Supplemental Data for Computational profiling of hiPSC-derived heart organoids reveals chamber defects associated with NKX2-5 deficiency

Supplemental Data LegendsSupplemental Data 1: Inter-cluster differentially expressed genes (DEGs) depicted in Figure 2Cii (fdr &lt; 0.001). At most, twenty top DEGs are reported for each cluster. The column labeled ‘cluster’ indicates which cluster the gene is up regulated in.Supplemental Data 2: Inter-cluster differentially expressed genes depicted in Figure 4Bii (fdr &lt; 0.001). At most, twenty top DEGs are reported for each cluster. The column labeled ‘cluster’ indicates which cluster the gene is up regulated in.Supplemental Data 3: Inter-cluster differentially expressed genes depicted in Figure S8Bii (fdr &lt; 0.1). At most, twenty top DEGs are reported for each cluster. The column labeled ‘cluster’ indicates which cluster the gene is up regulated in.Supplemental Data 4: Differentially expressed genes between stages and differentiation methods for each cardiac cell type depicted in Figure S11Ei-iii (fdr &lt; 0.001). The column labeled ‘cell_type’ indicates which cell type was used to calculate the DEGs, while the column labeled ‘stage_and_differentiation_method’ indicates which group (Day 15 Org, Day 15 ML, Day 30 Org, or Day 30 ML) the gene is up regulated in.Supplemental Data 5: Differentially expressed genes between wild type and mutant cells for each cardiac cell type depicted in Figure 9F (CMs) and Figure S14Ai (FBs), and Figure S14Bi (Endo_ECs) (fdr &lt; 0.001). The column labeled ‘cell_type’ indicates which cell type was used to calculate the DEGs, while the column labeled ‘WTvsMUT’ indicates which group (wild type vs mutant cells) the gene is up regulated in.Supplemental Data 6: Cell type annotations used for the training set, Cui et al.Supplemental Data 7: Cell type annotations used for the development set 1 from Asp et al.Supplemental Data 8: Cell type annotations used for the development set 2 from Miao et al.Supplemental Data 9: Important genes selected by the first random forest model and used as features in the second random forest model. The column labeled ‘classifier’ indicates which type of classifier (cell type, zone, or laterality) was being trained, while the column labeled ‘dataset’ indicates which test set (cross validation, development set 1, development set 2, wild type unsorted hiPSC, mutant unsorted hiPSC, or sorted hiPSC data) was being predicted on when the important genes were selected. For cross validation, the intersection of important genes for each iteration is reported.Supplemental Data 10: Spreadsheet containing source data used to generate main figures.<br><br>