Transcriptomic Analysis of TYLMS-1 Cell Clones

We created three clones of TYLMS-1 cells treated with TAPI + DAPT, three clones of untreated TYLMS-1 cells (dimethyl sulfoxide added), three clones of TYLMS-1 cells transfected with siEPCAM, and three clones of TYLMS-1 cells transfected with scrambled siRNA, for a total of 12 TYLMS-1 cell clones. Total RNA was extracted from the clones using a RNeasy Mini Kit (Qiagen). RNA quality was assessed using an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). RNA sequencing (RNA-seq) libraries were prepared using the Illumina Stranded-specific library preparation method (dUTP method) and sequenced as paired-end 150 base pair (bp) reads on a NovaSeq 6000 machine. Raw RNA-Seq data were subjected to FastQC for quality control. The data were processed using BioJupies [24 (link)] for the normalisation of mRNA expression and DEG analysis.