RNAseq, Caco2 cell line, knockout of CD133, clone 3
Total RNA was isolated from 310^6 Caco-2 cells (TRIM28-KO, CD133-KO, and reference clones) using the RecoverAll Total Nucleic Acid Isolation Kit (Thermo Fisher) per manufacturers instructions. RNA quantity and integrity were assessed with Qubit and Agilent RNA 6000 Nano (Agilent). rRNA depletion and library preparation used the KAPA RNA HyperPrep RiboErase kit; libraries were QCd by Qubit HS and TapeStation. Sequencing was performed on an Illumina NextSeq 550 (30 M reads/sample).