NadPrep EZ DNA Library Preparation Kit v2

Fig 1. Library yield of NadPrep EZ DNA Library Preparation Kit v2 for gDNA samples with different input amounts.The libraries were prepared by using NadPrep EZ DNA Library Preparation Module v2 (NadPrep Enfrag v2) coupled with A. NadPrep Universal Stubby Adapter (UDI) Module and NadPrep UDI Adapter Module (for Illumina^®), and B. NadPrep Universal Adapter (SI) Module (for MGI) and NadPrep Universal Adapter (MDI) Module (for MGI) respectively, with 25 min of enzymatic digestion and recommended PCR cycles.

 Fig 2. Library yield of NadPrep EZ DNA Library Preparation Kit v2 for different types of samples. The libraries were prepared by using NadPrep EZ DNA Library Preparation Module v2 coupled with A. NadPrep UDI Adapter Module (for Illumina^®) and B. NadPrep Universal Adapter (MDI) Module (for MGI) respectively, with enzymatic digestion duration and PCR cycles as protocol.
Note：The grading standards by electrophoresis are as follows: gDNA: one bright and non-trailing stripe with about 15 kb in size. FFPE B+: one clear stripe with slight diffusion and with about 15 kb in size. FFPE B: one indistinct stripe with about 15 kb in size, with medium diffusion. FFPE C: multiple stripes ranging from 200 bp to 2,500 bp, with severe diffusion. FFPE D: multiple stripes ranging from 250 bp to 1,000 bp, with severe diffusion.

Fig 3. Size distribution of libraries prepared with different types of samples under different enzymatic digestion conditions.A.he libraries were prepared from 250 ng of gDNA sample with different grades by using NadPrep EZ DNA Library Preparation Module v2 coupled with NadPrep UDI Adapter Module (for Illumina^®), with enzymatic digestion at different times as protocol, so as to obtain DNA fragments of different lengths.；B. The libraries were prepared from 50 ng of FFPE DNA samples of different grades, with enzymatic digestion at different times as protocol, so as to obtain DNA fragments of 250 bp.

Fig 4. Low GC bias in metagenomic library preparation using NadPrep EZ DNA Library Preparation Kit v2. After comparison of different library preparation schemes by using microbial community DNA standard (Zymo Research, D6306), the libraries prepared by using NadPrep EZ DNA Library Preparation Kit v2 show no significant difference in GC bias with those prepared by using sonication-based library preparation kits.
Note：NadPrep^® Sonication: NadPrep^®Both NadPrep Sonication: NadPrep DNA Universal Library Preparation Module (for Illumina^®) and NadPrep Enfrag v2: NadPrep EZ DNA Library Preparation Kit V2 can be used along with NadPrep UDI Adapter Module (for Illumina^®) for library preparation. (for Illumina^®)；

Fig 5. The abnormal reads ratio of libraries prepared with different types of samples by using different library preparation kits. The libraries were prepared with gDNA and different grades of FFPE DNA samples (50 ng each) with library preparation strategies, including NadPrep Sonication, NadPrep Enfrag v2, Vendor Q *, Vendor K* and Vendor V* enzymatic fragmentation library preparation kits. The multi-hybridization reaction was initiated with 500 ng of each library with the same library preparation scheme. The capture was performed by using NanOnco Plus Panel v2.0, with calculation of total reads. A. Library yield and the abnormal reads ratio of libraries prepared with gDNA samples (Illumina platform) with different library preparation schemes；B. Abnormal reads ratio of libraries prepared with different grades of FFPE DNA samples by using enzymatic fragmentation library preparation kit (MGI platform). Note: Artifact rate: the ratio of abnormal sequence introduced by enzymatic digestion by-products.

Figure 6 The capture performance of libraries prepared by the enzyme-based kit and the sonication-based kit.The libraries were prepared from 50 ng of FFPE DNA samples with different grades, using either NadPrep Sonication strategy or NadPrep Enfrag strategy, and the multi-hybridization reaction was initiated with 500 ng of each library with the same library preparation scheme by using NanOnco Plus Panel v2.0 (2.6 M) coupled with NadPrep Hybrid Capture Reagents and NadPrep NanoBlockers (for Illumina^®), and the sequencing data is analyzed by selecting 2 M reads pair randomly. The performance of capture data of different library preparation schemes was basically consistent inA.Mappability and On-target rate, but the performance in B. Fold 80 penalty,C. Duplication rate and D. Mate on differ chr was superior to that of competitive products.