Bulk RNA sequencing of ABCA3 mutant, and gene-corrected patient iPSC-derived iAEC2s

We performed transcriptomic profiling of patient induced pluripotent stem cell (iPSC)-derived iAEC2s containing E690K and W308R ABCA3 mutations as well as their syngeneic, gene-corrected iAEC2s (total of four iPSC-derived iAEC2 lines). We first reprogrammed iPSCs from 2 patients with two homozyguos ABCA3 mutations (E690K and W308R ABCA3 mutations). Next we utilized TALENs gene-editing technique previously published in Jacob et al. (2017) to monoallelically target the endogenous SFTPC locus with the tdTomato reporter, allowing for sorting and isolation of SFTPCtdTomato positive iAEC2s. Finally, we used CRISPR-Cas9 footprint-free gene-correction to generate syngeneic patient iPSCs which were dfferentiated into the corresponding iAEC2s for syngeneic comparisons. Following tripplicate differentiations of all 4 patient iPSC lines, we sorted the SFTPCtdTomato+ iAEC2s on day 43-44 of differentiation for transcriptomic analyses. Overall design: Global transcriptomic profiling of patient iPSC-derived iAEC2s containing homozygous ABCA3 mutations and their corresponding gene-corrected iAEC2s. Total of 4 patient iPSC-derived iAEC2s were differentiated in biological triplicate (n=3) separated from day 0 of directed differentiation: homozygous E690K mutant (E690K) line; gene-corrected E690 line (cE690);W308R mutant (W308R) line; gene-corrrected W308 line (cW308). Upon directed diifferentiation following protocol previously published by our lab (Jacob et al., 2017, 2019), SFTPCtdTomato+ iAEC2s were sorted onday 43-44 of differentiation for transcriptomic analyses.