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Clinical implementation of single-cell RNA sequencing using liver fine needle aspirate tissue sampling and centralized processing captures compartment specific immuno-diversity
Alex S. Genshaft, View ORCID ProfileSonu Subudhi, Arlin Keo, Juan D. Sanchez Vasquez, Nádia Conceição-Neto, Deeqa Mahamed, Lauke L. Boeijen, Nadia Alatrakchi, Chris Oetheimer, Mike Vilme, Riley Drake, Ira Fleming, Nancy Tran, Constantine Tzouanas, Jasmin Joseph-Chazan, Martin Arreola Villanueva, View ORCID ProfileHarmen J. G. van de Werken, Gertine W. van Oord, Zwier M.A. Groothuismink, Boris J. Beudeker, Zgjim Osmani, Shirin Nkongolo, Aman Mehrotra, Jordan Feld, Raymond T. Chung, Robert J. de Knegt, Harry L. A. Janssen, Jeroen Aerssens, Jacques Bollekens, Nir Hacohen, Georg M. Lauer, Andre Boonstra, Alex K. Shalek, Adam Gehring
doi: https://doi.org/10.1101/2021.11.30.470634
Alex S. Genshaft
1Institute for Medical Engineering and Science (IMES), Department of Chemistry, and Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology,
2The Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, 400 Technology Square, Cambridge, MA 02139, USA.
12Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
Sonu Subudhi
3Division of Gastroenterology and Liver Center, Massachusetts General Hospital and Harvard University, Boston, MA
Arlin Keo
4Department of Gastroenterology and Hepatology, Erasmus MC University Medical Center, Rotterdam, The Netherlands.
5Cancer Computational Biology Center, Erasmus MC Cancer Institute, University Medical Center, Rotterdam, the Netherlands.
Juan D. Sanchez Vasquez
6Toronto Centre for Liver Disease, Toronto General Hospital Research Institute, University Health Network, Toronto, Ontario, Canada
7Department of Immunology, University of Toronto, Toronto, Ontario, Canada
Nádia Conceição-Neto
8Infectious Diseases Biomarkers, Janssen Research and Development, Beerse, Belgium.
Deeqa Mahamed
6Toronto Centre for Liver Disease, Toronto General Hospital Research Institute, University Health Network, Toronto, Ontario, Canada
Lauke L. Boeijen
4Department of Gastroenterology and Hepatology, Erasmus MC University Medical Center, Rotterdam, The Netherlands.
Nadia Alatrakchi
3Division of Gastroenterology and Liver Center, Massachusetts General Hospital and Harvard University, Boston, MA
Chris Oetheimer
3Division of Gastroenterology and Liver Center, Massachusetts General Hospital and Harvard University, Boston, MA
Mike Vilme
1Institute for Medical Engineering and Science (IMES), Department of Chemistry, and Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology,
2The Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, 400 Technology Square, Cambridge, MA 02139, USA.
12Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
Riley Drake
1Institute for Medical Engineering and Science (IMES), Department of Chemistry, and Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology,
2The Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, 400 Technology Square, Cambridge, MA 02139, USA.
12Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
Ira Fleming
1Institute for Medical Engineering and Science (IMES), Department of Chemistry, and Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology,
2The Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, 400 Technology Square, Cambridge, MA 02139, USA.
12Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
Nancy Tran
1Institute for Medical Engineering and Science (IMES), Department of Chemistry, and Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology,
2The Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, 400 Technology Square, Cambridge, MA 02139, USA.
12Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
Constantine Tzouanas
1Institute for Medical Engineering and Science (IMES), Department of Chemistry, and Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology,
2The Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, 400 Technology Square, Cambridge, MA 02139, USA.
12Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
Jasmin Joseph-Chazan
1Institute for Medical Engineering and Science (IMES), Department of Chemistry, and Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology,
2The Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, 400 Technology Square, Cambridge, MA 02139, USA.
11Department of Immunology, Harvard Medical School, Boston, MA 02115, USA
12Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
Martin Arreola Villanueva
1Institute for Medical Engineering and Science (IMES), Department of Chemistry, and Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology,
2The Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, 400 Technology Square, Cambridge, MA 02139, USA.
10Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
12Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
Harmen J. G. van de Werken
4Department of Gastroenterology and Hepatology, Erasmus MC University Medical Center, Rotterdam, The Netherlands.
5Cancer Computational Biology Center, Erasmus MC Cancer Institute, University Medical Center, Rotterdam, the Netherlands.
9Department of Urology, Erasmus MC Cancer Institute, University Medical Center, Rotterdam, the Netherlands.
Gertine W. van Oord
4Department of Gastroenterology and Hepatology, Erasmus MC University Medical Center, Rotterdam, The Netherlands.
