Whole exome sequencing of Homo sapien: Adult female stomach
Leftover dissociated cells from the Barrett's esophagus biopsy for Patient 6 that did not go toward 10x were stored in 80% methanol, first at -20 °C for 24 hours followed by long-term storage at -80 °C; approximately 1e5 cells were saved. Total DNA was extracted from these cells following centrifugation and resuspension in 200 uL DPBS using the QIAamp DNA Mini Kit (Qiagen, 51304). 600 ng DNA were recovered, confirming our cell number estimate. Total DNA was also extracted from whole normal esophagus and gastric cardia biopsies taken from the same patient and stored in CryoStor CS10 in liquid nitrogen. Once thawed and washed in DPBS, the biopsies were chopped coarsely before being processed using the QIAamp DNA Mini Kit with the manufacturer's recommended protocol for tissue.   Whole-exome sequencing library preparation was performed using the Twist Exome 2.0 plus Comprehensive Exome Spike-in Kit (Twist Biosciences, 105036) and sequenced on an Illumina NovaSeq 6000 at the Center for Applied Genomics at the Children's Hospital of Philadelphia with at least 100x coverage.