The effect of Foxc1 deficiency on undifferentiated and differentiated human primary keratinocytes

In this study, we used a RNA-sequencing (RNA-seq) approach to analyze the whole transcriptomes of human primary Keratinocytes (KC) at undifferentiated stage and differentiated stage with and without FOXC1 knockdown. Each treatment condition have 2 or 3 replicates. 10 million reads were collected. A total of 8202 genes were designated as present (RPKM>5 in at least one sample). 635 genes were differentially expressed (FDR<0.01, P<0.000774201). FOXC1 knock-down significantly impaired keratinocytes differentiation process. Proliferating foreskin normal human keratinocytes were seeded in 24 well-dishes and transfected with scrambled siRNA and FOXC1 siRNA duplexes. The following day, half of the wells were differentiated in vitro by increasing Ca2+ concentration in culture media from 0.06mM to 1.3 mM for 5 days. The other half wells of cells were cultured in 0.06mM CaCl2. Both undifferentiated and differentiated cells were harvested for total RNA extraction. RNA sequencing libraries were made using Illumina RNA sequencing library construction protocol. RNA libraries were sequenced by 100bp reads on Illumina Hi-seq 2000.