To obtain comprehensive transcripts of the CD44⁺ colon CSCs and an overview of their gene expression profiles, total RNAs were isolated from the CD44⁺ colon CSCs (CD44⁺) and CD44⁻ control cells (CD44⁻). DGE profiling was performed using the Illumina platform. A total of 9,957,439 and 8,463,165 reads were obtained for CD44⁺ and CD44⁻, respectively, corresponding to more than 1.7 billion base pairs of sequence data (Table 2). Sequence quality and GC content distribution were inspected (Supplementary Figs. S1 and S2), and results showed that DEG sequencing possessed high quality score and exactly matched GC content distribution.