RNA velocity analysis for Pertrub-Seq
Name
1227275866-MIT.pdf
Size
4.88 MB
Format
Adobe PDF
Checksum (MD5)
22c7de2df4b9714e4add1b2eefec09bd
Author(s)
Kebed, Mesert.
Advisor(s)
Aviv Regev.
Alternative Title
Ribonucleic acid velocity analysis for Pertrub-Seq
Date Issued
2020
Publisher
Massachusetts Institute of Technology
Abstract
Recent developments in single-cell RNA seq and CRISPR based perturbations have enabled researchers to carry out hundreds of perturbation experiments in a pooled format in an experimental approach called Perturb-Seq [7]. Prior analysis of Perturb-Seq measured the overall effect of a perturbation on each gene, however it remains difficult to capture temporal responses to a perturbation. In this thesis, we compare the effectiveness of three RNA velocity informed models and two cell-cell similarity based models in providing a pseudo-temporal ordering of cells. We find pseudotime estimated with the dynamical model for computing velocity provides the most reliable ordering of cells. We use this pseudo-temporal ordering to bin cells into three time resolved groups and compute the effect of a perturbation at each time point. This analysis provides a promising start to understanding the temporal effects of a perturbation.
Description
Thesis: M. Eng., Massachusetts Institute of Technology, Department of Electrical Engineering and Computer Science, September, 2020
Cataloged from student-submitted PDF of thesis.
Includes bibliographical references (pages 67-69).
Subjects
Electrical Engineering and Computer Science.
MIT Department
Massachusetts Institute of Technology. Department of Electrical Engineering and Computer Science
Terms of Use
MIT theses may be protected by copyright. Please reuse MIT thesis content according to the MIT Libraries Permissions Policy, which is available through the URL provided.
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