Product details

NadPrep DNA Universal Library Preparation Kit (for MGI)

Catalog Number:

#1002211 #1002212
#1003611 #1003621 #1003622 #1003620
#1003711 #1003721 #1003722 #1003725 #1003726 #1003751 #1003752 #1003753 #1003754

NadPrep DNA Universal Library Preparation Kit (for MGI) is designed for preparation of high-quality libraries from double-stranded DNA (dsDNA) on MGI platforms. This A-T ligation based kit offers a stable and efficient library preparation solution for a various of applications.

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Kit Content
FAQ
Ordering Information
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Features

Suitable for various sample types including gDNA, FFPE DNA and cell-free DNA
Provide DNA purification magnetic beads and optimized size-selection solution
Optional with Single Index (SI) Adapters and MGI Unique Dual Index (MDI) Adapters
Generate high quality libraries from low input

Applications

Application	Sample type	Recommended input
Whole Genome Sequencing	Animal or plant gDNA (without serious degradation)	50-500 ng
	Cell-free DNA(no large fragment contamination)	≥ 1 ng (analytical sensitivity dependent)
	Microbial gDNA (without serious degradation)	1-500 ng
Targeted Sequencing	gDNA (without serious degradation)	≥ 50 ng (quality dependent)
	FFPE DNA (with average size＞500 bp)	≥ 100 ng (quality dependent)
	Cell-free DNA(no large fragment contamination)	≥ 1 ng (analytical sensitivity dependent)

Workflow

Performance

High Efficiency

Fig 1. Efficiency of NadPrep DNA Universal Library Preparation Kit (for MGI). A. Library yields prepared with NadPrep Universal Adapter (SI) Module and NadPrep Universal Adapter (MDI) Module. B-C. Size distribution of one gDNA library prepared with SI Adapters and MDI Adapters, respectively (Agilent 2100 Bioanalyzer).).

Unbiased Coverage

Figure 2. Uniform coverage of regions with various GC content. Coverage distribution for libraries generated from 10 ng of DNA of A. Staphylococcus aureus (GC%=33), B. Salmonella enterica LT2 (GC%=52) and C. Pseudomonas aeruginosa (GC%=67). GC% distribution per 100 bp bin is indicated by histograms and normalized coverage is represented by lines.

Fig 3.Low GC bias in metagenomic library preparation using NadPrep DNA Universal Library Preparation Kit(for MGI).The DNA libraries were prepared from 10 ng Microbial Community DNA Standard(Zymo Research,D6306)

For research use only. Not for use in diagnostic procedures.

NadPrep DNA Library Preparation Module

Package	Color of Tube Cap	Component	Volume 1002211(24 rxn)	Volume 1002212 (96 rxn)
Box1		EndRepair & A-Tailing Buffer	180 µL	690 µL
		End Repair & A-Tailing Enzyme	120 µL	460µL
		Ligation Buffer	750 µL	2×1500 µL
		DNA Ligase	65 µL	250 µL
		2X HiFi PCR Master Mix	720 µL	2×1600 µL
		NadPrep M-Amplification Primer Mix (for MGI, SI)	20 µL	75 µL
		NadPrep M-Amplification Primer Mix (for MGI, DI)	20 µL	75 µL
		NadPrep M-Amplification Primer Mix (for MGI, DI)	20 µL	75 µL
	/	Nuclease Free Water	2.5 mL	8 mL
		TE Solution	1 mL	4 mL
Box2	/	NadPrep SP Beads	4 mL	15 mL

Single index(SI) adapter module

Color Of Tube Cap	Component	Volume 1003611 (24 rxn)	Volume 1003621 (96 rxn)	Volume 1003622(96 rxn)
	NadPrep M-Index (SI) Primer Mix #	12×15 µL	24×25 µL	24×25 µL
	NadPrep M-Adapter	60 µL	230 µL	230 µL

Color of Tube	Component	Volume
Color of Tube	Component	1003641* (96 rxn)
	NadPrep M-Index (SI) Primer Mix #	96×8 µL (Plate)
	NadPrep M-Adapter (SI)	260 µL (Tube)
	NadPrep M-Amplification Primer Mix (for MGI, SI)	75 µL (Tube)

Unique Dual Index (MDI) Adapters

Color of

Tube Cap

Component

Volume
1003711 (24 rxn)

