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A Robust Approach to Identifying Tissue-Specific Gene Expression Regulatory Variants Using Personalized Human Induced Pluripotent Stem Cells

Figure 11

Changes in ASE during iPS differentiation.

(A) A biological replicate of PGP1Bx1 iPS1 cells were used for in vitro differentiation, using 100-µM trans-retinoic acid for 12 hours or embryoid body formation for 7 days. ASE loci with high confidence scores are shown. The expression SNPs in the upper left and the lower right quadrant represent those that have significantly altered their preference of parental alleles (5–13%). (B) Variations in ASE across six differentiated samples (3 RA-induced and 3 EBs) were analyzed according to their chromosomal locations. The ASE ratio variance from Chromosome 6 was compared to the ASE ratio variance from all other chromosomes.

Figure 11

doi: https://doi.org/10.1371/journal.pgen.1000718.g011