RNA-seq of DLD1 cells with CDX2 knocked out (clone D3): Sample BP105
RNA was extracted using Trizol (Ambion 15596026) per the manufacturer's instructions then purified using the Qiagen QiaEasy RNA clean up kit (74204). RNA quality was analyzed by Bioanalyzer (Agilent RNA Pico). Poly-A pull-down was used to enrich mRNAs from total RNA samples. Libraries were constructed using Illumina TruSeq stranded mRNA kit. RTA (Illumina) was used for base calling and bcl2fastq2 (version 2.20) was used for converting BCL to fast format, coupled with adaptor trimming.