Study 4- RNA-seq of male KOLF2.2J hiPSC-derived cortical brain organoids and extra-embryonic lineages homozygous null for six different transcription factors

This study aimed to phenotype iPSC-derived cortical brain organoids that contain homozygous null alleles for transcription factors DMRTA1 and TBR1 and to phenotype iPSC-derived extra-embryonic cell lineages that contain homozygous null alleles for transcription factors OVOL1, PITX1, LMO2, and ZBTB7C. 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 28 samples, comprising 10 differentiated into cortical brain organoids (with dorsal forebrain patterning) and 18 differentiated into the trophoblast lineage, promoting the formation of a primitive syncytium. Three biological replicates were run for each gene KO line. Additionally, three biological replicates were run of wild-type KOLF2.2J cells (the parental male cell line in which the KOs were generated) under the same differentiation conditions.