RNA velocity analysis for Pertrub-Seq
Ribonucleic acid velocity analysis for Pertrub-Seq
Massachusetts Institute of Technology. Department of Electrical Engineering and Computer Science.
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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 . 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.
Thesis: M. Eng., Massachusetts Institute of Technology, Department of Electrical Engineering and Computer Science, September, 2020Cataloged from student-submitted PDF of thesis.Includes bibliographical references (pages 67-69).
DepartmentMassachusetts Institute of Technology. Department of Electrical Engineering and Computer Science
Massachusetts Institute of Technology
Electrical Engineering and Computer Science.