Bulk RNA-seq study 10- RNA-seq of male KOLF2.2J hiPSC-derived endoderm and mesoderm homozygous null for three different transcription factors.

This study aims to phenotype iPSC-derived early endoderm and mesoderm that contain homozygous null alleles for the following transcription factors: ISL1, NKX2-1, and EOMES. Null alleles were generated using insertion of a premature termination codon with frameshift (PTC+1) in the case of ISL1 or full protein coding region deletion (KO) for NKX2-1 and EOMES. RNA-seq data was generated after 5 days of initiating differentiation from iPSCs. This analysis allowed the investigation of early embryonic development, cell fate mapping, and lineage analysis. The study involved the generation of RNA-seq on 15 samples. Two of the transcription factors were analyzed in the endoderm differentiation scheme and one in the early mesoderm scheme. Three biological replicates were run for each gene. 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. This comprehensive design allowed the investigation of the effects of transcription factor manipulation during early embryonic development.