Towards sequencing by synthesis In Situ

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.

Department dc:contributor.department

Program in Media Arts and Sciences (Massachusetts Institute of Technology)

Grantor dc:publisher

Massachusetts Institute of Technology

Year dc:date.issued

2017

Author dc:creator

• Payne, Andrew C. (Andrew Colin)

Advisor dc:contributor.advisor

• Edward S. Boyden.

• Program in Media Arts and Sciences ()

Statement dc:rights

• 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.

Licence dc:rights.uri

• http://dspace.mit.edu/handle/1721.1/7582

Language dc:language.iso

eng

Handle dc:identifier.uri

http://hdl.handle.net/1721.1/113770

OAI identifier oai:identifier

oai:dspace.mit.edu:1721.1/113770