2026-09-19T10:35:29Zhttps://dspace.mit.edu/server/oai/requestoai:dspace.mit.edu:1721.1/1137702021-07-05T14:03:20Zcom_1721.1_7582com_1721.1_7581col_1721.1_131023
Edward S. Boyden.
Payne, Andrew C. (Andrew Colin)
Program in Media Arts and Sciences (Massachusetts Institute of Technology)
Program in Media Arts and Sciences (Massachusetts Institute of Technology)
2018-02-16T20:05:07Z
2018-02-16T20:05:07Z
2017
2017
http://hdl.handle.net/1721.1/113770
1022284037
Thesis: S.M., Massachusetts Institute of Technology, School of Architecture and Planning, Program in Media Arts and Sciences, 2017.
Cataloged from PDF version of thesis.
Includes bibliographical references (pages 53-55).
The development of fluorescence in situ nucleic acid sequencing (FISSEQ) will permit investigators to answer scientific questions in which the spatial context of gene expression rather than just identity and abundance - must be taken into account; recent progress in biological sample engineering, including physical expansion of tissue (i.e. Expansion Microscopy), will radically empower this technology (ExSEQ). However, in situ sequencing is technically difficult to implement, requiring an investigator to be familiar with a wide variety of techniques in molecular biology, microfluidics, fluorescence microscopy, image processing, and bioinformatics, and improvements are still needed before it is widely practicable. In this work, we investigate the use of sequencing by synthesis - as opposed to the currently practiced method of sequencing by ligation - in order to realize improvements in usability and performance. We demonstrate the viability of sequencing by synthesis reactions in situ, characterize their performance, and describe a route from demonstration to practice.
by Andrew C. Payne.
S.M.
55 pages
eng
Massachusetts Institute of Technology
MIT theses are protected by copyright. They may be viewed, downloaded, or printed from this source but further reproduction or distribution in any format is prohibited without written permission.
http://dspace.mit.edu/handle/1721.1/7582
Program in Media Arts and Sciences ()
Towards sequencing by synthesis In Situ
Thesis
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<Abstract>The development of fluorescence in situ nucleic acid sequencing (FISSEQ) will permit investigators to answer scientific questions in which the spatial context of gene expression rather than just identity and abundance - must be taken into account; recent progress in biological sample engineering, including physical expansion of tissue (i.e. Expansion Microscopy), will radically empower this technology (ExSEQ). However, in situ sequencing is technically difficult to implement, requiring an investigator to be familiar with a wide variety of techniques in molecular biology, microfluidics, fluorescence microscopy, image processing, and bioinformatics, and improvements are still needed before it is widely practicable. In this work, we investigate the use of sequencing by synthesis - as opposed to the currently practiced method of sequencing by ligation - in order to realize improvements in usability and performance. We demonstrate the viability of sequencing by synthesis reactions in situ, characterize their performance, and describe a route from demonstration to practice.</Abstract>
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