Volume
1003721 (96 rxn)

Volume
1003722(96 rxn)

Volume
1003725 (96 rxn)

Volume
1003726 (96 rxn)

NadPrep M-Index (MDI) Primer Mix #

12×15 µL

24×25 µL

NadPrep M-Adapter

60 µL

230 µL

Color of Tube	Component	Volume	Volume	Volume	Volume
Color of Tube	Component	*1003751 (96 rxn)**	*1003752 (96 rxn)**	1003753 (96 rxn)	1003754 (96 rxn)
	NadPrep M-Index (MDI) Primer Mix #	96×8 µL (Plate)	96×8 µL (Plate)	96×8 µL (Plate)	96×8 µL (Plate)
	NadPrep M-Adapter (DI)	260 µL (Tube)	260 µL (Tube)	260 µL (Tube)	260 µL (Tube)
	NadPrep M-Amplification Primer Mix (for MGI, DI)	75 µL (Tube)	75 µL (Tube)	75 µL (Tube)	75 µL (Tube)

Which DNA extraction kit is recommended?

Title: Which DNA extraction kit is recommended?

Based on our experience, the kits for DNA extraction are recommended as follows.

Item	Recommendations
Extraction kit	gDNA	DNeasy Blood & Tissue Kit (Qiagen, Cat # 69504 & 69506) TIANamp Genomic DNA Kit (TIANGEN, Cat # DP304)
	cfDNA	QIAamp Circulating Nucleic Acid Kit (Qiagen, Cat # 55114)
	FFPE gDNA	QIAamp DNA FFPE Tissue Kit (Qiagen, Cat # 56404)
Dissolvent	Nuclease-free water, 0.1 x TE (low TE), 10 mM Tris-HCl (pH 8.0-8.5) or Buffer provided in extraction kit should be used to dissolve DNA.

What are the DNA input requirements for NadPrep DNA Library Preparation Module (for MGI)?

Title: What are the DNA input requirements for NadPrep DNA Library Preparation Module (for MGI)?

This kit is compatible with types of dsDNA inputs, including DNA extracted from blood, tissues, FFPE and body fluid. This kit can be used to construct libraries for dsDNA input ranging from 1 to 500 ng.

For samples with suboptimal quality such as FFPE tissue samples, careful quality control (QC) and stratification on DNA integrity is highly recommended.

For common usage, the QC metrics are recommended as follows.

Item	Recommendations
Quantification	NanoDrop (based on the spectrophotometer principle), Qubit® or PicoGreen® (based on double-stranded DNA fluorescent dye).
Quality	OD₂₆₀/OD₂₈₀= 1.8 - 2.0; OD₂₆₀/OD₂₃₀= 2.0 - 2.5. OD₂₆₀/OD₂₈₀> 1.9 indicates RNA contamination while < 1.6 indicates protein, phenol or other contamination; OD₂₆₀/OD₂₃₀< 2.0 indicates carbohydrates, salts or organic solvent contamination.
Fragment distribution	gDNA	A clear band > 15 kb when running on a 1% agarose gel.
	cfDNA	A peak at ~ 160 bp followed by a peak at ~ 320 bp on Bioanalyzer or Bioptic (Qsep).
	FFPE gDNA	DNA integrity assessment by running on a 1% agarose gel or Bioanalyzer.

Does NadPrep DNA Library Preparation Module (for MGI) support PCR-free library construction?

Title: Does NadPrep DNA Library Preparation Module (for MGI) support PCR-free library construction?

No. PCR with indexing primers is necessary to generate full-length library.

What is the recommended sample fragmentation method?

Title: What is the recommended sample fragmentation method?

The kit is compatible with ultrasonic and enzymatic fragmentation methods. For enzymatic fragmentation, NEBNext® dsDNA Fragmentase® (NEB; Cat M0348) or Custom 5X DNA Shearing Mix (Qiagen; Cat CM0162) is recommended; For ultrasonic fragmentation, it is recommended to use Covaris (M220 Focused-ultrasonicator, 50 μL interruption tube) or similar.

How to choose adapter module?

Title: How to choose adapter module?

For different applications, adapter module is recommended as follows.

