Bulk RNA-seq study 9- RNA-seq of male KOLF2.2J hiPSC-derived cortical brain organoids homozygous null for eight different transcription factors.

This study aims to phenotype iPSC-derived cortical brain organoids that contain homozygous null alleles for transcription factors expressed in the early neuroectoderm. Null alleles were generated using insertion of a premature termination codon with frameshift (PTC+1). RNA-seq data was generated at the indicated day post initiation of differentiation from hiPSCs. The study included the homozygous null alleles for the following transcription factors: EMX2, FOXG1, POU3F2, SOX1, HES5, SOX21, POU3F1 and SP8. This analysis provided insight into the impact of loss of function for these transcription factors in cortical brain organoid differentiation. The study involved the generation of RNA-seq on 39 samples. Different time points of differentiation to cortical brain organoids were chosen according to the initiation of the transcription factor in wildtype cells within this differentiation scheme. Three biological replicates were run for gene. Additionally, three biological replicates were run of wildtype KOLF2.2J cells (the parental male cell line in which the KOs were generated) under the same differentiation conditions in the different time points. This comprehensive design allowed for a robust analysis of the effects of transcription factor manipulation on brain organoid formation.