Single-cell RNA-seq of differentiating inducible knockdown (with CTCF and GATA4 shRNA) Left Ventricle cardioids
This dataset comprises droplet-based single-cell RNA-seq (10x Genomics) from first heart field–derived left ventricle (LV) cardioids generated from WTC11 hiPSCs (TTN-mEGFP) carrying tetracycline-inducible shRNAs targeting GATA4 or CTCF, as well as a scrambled (SCR) control. Cardioids were profiled at day 4.5 and day 7.5 to capture early and later stages of LV differentiation under ± tetracycline (isogenic) conditions, with two biological replicates per time point. The dataset enables comparison of cellular composition, cardiomyocyte maturation trajectories (pseudotime), and knockdown-specific shifts in LV development. In brief, GATA4 KD expands immature/mesodermal populations and yields less-mature CM clusters, whereas CTCF KD produces more-mature CM states at day 4.5 and alters CM abundance by day 7.5 (as readouts; see figure panels for details). Each cell is annotated with the following information: line/perturbation (GATA4, CTCF, SCR), treatment (±Tet), time point (d4.5, d7.5), and replicate. Method details for scRNA-seq preparation (pooling 16 cardioids/condition, CMO multiplexing, FACS, library prep, and sequencing) are provided in the paper's Methods and Supplementary Methods.