Gm12891

To mimic clinically derived formalin-fixed paraffin-embedded (FFPE) material using reference samples, DNA was generated from two different human cell lines (GM12891 and GM12892, Coriell Institute) and pellets subject to formaldehyde treatment. Briefly, pellets containing 30–50 million cells were flash-frozen on dry-ice and carefully submerged in 15 ml of neutral buffered formalin or zinc formalin without disturbing the pellet. Cells were incubated for 72 h at 37 °C. Formalin was removed and replaced with 20 ml of 70% EtOH without resuspending the pellet. The cells were kept at 4 °C until further processing.
The pellet was dehydrated with the Tissue-Tek VIP6 robot (Sakura) using the nerve program. The cassette with the pellet was subsequently embedded in paraffin. Scrolls were created by sectioning the paraffin block with the microtome (thickness of 15 µm).

Lymphoblastoid cell lines (GM12878, GM12891, and GM12892) were obtained from the Coriell Institute for Medical Research and cultured in Roswell Park Memorial Institute 1640 medium (Corning Life Sciences, Tewksbury, MA, USA), supplemented with 15% fetal bovine serum (FBS, Corning). Embryonic stem cell lines (H1, H7, and H9) were obtained from the WiCell Research Institute (Madison, WI, USA) and cultured feeder-free on Matrigel culture matrix in mTeSR™ 1 medium (WiCell). Tumor-derived cell lines (MCF-7, RKO, and HCT-116) were obtained from the American Type Culture Collection. MCF-7 and RKO cells were cultured in Eagle’s minimum essential medium (Corning), supplemented with 10% FBS. HCT-116 cells were cultured in McCoy’s 5a medium (Corning), supplemented with 10% FBS. All cell lines were grown at 37 °C in a 5% CO₂ atmosphere.