Towards mapping spatial transcriptome of an entire vertebrate brain

Both the brain’s substantial complexity and technical challenges in monitoring and manipulating brains present challenges for understanding this essential organ. Zebrafish, for their modest brain size and transparency in the larval stage, serve as a model organism for whole-brain in vivo imaging and modeling. While calcium imaging generates substantial amounts of neural activity data, the lack of molecular information for individual neurons in a purely activity readout approach limits further biological interpretation. Recent advancements in in situ sequencing allow RNA profiling in its spatial context, which provides rich information on cell types and cell states. In this thesis, we adapted the expansion in situ sequencing(ExSeq) protocol for larval zebrafish brain slices. In brief, performing two rounds of expansion on zebrafish brain slices enabled us to obtain spatially localized sequencing readouts. This lays the foundation for mapping the spatial transcriptome of an entire vertebrate brain.

Name thesis:degree_name

Master

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

2021

Author dc:creator

• Zhang, Ruihan

Advisor dc:contributor.advisor

• Jacobson, Joseph M.

Statement dc:rights

• In Copyright - Educational Use Permitted
• Copyright MIT

Licence dc:rights.uri

• http://rightsstatements.org/page/InC-EDU/1.0/

Handle dc:identifier.uri

https://hdl.handle.net/1721.1/141957

OAI identifier oai:identifier

oai:dspace.mit.edu:1721.1/141957