Assessment of random monoallelic expression. (a) Examples of X-chromosome inactivation in clonal cell lines from females. Each column represents an individual clone and each row represents an individual SNP within a known gene. Inset is the key for color coding. By focusing our analyses on the X-chromosome rather than autosomes, we can observe the expected chromosome-wide inactivation of one of the two X-chromosomes. (b) Examples of random monoallelic expression (RMAE) in autosomal genes. Colors have the same meaning as in (a). To be 'assessed,' a gene had to have either a G-score > 1 (classified as RMAE class I), equal to 1 (RMAE class II), or a G-score of 0 with 2 or more informative clones (classified as biallelic expression). See detailed explanation in Note 4 in Additional file 1
. (c) Validation of RMAE calls with Sanger sequencing of cDNA from clonal cell lines. Comparison against the gDNA relative allelic balance is necessary to ensure that allelic imbalance seen in the nuclear cDNA did not result from PCR bias or loss of heterozygosity. The extent of allelic bias shown above (heterozygosity in the gDNA contrasted with an extreme allelic imbalance in the cDNA) is typical of RMAE genes. At the bottom is the summary of validation for randomly selected RMAE genes. Additional genes were also validated and these results, along with details on all validation experiments, are found in Table S2 in Additional file 1.