Genomics Netherlands ( email )

Universiteitsweg 100
Utrecht, 3584 CG
Netherlands

The Netherlands Cancer Institute - Oncode Institute ( email )

Plesmanlaan 121
Amsterdam, 1066 CX
Netherlands

Aditya Barve

Royal Netherlands Academy of Arts and Sciences - Hubrecht Institute‐KNAW ( email )

Amsterdam, 1000 GC
Netherlands

Utrecht University, University Medical Center (Utrecht), Division Biomedical Genetics, Cancer Genomics Netherlands ( email )

Universiteitsweg 100
Utrecht, 3584 CG
Netherlands

The Netherlands Cancer Institute - Oncode Institute ( email )

Plesmanlaan 121
Amsterdam, 1066 CX
Netherlands

Mauro Muraro

Royal Netherlands Academy of Arts and Sciences - Hubrecht Institute‐KNAW

Amsterdam, 1000 GC
Netherlands

Utrecht University, University Medical Center (Utrecht), Division Biomedical Genetics, Cancer Genomics Netherlands

Universiteitsweg 100
Utrecht, 3584 CG
Netherlands

The Netherlands Cancer Institute - Oncode Institute

Plesmanlaan 121
Amsterdam, 1066 CX
Netherlands

Single Cell Discoveries

Utrecht
Netherlands

Gitanjali Dharmadhikari

Royal Netherlands Academy of Arts and Sciences - Hubrecht Institute‐KNAW ( email )

Amsterdam, 1000 GC
Netherlands

Utrecht University, University Medical Center (Utrecht), Division Biomedical Genetics, Cancer Genomics Netherlands ( email )

Universiteitsweg 100
Utrecht, 3584 CG
Netherlands

Reinier Van der Linden

Royal Netherlands Academy of Arts and Sciences - Hubrecht Institute‐KNAW ( email )

Amsterdam, 1000 GC
Netherlands

Utrecht University, University Medical Center (Utrecht), Division Biomedical Genetics, Cancer Genomics Netherlands ( email )

Universiteitsweg 100
Utrecht, 3584 CG
Netherlands

Anna Lyubimova

Royal Netherlands Academy of Arts and Sciences - Hubrecht Institute‐KNAW ( email )

Amsterdam, 1000 GC
Netherlands

Utrecht University, University Medical Center (Utrecht), Division Biomedical Genetics, Cancer Genomics Netherlands ( email )

Universiteitsweg 100
Utrecht, 3584 CG
Netherlands

The Netherlands Cancer Institute - Oncode Institute ( email )

Plesmanlaan 121
Amsterdam, 1066 CX
Netherlands

Eelco JP De Koning

Royal Netherlands Academy of Arts and Sciences - Hubrecht Institute‐KNAW ( email )

Amsterdam, 1000 GC
Netherlands

Utrecht University, University Medical Center (Utrecht), Division Biomedical Genetics, Cancer Genomics Netherlands ( email )

Universiteitsweg 100
Utrecht, 3584 CG
Netherlands

Leiden University, Medical Center (LUMC), Department of Medicine, Section of Nephrology and Section of Endocrinology ( email )

Leiden
Netherlands

Alexander Van Oudenaarden (Contact Author)

Royal Netherlands Academy of Arts and Sciences - Hubrecht Institute‐KNAW ( email )

Amsterdam, 1000 GC
Netherlands

Utrecht University, University Medical Center (Utrecht), Division Biomedical Genetics, Cancer Genomics Netherlands ( email )

Universiteitsweg 100
Utrecht, 3584 CG
Netherlands

The Netherlands Cancer Institute - Oncode Institute ( email )

Plesmanlaan 121
Amsterdam, 1066 CX
Netherlands

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