Comprehensive analysis of gene expression changes induced by SOX4 in keratinocytes

To investigate the changes in gene expression profile of keratinocytes induced by the transcription factor SOX4, we used the tetracycline-dependent inducible system to regulate the activity of SOX4. The pRetroX-TetOne-TY1-SOX4 was generated by inserting DNA fragments corresponding to TY-1-taged SOX4 cDNA into the pRetroX-TetOne-Puro retroviral Tet-on Vector. pRetroX-TetOne-TY1-SOX4 was transfected into the GP2-293 cells. the virus-containing supernatants were added to the HaCaT cell growth medium. Thus, we generated a doxycycline (DOX)-dependent SOX4 overexpressing cell line (TY1-SOX4). RNA-seq was performed in DOX-treated or -untreated TY1-SOX4. Total RNA of TY1-SOX4 with or without DOX-treatment were extracted using ISOGEN. Thereafter, the resulting total RNA was converted to an Illumina sequencing library. Sequencing was performed on NextSeq 500 with paired-end 36 base-read options. Reads were mapped to the hg19 human reference genome and quantified using STAR. To estimate the expression patterns of transcripts, read counts were normalized by calculating the number of reads per kilobase per million for each transcript in individual samples, using CLC Genomics Workbench version 12.0. The filtering characteristics of fold change -2 to 2 (false discovery rate [FDR] at p < 0.05) were used to identify the differentially expressed genes (DEGs). Overall design: DEGs between non-treated TY1-SOX4 and DOX-treated TY1-SOX4.