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Deep learning and alignment of spatially-resolved whole transcriptomes of single cells in the mouse brain with Tangram

View ORCID ProfileTommaso Biancalani, View ORCID ProfileGabriele Scalia, View ORCID ProfileLorenzo Buffoni, View ORCID ProfileRaghav Avasthi, View ORCID ProfileZiqing Lu, View ORCID ProfileAman Sanger, View ORCID ProfileNeriman Tokcan, View ORCID ProfileCharles R. Vanderburg, View ORCID ProfileAsa Segerstolpe, View ORCID ProfileMeng Zhang, View ORCID ProfileInbal Avraham-Davidi, View ORCID ProfileSanja Vickovic, View ORCID ProfileMor Nitzan, Sai Ma, View ORCID ProfileJason Buenrostro, View ORCID ProfileNik Bear Brown, View ORCID ProfileDuccio Fanelli, View ORCID ProfileXiaowei Zhuang, View ORCID ProfileEvan Z. Macosko, View ORCID ProfileAviv Regev
doi: https://doi.org/10.1101/2020.08.29.272831
Tommaso Biancalani
1Broad Institute of MIT and Harvard, Cambridge, MA 02142
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  • ORCID record for Tommaso Biancalani
  • For correspondence: tbiancal@broadinstitute.org aregev@broadinstitute.org
Gabriele Scalia
1Broad Institute of MIT and Harvard, Cambridge, MA 02142
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  • ORCID record for Gabriele Scalia
Lorenzo Buffoni
2Department of Physics and Astrophysics, University of Florence, Florence, Italy
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  • ORCID record for Lorenzo Buffoni
Raghav Avasthi
1Broad Institute of MIT and Harvard, Cambridge, MA 02142
3Northeastern University, Boston, MA 02115
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  • ORCID record for Raghav Avasthi
Ziqing Lu
1Broad Institute of MIT and Harvard, Cambridge, MA 02142
3Northeastern University, Boston, MA 02115
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  • ORCID record for Ziqing Lu
Aman Sanger
1Broad Institute of MIT and Harvard, Cambridge, MA 02142
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  • ORCID record for Aman Sanger
Neriman Tokcan
1Broad Institute of MIT and Harvard, Cambridge, MA 02142
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  • ORCID record for Neriman Tokcan
Charles R. Vanderburg
1Broad Institute of MIT and Harvard, Cambridge, MA 02142
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  • ORCID record for Charles R. Vanderburg
Asa Segerstolpe
1Broad Institute of MIT and Harvard, Cambridge, MA 02142
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  • ORCID record for Asa Segerstolpe
Meng Zhang
4Department of Chemistry and Chemical Biology, Department of Physics, Harvard University
6Howard Hughes Medical Institute
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  • ORCID record for Meng Zhang
Inbal Avraham-Davidi
1Broad Institute of MIT and Harvard, Cambridge, MA 02142
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Sanja Vickovic
1Broad Institute of MIT and Harvard, Cambridge, MA 02142
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Mor Nitzan
1Broad Institute of MIT and Harvard, Cambridge, MA 02142
5School of Engineering and Applied Sciences, Harvard University
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  • ORCID record for Mor Nitzan
Sai Ma
1Broad Institute of MIT and Harvard, Cambridge, MA 02142
7Department of Biology, MIT, Cambridge, MA 02140
8Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, 02138 USA
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Jason Buenrostro
1Broad Institute of MIT and Harvard, Cambridge, MA 02142
8Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, 02138 USA
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Nik Bear Brown
3Northeastern University, Boston, MA 02115
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Duccio Fanelli
2Department of Physics and Astrophysics, University of Florence, Florence, Italy
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  • ORCID record for Duccio Fanelli
Xiaowei Zhuang
4Department of Chemistry and Chemical Biology, Department of Physics, Harvard University
6Howard Hughes Medical Institute
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Evan Z. Macosko
1Broad Institute of MIT and Harvard, Cambridge, MA 02142
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  • ORCID record for Evan Z. Macosko
Aviv Regev
1Broad Institute of MIT and Harvard, Cambridge, MA 02142
6Howard Hughes Medical Institute
7Department of Biology, MIT, Cambridge, MA 02140
9Genentech, 1 DNA Way, South San Francisco, CA, 94080
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  • For correspondence: tbiancal@broadinstitute.org aregev@broadinstitute.org
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Article Information

doi 
https://doi.org/10.1101/2020.08.29.272831
History 
  • August 30, 2020.

