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...
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| Format: | Thesis |
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Massachusetts Institute of Technology
2022
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| Online Access: | https://hdl.handle.net/1721.1/141957 |
| _version_ | 1826215641652133888 |
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| author | Zhang, Ruihan |
| author2 | Jacobson, Joseph M. |
| author_facet | Jacobson, Joseph M. Zhang, Ruihan |
| author_sort | Zhang, Ruihan |
| collection | MIT |
| description | 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. |
| first_indexed | 2024-09-23T16:37:09Z |
| format | Thesis |
| id | mit-1721.1/141957 |
| institution | Massachusetts Institute of Technology |
| last_indexed | 2024-09-23T16:37:09Z |
| publishDate | 2022 |
| publisher | Massachusetts Institute of Technology |
| record_format | dspace |
| spelling | mit-1721.1/1419572022-04-20T03:02:00Z Towards mapping spatial transcriptome of an entire vertebrate brain Zhang, Ruihan Jacobson, Joseph M. Program in Media Arts and Sciences (Massachusetts Institute of Technology) 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. S.M. 2022-04-19T19:59:53Z 2022-04-19T19:59:53Z 2021-06 2022-02-27T16:51:05.025Z Thesis https://hdl.handle.net/1721.1/141957 0000-0002-1564-5907 In Copyright - Educational Use Permitted Copyright MIT http://rightsstatements.org/page/InC-EDU/1.0/ application/pdf Massachusetts Institute of Technology |
| spellingShingle | Zhang, Ruihan Towards mapping spatial transcriptome of an entire vertebrate brain |
| title | Towards mapping spatial transcriptome of an entire vertebrate brain |
| title_full | Towards mapping spatial transcriptome of an entire vertebrate brain |
| title_fullStr | Towards mapping spatial transcriptome of an entire vertebrate brain |
| title_full_unstemmed | Towards mapping spatial transcriptome of an entire vertebrate brain |
| title_short | Towards mapping spatial transcriptome of an entire vertebrate brain |
| title_sort | towards mapping spatial transcriptome of an entire vertebrate brain |
| url | https://hdl.handle.net/1721.1/141957 |
| work_keys_str_mv | AT zhangruihan towardsmappingspatialtranscriptomeofanentirevertebratebrain |