Modification of Seurat v4 for the Development of a Phase Assignment Tool Able to Distinguish between G2 and Mitotic Cells

• Published in: International journal of molecular sciences Vol. 25; no. 9; p. 4589
• Main Authors: Watson, Steven, Porter, Harry, Sudbery, Ian, Thompson, Ruth
• Format: Journal Article
• Language: English
• Published: Switzerland MDPI AG 01-05-2024
• Subjects: bioinformatics; Cell cycle; Computational Biology - methods; Confidence; Cyclones; Datasets; Ethylenediaminetetraacetic acid; Flow cytometry; G2 Phase - genetics; Gene expression; Gene Expression Profiling - methods; Genes; Histones - genetics; Histones - metabolism; Humans; mitosis; Mitosis - genetics; phase assignment; RNA; RNA sequencing; Scientific equipment and supplies industry; Sequence Analysis, RNA - methods; Single-Cell Analysis - methods; Software; Telomerase; United States; United Kingdom; RNA sequencing; phase assignment; mitosis; cell cycle; bioinformatics
• ISSN: 1422-0067; 1661-6596; 1422-0067
• DOI: 10.3390/ijms25094589

Single-cell RNA sequencing (scRNAseq) is a rapidly advancing field enabling the characterisation of heterogeneous gene expression profiles within a population. The cell cycle phase is a major contributor to gene expression variance between cells and computational analysis tools have been developed to assign cell cycle phases to cells within scRNAseq datasets. Whilst these tools can be extremely useful, all have the drawback that they classify cells as only G1, S or G2/M. Existing discrete cell phase assignment tools are unable to differentiate between G2 and M and continuous-phase-assignment tools are unable to identify a region corresponding specifically to mitosis in a pseudo-timeline for continuous assignment along the cell cycle. In this study, bulk RNA sequencing was used to identify differentially expressed genes between mitotic and interphase cells isolated based on phospho-histone H3 expression using fluorescence-activated cell sorting. These gene lists were used to develop a methodology which can distinguish G2 and M phase cells in scRNAseq datasets. The phase assignment tools present in Seurat were modified to allow for cell cycle phase assignment of all stages of the cell cycle to identify a mitotic-specific cell population.