Zwier M.A. Groothuismink
4Department of Gastroenterology and Hepatology, Erasmus MC University Medical Center, Rotterdam, The Netherlands.
Boris J. Beudeker
4Department of Gastroenterology and Hepatology, Erasmus MC University Medical Center, Rotterdam, The Netherlands.
Zgjim Osmani
4Department of Gastroenterology and Hepatology, Erasmus MC University Medical Center, Rotterdam, The Netherlands.
Shirin Nkongolo
6Toronto Centre for Liver Disease, Toronto General Hospital Research Institute, University Health Network, Toronto, Ontario, Canada
Aman Mehrotra
6Toronto Centre for Liver Disease, Toronto General Hospital Research Institute, University Health Network, Toronto, Ontario, Canada
Jordan Feld
6Toronto Centre for Liver Disease, Toronto General Hospital Research Institute, University Health Network, Toronto, Ontario, Canada
Raymond T. Chung
3Division of Gastroenterology and Liver Center, Massachusetts General Hospital and Harvard University, Boston, MA
Robert J. de Knegt
4Department of Gastroenterology and Hepatology, Erasmus MC University Medical Center, Rotterdam, The Netherlands.
Harry L. A. Janssen
6Toronto Centre for Liver Disease, Toronto General Hospital Research Institute, University Health Network, Toronto, Ontario, Canada
Jeroen Aerssens
8Infectious Diseases Biomarkers, Janssen Research and Development, Beerse, Belgium.
Jacques Bollekens
8Infectious Diseases Biomarkers, Janssen Research and Development, Beerse, Belgium.
Nir Hacohen
11Department of Immunology, Harvard Medical School, Boston, MA 02115, USA
12Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
Georg M. Lauer
2The Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, 400 Technology Square, Cambridge, MA 02139, USA.
Andre Boonstra
4Department of Gastroenterology and Hepatology, Erasmus MC University Medical Center, Rotterdam, The Netherlands.
Alex K. Shalek
1Institute for Medical Engineering and Science (IMES), Department of Chemistry, and Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology,
2The Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, 400 Technology Square, Cambridge, MA 02139, USA.
12Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
Adam Gehring
6Toronto Centre for Liver Disease, Toronto General Hospital Research Institute, University Health Network, Toronto, Ontario, Canada
7Department of Immunology, University of Toronto, Toronto, Ontario, Canada
Posted December 02, 2021.
Clinical implementation of single-cell RNA sequencing using liver fine needle aspirate tissue sampling and centralized processing captures compartment specific immuno-diversity
Alex S. Genshaft, Sonu Subudhi, Arlin Keo, Juan D. Sanchez Vasquez, Nádia Conceição-Neto, Deeqa Mahamed, Lauke L. Boeijen, Nadia Alatrakchi, Chris Oetheimer, Mike Vilme, Riley Drake, Ira Fleming, Nancy Tran, Constantine Tzouanas, Jasmin Joseph-Chazan, Martin Arreola Villanueva, Harmen J. G. van de Werken, Gertine W. van Oord, Zwier M.A. Groothuismink, Boris J. Beudeker, Zgjim Osmani, Shirin Nkongolo, Aman Mehrotra, Jordan Feld, Raymond T. Chung, Robert J. de Knegt, Harry L. A. Janssen, Jeroen Aerssens, Jacques Bollekens, Nir Hacohen, Georg M. Lauer, Andre Boonstra, Alex K. Shalek, Adam Gehring
bioRxiv 2021.11.30.470634; doi: https://doi.org/10.1101/2021.11.30.470634
Clinical implementation of single-cell RNA sequencing using liver fine needle aspirate tissue sampling and centralized processing captures compartment specific immuno-diversity
Alex S. Genshaft, Sonu Subudhi, Arlin Keo, Juan D. Sanchez Vasquez, Nádia Conceição-Neto, Deeqa Mahamed, Lauke L. Boeijen, Nadia Alatrakchi, Chris Oetheimer, Mike Vilme, Riley Drake, Ira Fleming, Nancy Tran, Constantine Tzouanas, Jasmin Joseph-Chazan, Martin Arreola Villanueva, Harmen J. G. van de Werken, Gertine W. van Oord, Zwier M.A. Groothuismink, Boris J. Beudeker, Zgjim Osmani, Shirin Nkongolo, Aman Mehrotra, Jordan Feld, Raymond T. Chung, Robert J. de Knegt, Harry L. A. Janssen, Jeroen Aerssens, Jacques Bollekens, Nir Hacohen, Georg M. Lauer, Andre Boonstra, Alex K. Shalek, Adam Gehring
bioRxiv 2021.11.30.470634; doi: https://doi.org/10.1101/2021.11.30.470634
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