RNASeq to investigate SOX2 and SOX9 function in human fetal lung tip progenitor cells

In order to understand transcription factor SOX2 and SOX9 function, we have knocked down SOX2 and SOX9 in human fetal lung tip progenitor organoids using an inducible CRISPRi system. We discovered that SOX2 knockdown didn't appear to influence organoid cell survival and led to minimal gene expression changes at transcriptome level. By contrast, SOX9 knockdown led to organoid cell self-renewal defects and we have detected hundreds of genes differentially expressed after SOX9 knockdown. We used 2 independent organoid parental lines infected with inducible CRISPRi system. 2 different non-targeting control (NT) gRNAs, which do not bind to anywhere of the genome, 2 different gRNAs targeting for SOX2 knockdown, and 2 different gRNAs targeting for SOX9 knockdown were used to control non-specific effect from organoid lines, lentiviral infection and different gRNAs.