Episonic multi functional bioprocessor 1100

12.3 to 96.1 ng of gDNA, quantified with Qubit dsDNA BR Assay kit (Thermo Fisher Scientific), was fragmented with Episonic Multi-Functional Bioprocessor 1100 (Epigentek Group Inc., Farmingdale, NY, USA). The libraries were created with Thruplex DNA-seq 96D kit (Rubicon Genomics) according to manufacturer’s protocol. 10–50 ng of DNA was used for library preparation. Five amplification cycles were used. The amplified libraries were purified with 50 µl of NucleoMag NDS Clean-up and Size Select beads and eluted to 30 µl of PCR grade water. The libraries were quantified with LabChip GX HT DNA HiSens chip (PerkinElmer, Waltham, MA, USA) (Supplementary Data 2).

Five to 150 ng of lysate gDNA was quantified with Qubit dsDNA BR Assay kit (ThermoFisher, Waltham, MA, USA) and fragmented with Episonic Multi-Functional Bioprocessor 1100 (Epigentek Group Inc., Farmingdale, NY, USA). The libraries were created with Accel-NGS 1S Plus DNA Library Kit (Swift Biosciences, Ann Arbor, MI, USA) according to manufacturer’s protocol. Four to 40 ng of DNA were used for library preparation. Seven amplification cycles in PCR were used for all the samples. Agencourt AMPure XP beads (Beckman Coulter, Brea, CA, USA) in 1.8 times the reaction volume were used for purifications. 1S Plus Dual Indexing Kit was used for all the samples. The libraries were quantified with LabChip GX HT DNA HiSens chip.

The whole-genome-amplified products or genomic DNA extracts were fragmented using an EpiSonic Multi-Functional Bioprocessor 1100 (Epigentek) to generate a 150~250-bp fragment distribution. The fragmented products underwent Illumina library preparation for end repair, 3′dA-tailing, adaptor ligation, and PCR amplification according to the manufacturers’ instructions. We used the Celemics NGS Library Preparation Kit (LI1096, Celemics, Seoul, Korea) for the whole-genome sequencing library preparation, SureSelectXT (Agilent, CA, USA) for whole-exome sequencing, and the Celemics Customized Target Enrichment Kit (SICT96, Celemics, Seoul, Korea) for targeted sequencing. DNA purification was performed by ^TOPQXSEP MagBead (XB6050, Celemics, Seoul, Korea), and DNA libraries were amplified using the KAPA Library Amplification Kit (KAPA Biosystems, KK2602). Finally, the products were quantified by TapeStation 2200 (Agilent, CA, USA). We used a HiSeq 2500 50SE (Illumina) to generate 0.16 Gb/sample for whole-genome sequencing and a HiSeq 2500 150PE (Illumina) to generate 5 G/sample and 0.88G/sample for whole-exome and targeted sequencing, respectively.