scRNA-seq in 79 fibroblast cell lines and 31 reprogrammed induced pluripotent stem cell lines for sceQTL analysis

Here, we performed scRNA-seq on 64,018 fibroblasts from 79 donors and mapped expression quantitative trait loci (eQTLs) at the level of individual cell types. We demonstrate that the majority of eQTLs detected in fibroblasts are specific to an individual cell subtype. To address if the allelic effects on gene expression are maintained following cell reprogramming, we generated scRNA-seq data in 19,967 iPSCs from 31 reprogramed donor lines. We again identify highly cell type specific eQTLs in iPSCs, and show that that the eQTLs in fibroblasts almost entirely disappear during reprogramming.