Seurat function FindAllMarkers was used to find the cell type specific genes or differentially expressed genes between PBC and control samples with “logfc.threshold = 0.4, test.use = “MAST”” and “logfc.threshold = 0.3, test.use = “MAST”” respectively. The P values were adjusted by Bonferroni test. Most marker genes and differentially expressed genes are provided in Supplementary Data 2-10,11-17. For genes that may have a close relationship with the progression of PBC disease but have log-transformed fold changes less than 0.3, we have described the fold changes and adjusted P-values of these genes in the results section. R package clusterProfiler (v3.12) was applied to perform pathway enrichment analysis of given gene sets60.
Do you have any questions about this protocol?
Post your question to gather feedback from the community. We will also invite the authors of this article to respond.
Tips for asking effective questions
+ Description
Write a detailed description. Include all information that will help others answer your question including experimental processes, conditions, and relevant images.