scRNA-seq
For Caco2 cells stably expressed shRNA targeting SETDB1 and shScramble, we used 10X Genomics Chromium machine to capture single cells and cDNA preparation. 3000 cells were loaded on a Chromium Single Cell Instrument to generate single cell nanoliter-scale Gel Bead-In-EMulsions (GEMs). The barcoded cDNA was then amplified in PCR and the single-cell RNA sequencing libraries were prepared using version 1 Chromium Single Cell 3 Library, Gel beads and Multiplex kit (10X Genomics). The libraries were quantified using qPCR according to the qPCR Quantification Protocol Guide (KAPA Library Quantificatoin kits for Illumina Sequecing platforms) and qualified using the TapeStation D1000 ScreenTape (Agilent Technologies, Waldbronn, Germany). Indexed libraries were then sequenced using the HiSeq2500 platform (Illumina) by the Macrogen Incorporated.