Genomic DNA and plasma derived cfDNA were isolated from fresh tissue, FFPE and blood-isolated PBMC, as previously described.16 (link)
For trtDNA extraction, at least 100 mL of urine was concentrated to 4 mL using Vivacell 100 concentrators (Sartorius Corp) and incubated with 700 ul of Q-sepharose Fast Flow quaternary ammonium resin (GE Healthcare). We modified the previously used protocol for trtDNA isolation from urine and performed a double-step ultrafiltration to separate the low molecular weight from the high molecular weight fragments, and treated them as individual samples until the end of the procedure.14 (link) trtDNA fragment size distribution was assessed using the 2100 Bioanalyzer High-Sensitivity DNA assay kit (Agilent Technologies) according to the manufacturer’s instructions.
For trtDNA extraction, at least 100 mL of urine was concentrated to 4 mL using Vivacell 100 concentrators (Sartorius Corp) and incubated with 700 ul of Q-sepharose Fast Flow quaternary ammonium resin (GE Healthcare). We modified the previously used protocol for trtDNA isolation from urine and performed a double-step ultrafiltration to separate the low molecular weight from the high molecular weight fragments, and treated them as individual samples until the end of the procedure.14 (link) trtDNA fragment size distribution was assessed using the 2100 Bioanalyzer High-Sensitivity DNA assay kit (Agilent Technologies) according to the manufacturer’s instructions.