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Highly multiplexed immunofluorescence images and single-cell data of immune markers in tonsil and lung cancer

View ORCID ProfileRumana Rashid, Giorgio Gaglia, Yu-An Chen, View ORCID ProfileJia-Ren Lin, Ziming Du, Zoltan Maliga, Denis Schapiro, Clarence Yapp, Jeremy Muhlich, Artem Sokolov, Peter Sorger, Sandro Santagata
doi: https://doi.org/10.1101/704114
Rumana Rashid
1Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA
2Laboratory for Systems Pharmacology, Harvard Medical School, Boston, MA
3Ludwig Center at Harvard, Harvard Medical School, Boston, MA
4Department of Biomedical Informatics, Harvard Medical School, Boston, MA
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  • ORCID record for Rumana Rashid
Giorgio Gaglia
1Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA
2Laboratory for Systems Pharmacology, Harvard Medical School, Boston, MA
3Ludwig Center at Harvard, Harvard Medical School, Boston, MA
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Yu-An Chen
2Laboratory for Systems Pharmacology, Harvard Medical School, Boston, MA
3Ludwig Center at Harvard, Harvard Medical School, Boston, MA
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Jia-Ren Lin
2Laboratory for Systems Pharmacology, Harvard Medical School, Boston, MA
3Ludwig Center at Harvard, Harvard Medical School, Boston, MA
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  • ORCID record for Jia-Ren Lin
Ziming Du
1Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA
2Laboratory for Systems Pharmacology, Harvard Medical School, Boston, MA
3Ludwig Center at Harvard, Harvard Medical School, Boston, MA
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Zoltan Maliga
2Laboratory for Systems Pharmacology, Harvard Medical School, Boston, MA
3Ludwig Center at Harvard, Harvard Medical School, Boston, MA
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Denis Schapiro
2Laboratory for Systems Pharmacology, Harvard Medical School, Boston, MA
5Broad Institute of MIT and Harvard, Cambridge, MA
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Clarence Yapp
2Laboratory for Systems Pharmacology, Harvard Medical School, Boston, MA
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Jeremy Muhlich
2Laboratory for Systems Pharmacology, Harvard Medical School, Boston, MA
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Artem Sokolov
2Laboratory for Systems Pharmacology, Harvard Medical School, Boston, MA
4Department of Biomedical Informatics, Harvard Medical School, Boston, MA
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Peter Sorger
2Laboratory for Systems Pharmacology, Harvard Medical School, Boston, MA
3Ludwig Center at Harvard, Harvard Medical School, Boston, MA
6Department of Systems Biology, Harvard Medical School, Boston, MA
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  • For correspondence: ssantagata@bics.bwh.harvard.edu peter_sorger@hms.harvard.edu
Sandro Santagata
1Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA
2Laboratory for Systems Pharmacology, Harvard Medical School, Boston, MA
3Ludwig Center at Harvard, Harvard Medical School, Boston, MA
7Department of Oncologic Pathology, Dana Farber Cancer Institute, Boston, MA
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  • For correspondence: ssantagata@bics.bwh.harvard.edu peter_sorger@hms.harvard.edu
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ABSTRACT

In this data descriptor, we document a dataset of multiplexed immunofluorescence images and derived single-cell measurements of immune lineage and other markers in formaldehyde-fixed and paraffin-embedded (FFPE) human tonsil and lung cancer tissue. We used tissue cyclic immunofluorescence (t-CyCIF) to generate fluorescence images which we artifact corrected using the BaSiC tool, stitched and registered using the ASHLAR algorithm, and segmented using ilastik software and MATLAB. We extracted single-cell features from these images using HistoCAT software. The resulting dataset can be visualized using image browsers and analyzed using high-dimensional, single-cell methods. This dataset is a valuable resource for biological discovery of the immune system in normal and diseased states as well as for the development of multiplexed image analysis and viewing tools.

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  • https://www.synapse.org/#!Synapse:syn17865732/wiki/592782

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted July 17, 2019.
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Highly multiplexed immunofluorescence images and single-cell data of immune markers in tonsil and lung cancer
Rumana Rashid, Giorgio Gaglia, Yu-An Chen, Jia-Ren Lin, Ziming Du, Zoltan Maliga, Denis Schapiro, Clarence Yapp, Jeremy Muhlich, Artem Sokolov, Peter Sorger, Sandro Santagata
bioRxiv 704114; doi: https://doi.org/10.1101/704114
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Highly multiplexed immunofluorescence images and single-cell data of immune markers in tonsil and lung cancer
Rumana Rashid, Giorgio Gaglia, Yu-An Chen, Jia-Ren Lin, Ziming Du, Zoltan Maliga, Denis Schapiro, Clarence Yapp, Jeremy Muhlich, Artem Sokolov, Peter Sorger, Sandro Santagata
bioRxiv 704114; doi: https://doi.org/10.1101/704114

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