Study 6- RNA-seq of female WIBJ2 hiPSC-derived cortical brain organoids and extra-embryonic lineages homozygous null for five different transcription factors

This study aimed to phenotype iPSC-derived cortical brain organoids that contain homozygous null alleles for transcription factor PAX6 and to phenotype iPSC-derived extra-embryonic cell lineages that contain homozygous null alleles for transcription factors PPARG, EPAS1, GCM1, and GRHL1. Null alleles were generated by the insertion of a premature termination codon with frameshift (PTC+1). This analysis provided insight into the impact of loss of function for these transcription factors in the respective cell lineages. The study involved the generation of RNA-seq on 27 samples, comprising cells differentiated into cortical brain organoids (with dorsal forebrain patterning) and differentiated into the trophoblast lineage, promoting the formation of a primitive syncytium. Three biological replicates were run for each gene KO line. The hypoxia-inducible factor (EPAS1) was differentiated under both 20% oxygen and 3% (~ level present at peri-implantation) oxygen concentrations. Additionally, three biological replicates were run of wild-type WIBJ2 cells (the parental female cell line in which the KOs were generated) under the same differentiation conditions.