JAX Study 1 and Study 2 - RNA-seq of male KOLF2.2J hiPSC-derived trophoblast cell lines homozygous null for 14 different transcription factors

This SuperSeries is composed of the SubSeries listed below. This study aims to phenotype iPSC-derived trophoblast lines that contain homozygous null alleles for transcription factors expressed within the extra-embryonic lineage, with a focus on differentiation toward either primitive syncytium or extra-embryonic mesenchymal cells, depending on the TF being analyzed. Null alleles were generated using three distinct genetic engineering approaches: full protein coding region deletion (KO), critical exon deletion (CE), and insertion of a premature termination codon with frameshift (PTC+1). RNA-seq data was generated after 6 days of initiating differentiation from iPSCs. The study included the homozygous null alleles for the following transcription factors: GRHL1, POU2F3, EPAS1, FOSB, GCM1, PPARG, and ISL1, MEIS1, MXD1, MEIS2, RUNX1, MEF2C, NCOA3, and BHLHE40. Notably, the hypoxia-inducible factor EPAS1 was evaluated under both 20% oxygen and 3% (~ level present at peri-implantation) oxygen concentrations. This analysis provided insight into the differences between the various CRISPR-Cas9-based approaches and the impact of loss of function for these transcription factors in trophoblast lineage differentiation.