gDNA RRBS, control, patient #6
Patient samples and unidentified data were supplied under the UChicago protocol (IRB#10-209-A). The protocol involves data and sample collection from newly diagnosed patients with non-metastatic colorectal cancer, and non-cancer controls undergoing colonoscopies found to have a negative exam at UChicago medicine. Blood from patients with CRC was collected prior to surgical operation using EDTA-containing vials and processed within six hours for plasma. Biopsies of primary tumor and adjacent normal-appearing colonic mucosa was also collected and were stored into RNAlater solution (ThermoFisher).  Plasma and tissues in RNAlater were stored in -80C before gDNA and cfDNA extraction. gDNA was extracted using AllPrep DNA/RNA/miRNA Universal Kit (Cat. No. 80244) following the instruction of the protocol. In brief, the tissue was removed from RNAlater solution for lysis and homogenization, and DNA was collected through transferring the lysate through AllPrep DNA Mini spin column (Qiagen).  cfDNA was extracted from plasma QIAamp Circulating Nucleic Acid Kit (Qiagen) following the instruction of the protocol. 1ml plasma were used. RRBS processing using Zymo-seq RRBS Library Kit: after 4-hr Mspl restriction enzyme digestion, adapter ligation, bisulfite conversion, index Primer Amplification, the enriched libraries were sequenced at PE100 using NovaSeqX aiming >30 million paired reads /each sample.