Application	Recommended adapter module	Optional
Whole-genome, metagenomic and targeted capture sequencing	Universal Adapter (SI) Module	BMI Adapter (SI) Module
RNA sequencing	BMI Adapter (SI) Module	Universal Adapter (SI) Module
Low frequency mutation detection (e.g. ≤ 1% variant frequency)	BMI Adapter (SI) Module	-

How to improve cleanup efficiency?

Title: How to improve cleanup efficiency?

The following tips help to improve the cleanup efficiency.

1) never overdry the beads;

2) increase incubation time;

3) increase the volume of magnetic beads (NOT suitable for size selection step);

4) use freshly prepared 80% ethanol.

When using Adapter and Primer Module, how to cope with the adapters?

Title: When using Adapter and Primer Module, how to cope with the adapters?

Adapter: insert molar ratio is essential. Excessive adapter will result in residues of adapter or adapter dimers. Insufficient adapter will affect ligation efficiency and therefore reduce library yield. For universal adapters, please refer to the listed table to calculate the dilution fold of adapters so as to achieve the best yield.

* ~ 250 bp is commonly used for gDNA fragmentation, and ~ 160 bp is peak size observed for cfDNA in plasma. Other recommendations for handling adapters are as follows.

• Diluent: Use TE Solution in the kit to dilute adapters. Diluted adapters are not recommended for long-term storage;

• Storage: Aliquot to avoid repeated freezing and thawing.

While pipetting, there is solution remaining on the pipette tips. How to solve it?

Title: While pipetting, there is solution remaining on the pipette tips. How to solve it?

Ligation Buffer, DNA Ligase and End Repair & A-Tailing Enzyme are relatively viscous. It is recommended to use low-absorption tips and pipetting slowly. If residue remains in tip, repeatedly pipette or use the reverse pipetting.

Is the library compatible with Agilent, Roche and other targeted capture systems?

Title: Is the library compatible with Agilent, Roche and other targeted capture systems?

We provided a total solution for targeted capture sequencing. The library kit is compatible with a variety of targeted capture systems, such as SureSelect (Agilent) and NimbleGen™ SeqCap™ EZ (Roche).

Product	Scale	Catalog#
NadPrep DNA Library Preparation Module (for MGI, 24 rxn	24 rxn	1002211
NadPrep DNA Library Preparation Module (for MGI), 96 rxn	96 rxn	1002212
NadPrep Universal Adapter (SI) Module Set A1 (for MGI), 24 rxn	SI 1-12	1003611
NadPrep Universal Adapter (SI) Module Set E1 (for MGI), 96 rxn	SI 1-96	1003641
NadPrep Universal Adapter (SI) Module Set B1 (for MGI), 96 rxn	SI 1-24	1003621
NadPrep Universal Adapter (SI) Module Set B2 (for MGI), 96 rxn	SI 25-48	1003622
NadPrep Universal Adapter (MDI) Module Set A1 (for MGI), 24 rxn	MDI 1-12	1003711
NadPrep Universal Adapter (MDI) Module Set B1 (for MGI), 96 rxn	MDI 1-24	1003721
NadPrep Universal Adapter (MDI) Module Set B2 (for MGI), 96 rxn	MDI 25-48	1003722
NadPrep Universal Adapter (MDI) Module Set B3 (for MGI),96 rxn	MDI 49-72	1003725
NadPrep Universal Adapter (MDI) Module Set B4 (for MGI), 96 rxn	MDI 73-96	1003726
NadPrep Universal Adapter (MDI) Module Set E1 (for MGI),96 rxn	MDI 1-96	1003751
NadPrep Universal Adapter (MDI) Module Set E2 (for MGI), 96 rxn	MDI 97-192	1003752
NadPrep Universal Adapter (MDI) Module Set E3 (for MGI),96 rxn	MDI 193-288	1003753
NadPrep Universal Adapter (MDI) Module Set E4 (for MGI), 96 rxn	MDI 289-384	1003754

For research use only. Not for use in diagnostic procedures.

Product Sheet

Application Note

Demo Data

NadPrep for MGI Hema Research gDNA Promega female G1521

Title: NadPrep for MGI Hema Research gDNA Promega female G1521 DNA library was created from human gDNA (Promega, G1521) using Nanodigmbio NadPrep library preparation kit (for MGI). The library was enriched in a capture using the Hema Research Panel v1.0, then sequenced.

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