NadPrep Single Cell WGA Kit

Catalog Number:

#1300101
#1300102

NadPrep Single Cell WGA Kit is designed for whole-genome amplification (WGA) of genomic DNA (gDNA) from single cells or ultra-low amounts of purified gDNA. Utilizing optimized buffers and enzymes, whole-genome amplification can be completed within 3 hr. The kit features a simple, streamlined workflow including cell lysis, preamplification, and amplification to generate microgram-level gDNA with high coverage and uniformity.

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Feature

● Designed for single/multiple cells (1-10) or ultra-low gDNA (> 30 pg) inputs
● Enhances sequencing coverage and uniformity, thereby improving accuracy of variants detection
● Broadly compatible with downstream applications including WGS, large fragment CNVs analysis, qPCR analysis, etc.

Workflow

Performance

High Concordance in CNVs Analysis

Figure 1. Comparison of CNVs analysis results between single-cell DNA-Seq and bulk DNA-Seq in 293T cells. The correlation of average copy numbers across different libraries demonstrates high concordance between single-cell DNA-Seq from Nanodigmbio’s solution and bulk DNA-Seq (R² = 0.9141). Single-cell DNA-Seq libraries were prepared from 5-10 cells amplified with different WGA kits (Nanodigmbio, Vendor T* and Vendor Y*). 100 ng of each amplified DNA were used for library preparation with NadPrep EZ DNA Library Preparation Module v2 and NadPrep Universal Stubby Adapter (UDI) Module. Bulk DNA-Seq libraries were prepared from 100 ng gDNA extracted from cell lines. Libraries were sequenced on Illumina NovaSeq 6000 (PE150), generating approximately 1 Gb of raw data per sample. Variant analysis was performed with CNVkit in 1,000-kb bin sizes.

Note: Samples were cultured 293T cells characterized by pronounced aneuploidy.

Figure 2. Analysis using the Nanodigmbio’s solution demonstrates concordance with previously characterized aneuploidies in defined mixtures. 30 pg of gDNA were amplified using NadPrep Single Cell WGA Kit. 100 ng of each amplified DNA were used for library preparation with NadPrep EZ DNA Library Preparation Module v2 and NadPrep Universal Stubby Adapter (UDI) Module. Libraries were sequenced on Illumina NovaSeq 6000 (PE150), generating approximately 1.5 Gb of raw data per sample. Variant analysis was performed with CNVkit in 100-kb bin sizes.

Note: Positive samples were cell line-derived gDNA reference standards characterized by pronounced trisomy 13/18/21 (LDT Bioscience, C2337T/C2338T/C2339T). Negative samples were Human Genomic DNA (Promega, G1471) known as euploidy. Defined mixtures were generated by mixing two gDNA standards (C2337T/C2338T/C2339T and G1471) at the indicated ratios, containing aneuploidies at varying proportions across different genomic locations.

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

Click here for more details on the "End-to-End Solution for PGT-A by LP-WGS".

#Package	Cap Color	Component	Volume 1300101 (24 rxn)	Volume 1300102 (96 rxn)
Box 1		Cell Lysis Buffer	130 μL	520 μL
		Cell Lysis Enzyme	16 μL	65 μL
		1^st Amplification Buffer	320 μL	1,270 μL
		1^st Amplification Enzyme	32 μL	130 μL
		2^nd Amplification Buffer	810 μL	2×1,615 μL
		2^nd Amplification Enzyme	65 μL	250 μL
	/	NadPrep SP Beads	2.5 mL	8 mL

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

What are possible causes of no amplification product or low amplification yield when using the NadPrep Single Cell WGA Kit? How to solve them?

Cell loss during isolation: if cells are lost during isolation or transfer, inspect and optimize the cell isolation and collection workflow. Recollect samples and confirm that each reaction tube contains a cell before proceeding.

Insufficient purity of gDNA: residual wash buffers, ethanol or other contaminants remaining after purification can inhibit the amplification reaction. Ensure ethanol is fully evaporated after purification, resuspend/dilute purified gDNA in Nuclease Free Water, and verify accurate quantification of the input samples.

Although microgram-level amplified DNA was obtained using the NadPrep Single Cell WGA Kit, what may cause abnormal allelic loss or chromosomal abnormalities, and how to solve them?

I. If the initial input samples are cells: apoptosis of cells prior to lysis can lead to DNA degradation, which may produce allelic loss or chromosomal abnormalities. It is recommended to assess cell viability and proceed with lysis and amplification immediately when the cell status is acceptable. If immediate amplification is not possible, store lysed cells at -25 ~ -15℃ for ≤ 7 days to preserve genomic integrity.

II. If the initial input samples are bulk DNA: partial degradation of the input gDNA can likewise cause such artifacts. Use intact, non-degraded gDNA, or increase the initial input amount as appropriate.

What are possible causes of non-specific amplification in negative control samples when using the NadPrep Single Cell WGA Kit? How to solve them?

Exogenous DNA contamination: this kit is highly sensitive to trace DNA; ultra-low amounts of contaminating DNA can yield microgram-level amplification products. Perform all procedures in a clean, DNA-free environment (e.g., PCR-clean area or laminar-flow hood), and use nuclease-free, DNA-free consumables and reagents. Thoroughly decontaminate work surfaces, pipettes and equipment, and include and closely monitor negative controls throughout the workflow to rapidly identify and trace contamination sources.

Type	Product	Scale	Catalog#
Single Cell WGA	NadPrep Single Cell WGA Kit, 24 rxn	24 rxn	1300101
Single Cell WGA	NadPrep Single Cell WGA Kit, 96 rxn	96 rxn	1300102