Protocol for classifying cellular senescence from single-cell and single-nucleus RNA sequencing data

Cellular senescence is a cell state characterized by stable cell-cycle arrest accompanied by coordinated molecular, metabolic, and functional changes. Here, we present a protocol to classify senescent cells from single-cell or single-nucleus RNA sequencing data using gene expression activity scoring of a senescence gene set provided by the user. We describe steps for data-driven optimization of estimated proportion of senescent cells per cell type via enrichment testing. We then detail procedures for differential expression analysis to define senescence-associated transcriptional programs. For complete details on the use and execution of this protocol, please refer to Lund et al. 1