microDNA-seq of B-ALL patient : Plasma sample at the end of treatment
The eluted microDNA was used for rolling-circle amplification using degenerate 6-mer primers and Phi29 DNA polymerase. We employed an in-house protocol using oligonucleotides containing internal C3 spacers to minimize the production of self-priming by-products [17, 18]. Amplified microDNA concatemers were purified using Amicon Ultra-0.5 centrifugal filter devices (MilliporeSigma, Burlington, MA, USA) and quantified using a Qubit dsDNA BR Assay Kit (Invitrogen, Thermo Fisher Scientific, Waltham, MA, USA). Five hundred nanograms of Amplified microDNA (500 ng) was fragmented using the Illumina DNA Prep kit to generate 5/ 21 dual-indexed paired-end libraries following the Illumina DNA protocol with IDT for Illumina Unique Dual Indexes (Set D, Cat. No. 20027216). The collected microDNA material was sequenced on an Illumina MiSeq platform using a 300-cycle MiSeq Micro v2 kit (~34 million paired-end 2150 bp reads per sample).