Fig. 1

Workflow for identifying escapee genes from single cells. a Quantitative properties of ChrX and Chr17 are listed according to GRCh37 (GRC Human Build 37). b A scheme for the analysis of single cell primary fibroblasts. The two colors for the nuclei represent the random choice of Xa. In the context of fibroblasts, each Xa exhibits a different pattern of expression for the hSNPs. Each of the iSNPs can be assigned to the reference (R) or the alternative allele (A). If one cell with one Xa will have an expression pattern of A R A, a cell with the alternative Xa will express R A R. Due to the random X inactivation, and the hSNPs not being phased, annotating a gene as an escapee is entirely based on having multiple evidence of iSNPs with biallelic expression. The illustrative table shows the analysis of iSNPs from each of the hSNPs (on the left) in each of the cells as A or R and the annotation of a gene according to the accumulation of the iSNPs evidence. The illustration marks hSNPs derived from 4 single cells (cell-1 to cell-4). The hSNPs are associated with 3 genes (marked as gene a to gene c). Gene a is the only gene with multiple biallelic iSNPs thus it is annotated as Escapee gene (Esc). The other two genes either do not have biallelic iSNPs (gene b) or have only a single iSNP as evidence for biallelic expression (gene c) and thus are annotated as Inactivated gene (Ina). c The scheme for the single cells clonal lymphoblasts. In contrast to primary fibroblasts (b), the parental origin of Xa is identical for all cells. In this case of GM12878 cell-line Xa is associated with the maternal (M) allele (symbolized by pink colored nuclei). For lymphoblasts, the occurrence of a paternal allele (marked as P) suffices the identification of an iSNP being expressed from Xi and thus can be potentially annotated an escapee. The table on the right emphasized lymphoblast escapee assignment. The categories of the table are the same as in (b). For details on the workflow and the applied protocols, see Additional file 1: Text and Figure S1