Applying genome editing and genomics for novel cellular tracking and measurement
Abstract/Contents
- Abstract
- The three projects comprising this thesis explore and apply genetic diversity to various biological processes. In the first project, I engineer updatable and diverse CRISPR-based sequence barcodes for lineage tracing applications. I demonstrate the potential of such CRISPR-based barcoding methods by illustrating the agreement between the fully known lineage of C. elegans and that obtained using dynamic sequence barcodes, delve into the challenge presented by sequence dropouts through a simulation-based approach, and underscore the technique's promise by establishing its information content. In the second project, I add a new tool to the CRISPR/Cas9 toolbox by exploring the genetic diversity of CRISPR systems and discovering IgnaviCas9, a Cas9 from a hyperthermophilic Ignavibacterium. IgnaviCas9 expands the temperature range at which targeted nucleic acid cleavage is possible, thus speeding the development of new biotechnological techniques. I demonstrate one such application by using IgnaviCas9 to deplete undesired amplicons during the amplification step of library preparation in sequencing workflows. In the final project, I enable the examination of how genetic diversity is created during the processes of sperm development. I apply microfluidic methods to capture and amplify DNA from single sperm cells. I then perform whole genome sequencing to understand selection processes during spermatogenesis.
Description
| Type of resource | text |
|---|---|
| Form | electronic resource; remote; computer; online resource |
| Extent | 1 online resource. |
| Place | California |
| Place | [Stanford, California] |
| Publisher | [Stanford University] |
| Copyright date | 2019; ©2019 |
| Publication date | 2019; 2019 |
| Issuance | monographic |
| Language | English |
Creators/Contributors
| Author | Schmidt, Stephanie Tzouanas |
|---|---|
| Degree supervisor | Quake, Stephen Ronald |
| Thesis advisor | Quake, Stephen Ronald |
| Thesis advisor | Bassik, Michael |
| Thesis advisor | Qi, Lei, (Professor of Bioengineering) |
| Degree committee member | Bassik, Michael |
| Degree committee member | Qi, Lei, (Professor of Bioengineering) |
| Associated with | Stanford University, Department of Bioengineering. |
Subjects
| Genre | Theses |
|---|---|
| Genre | Text |
Bibliographic information
| Statement of responsibility | Stephanie Tzouanas Schmidt. |
|---|---|
| Note | Submitted to the Department of Bioengineering. |
| Thesis | Thesis Ph.D. Stanford University 2019. |
| Location | electronic resource |
Access conditions
- Copyright
- © 2019 by Stephanie Tzouanas Schmidt
- License
- This work is licensed under a Creative Commons Attribution Non Commercial No Derivatives 3.0 Unported license (CC BY-NC-ND).
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