Hi all,i'm currently studying a brain sc-seq data by seurat package,and my cluster analysis seems to be profoundly influenced by genes that relate to ribosome(named Rpxxx).A few clusters is characterized by expression of these genes,and known markers of cell types seems to have little relation with these clusters.I have regressed cell cycle by ScaleData function,so i'm confused about what these ribosome-related dada means.Shall i delete these data?Or shall i study these ribosome-related clusters in other way?Thank all!
BTW,i have deleted blood cells from my data by hemoglobin-related genes
Hi,
I tend to be quite careful about removing genes in the data set if I see that the data quality is good. Have you performed cell quality control (filtering out cells based on counts/number of genes/mitochondrial RNA fraction) and adequate normalization and batch correction if necessary? I have also previously found clusters with a lot of ribosomal gene markers, but looking at known marker gene expression clarified this (in my case Stem cell markers).
Also, is your data set mouse or human? If it is mouse you could check out Linnarson's mouse brain atlas.
Good luck!