Bulk RNA sequencing of cardiac organoids differentiated from hiPSC-derived cell lines with knockdown of factors involved in early cardiac specification
This dataset was generated to investigate the role of two DNA-binding factors, CTCF and GATA4, in early cardiac specification. Three WTC11-derived hiPSC lines were employed, each carrying a stably integrated shRNA construct. Two of the constructs specifically target CTCF and GATA4, while the third expresses a scrambled, non-targeting shRNA that serves as a control. All shRNA systems are driven by a tetracycline-inducible promoter, enabling conditional knockdown.  Each of the three cell lines was differentiated into 3D cardiac organoids patterned toward right ventricle and atrium fates. Differentiations were carried out for 7.5 days, both in the presence and absence of tetracycline, thereby providing an isogenic control for each knockdown condition. For every condition, two independent differentiations were performed, ensuring biological replication.