A Highly Phenotyped Open Access Repository of Alpha-1 Antitrypsin Deficiency Pluripotent Stem Cells

We profiled the global transcriptomes of 10 featured AATD-patient specific iPSC that underwent directed differentiation towards a hepatic and lung lineage. We used digital gene expression (DGE), a platform for high-fidelity RNA sequencing, and in addition to differentiated iPSC-derived cell types mentioned above (iHeps and iPSC-Lung progenitors), we also collected RNA from undifferentiated iPSCs and from a panel of primary adult human hepatocytes (PHH) for comparison. Overall design: For digital gene expression (DGE) the concentrations of all samples were normalized and sent to the Broad Institute for library construction and sequencing. Reads were then aligned to the ENSEMBL human reference genome. The count matrix was filtered and normalized to facilitate linear model fitting and differential expression testing. A liver enrichment score was derived by identifying differentially expressed genes between PHH and undifferentiated iPSCs.