Article Versions

  • You are currently viewing Version 1 of this article (August 30, 2020 - 21:31).
  • Version 2 (September 15, 2020 - 17:37).
  • View Version 3, the most recent version of this article.
Copyright 
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 4.0 International license.

Author Information

  1. Tommaso Biancalani1,#,
  2. Gabriele Scalia1,
  3. Lorenzo Buffoni2,
  4. Raghav Avasthi1,3,
  5. Ziqing Lu1,3,
  6. Aman Sanger1,
  7. Neriman Tokcan1,
  8. Charles R. Vanderburg1,
  9. Asa Segerstolpe1,
  10. Meng Zhang4,6,
  11. Inbal Avraham-Davidi1,
  12. Sanja Vickovic1,
  13. Mor Nitzan1,5,
  14. Sai Ma1,7,8,
  15. Jason Buenrostro1,8,
  16. Nik Bear Brown3,
  17. Duccio Fanelli2,
  18. Xiaowei Zhuang4,6,
  19. Evan Z. Macosko1 and
  20. Aviv Regev1,6,7,9,#
  1. 1Broad Institute of MIT and Harvard, Cambridge, MA 02142
  2. 2Department of Physics and Astrophysics, University of Florence, Florence, Italy
  3. 3Northeastern University, Boston, MA 02115
  4. 4Department of Chemistry and Chemical Biology, Department of Physics, Harvard University
  5. 5School of Engineering and Applied Sciences, Harvard University
  6. 6Howard Hughes Medical Institute
  7. 7Department of Biology, MIT, Cambridge, MA 02140
  8. 8Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, 02138 USA
  9. 9Genentech, 1 DNA Way, South San Francisco, CA, 94080
  1. ↵#To whom correspondence should be addressed: tbiancal{at}broadinstitute.org (TB) aregev{at}broadinstitute.org (AR)
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Posted August 30, 2020.
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Deep learning and alignment of spatially-resolved whole transcriptomes of single cells in the mouse brain with Tangram
Tommaso Biancalani, Gabriele Scalia, Lorenzo Buffoni, Raghav Avasthi, Ziqing Lu, Aman Sanger, Neriman Tokcan, Charles R. Vanderburg, Asa Segerstolpe, Meng Zhang, Inbal Avraham-Davidi, Sanja Vickovic, Mor Nitzan, Sai Ma, Jason Buenrostro, Nik Bear Brown, Duccio Fanelli, Xiaowei Zhuang, Evan Z. Macosko, Aviv Regev
bioRxiv 2020.08.29.272831; doi: https://doi.org/10.1101/2020.08.29.272831
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Deep learning and alignment of spatially-resolved whole transcriptomes of single cells in the mouse brain with Tangram
Tommaso Biancalani, Gabriele Scalia, Lorenzo Buffoni, Raghav Avasthi, Ziqing Lu, Aman Sanger, Neriman Tokcan, Charles R. Vanderburg, Asa Segerstolpe, Meng Zhang, Inbal Avraham-Davidi, Sanja Vickovic, Mor Nitzan, Sai Ma, Jason Buenrostro, Nik Bear Brown, Duccio Fanelli, Xiaowei Zhuang, Evan Z. Macosko, Aviv Regev
bioRxiv 2020.08.29.272831; doi: https://doi.org/10.1101/2020.08.29.272831

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