Bulk RNA sequencing of wildtype and ABCA3 mutant human iPSC-derived mutant containing the ABCA3:GFP fusion reporter

We performed transcriptomic profiling of induced pluripotent stem cell (iPSC)-derived iAEC2s containing wildtype, E690K homozygous ABCA3 mutantion, and W308R homozygous ABCA3 mutation. We first performed CRISPR-Cas9 gene editing on a wildtype human iPSC line (BU3) to engineer a GFP reporter bi-allelically targeted at the stop codon of the endigenous ABCA3 locus, thus generating an ABCA3:GFP fusion reporter line (as previous published iin Sun. et al, 2021). Next we utilized CRISPR-Cas9 gene-mutagenesis to introduce two homozygous ABCA3 mutations (E690K and W308R), resulting in two, new ABCA3 mutant iPSC lines containg the ABCA3:GFP fusion reporter, totally a total of 3 ABCA3:GFP fusion iPSC lines (wildtype, E690K-AG, W308R-AG). Following triplicate distal lung directed differentiations of all 3 ABCA3:GFP fusion iPSC lines we sorted the ABCA3:GFP positive iAEC2s on day 43 for transcriptomic analyses. Overall design: Global transcriptomic profiling of human iPSC-derived iAEC2s containing mutant or wildtype ABCA3:GFP fusion reporter. Three total samples include: wildtype ABCA3 (WT), E690K mutant ABCA3 (E690K-AG), and W308R mutant ABCA3 (W308R-AG). ABCA3:GFP positive, live cells were on day 43 of human distal lung differentiation. Each sample have three biological replicates separated at day 0 (n=3). Prior to sorting for this bulk RNAseq run, the cells were previously sorted on day 15 using CD47hi/CD26low and on day 30 using CPM to enrich for NKX2-1.