Counts and analyses for single cell data

Read counts and analyses on single cell data from 81 cells. Worksheet 1 contains the raw read counts for 13,408 genes and 96 cells obtained as described in the methods. Worksheet 2 contains the same data filtered for low gene expression and low confidence cells resulting in 11,319 genes and 81 cells (see methods for details). These filtered data were then normalised and log transformed using DESeq2 (Worksheets 3 and 4; see methods for Details). Worksheet 5 contains the cell identifier and the cluster affiliation (see Figure 1A). Worksheets 6 and 7 are comprised of the marker genes for cluster A and B and their respective AUC and adjusted p-value (computed by M3Drop, see methods), whereas worksheets 8 and 9 contain the GO analyses for these marker genes. Worksheet 10 contains the p-values for the hypergeometric tests conducted to check whether any genes with specific cell cycle profiles are over- or underrepresented in the marker genes for cluster A and B (see methods).