Resolving cell cycling and non-cycling dynamics in scRNA-seq
department or school: Science, Faculty of
data provider: DSpace
degree campus: UBCV
creator: MacDonald, Haley
issued: 2025-02-05T00:07:13Z
issued: 2025
related degree: Master of Science - MSc
degree grantor: University of British Columbia
description: Controlled progression through and exit from the cell cycle is essential for normal development and healthy tissue function, while cell cycle dysregulation and sustained proliferation is a key hallmark of cancer. With the advent of large-scale single cell transcriptomics, a variety of methods were developed to detect cells in distinct phases of the cell cycle, including G1, S and G2/M, but characterization of non-cycling cellular states and their role in tumour evolution remains limited. Current tools for inferring cell cycle phase from single cell RNA sequencing (scRNA-seq) datasets have not been comprehensively benchmarked, and most are not compatible with heterogeneous samples containing multiple cell types. Here we present Ouroboros, a comprehensive package to accurately identify cell cycle phase and non-cycling cellular states in scRNA-seq datasets. Ouroboros facilitates integrated cell cycle visualization through the generation of representative cell cycle UMAPs and provides a random forest model that outperforms existing cell cycle tools while classifying two additional non-cycling states. Applied to heterogeneous developmental and tumour datasets, Ouroboros reveals complex cell state dynamics over pseudotime and between patient treatment time points. By enabling comprehensive visualization and classification of cycling and non-cycling cells, we anticipate that Ouroboros will offer a means to explore the complex interplay between cellular proliferation and quiescence in health and disease.
aggregated CHO: https://circle.library.ubc.ca/rest/handle/2429/90330
note: RESOLVING CELL CYCLING AND NON-CYCLING DYNAMICS IN SCRNA-SEQ by Haley MacDonald B.Sc., The University of Guelph, 2019 A THESIS SUBMITTED IN PARTIAL FULFILLMENT OF THE REQUIREMENTS FOR THE DEGREE OF MASTER OF SCIENCE in The Faculty of Graduate and Postdoctoral Studies (Bioinformatics) THE UNIVERSITY OF BRITISH COLUMBIA (Vancouver) February 2025 © Haley MacDonald, 2025 ii The following individuals certify that they have read, and recommend to the Faculty of Graduate and Postdoctoral Studies for acceptance, the thesis entitled: Resolving cell cycling and non-cycling dynamics in scRNA-seq submitted by Haley MacDonald in partial fulfilment of the requirements for the degree of Master of Science in Bioinformatics Examining Committee: Dr. Adi Steif, Department of Medical Genetics, UBC Supervisor Dr. Marco Marra, Department of Medical Genetics, UBC Supervisory Committee Member Dr. Yongjin Park, Department of Pathology and Laboratory Medicine, UBC Supervisory Committee Member iii Abstract Controlled progression through and exit from the cell cycle is essential for normal development and healthy tissue function, while cell cycle dysregulation and sustained proliferation is a key hallmark of cancer. With the advent of large-scale single cell transcriptomics, a variety of methods were developed to detect cells in distinct phases of the cell cycle, including G1, S and G2/M, but characterization of non-cycling cellular states and their role in tumour evolution remains limited. Current tools for inferring cell cycle phase from single cell RNA sequencing (scRNA-seq) datasets have not been comprehensively benchmarked, and most are not compatible with heterogeneous samples containing multiple cell types. Here we present Ouroboros, a comprehensive package to accurately identify cell cycle phase and non-cycling cellular states in scRNA-seq datasets. Ouroboros facilitates integrated cell cycle visualization through the generation of representative cell cycle UMAPs and provides a random …
has type: Thesis/Dissertation
date issued: 2025-05
is shown at: 10.14288/1.0447974
language: eng
degree discipline: Bioinformatics
provider: Vancouver : University of British Columbia Library
publisher: University of British Columbia
rights: Attribution-NonCommercial-NoDerivatives 4.0 International
rights URI: http://creativecommons.org/licenses/by-nc-nd/4.0/
scholar level: Graduate
contributor: Steif, Adi
type: Text
identifier URI: http://hdl.handle.net/2429/90330