QIAseq UPX Single Cell DNA Lib Kit

• Pool together 24 samples into a single library following Repli-g whole genome amplification (WGA)
• Compatible with low-pass sequencing or hybrid-capture enrichment panels such as QIAseq xHYB Human Hybrid Capture Panels
• REPLI-g DNA polymerase MDA delivers PCR-free high-fidelity amplification and reduces false-positives
• Includes unique dual indices (UDI) to minimize sequencing artifacts due to “index hopping” on Illumina NGS instruments
• REPLI-g MDA buffers and reagents undergo a unique decontamination procedure to avoid amplification of contaminating DNA

The QIAseq UPX Single Cell DNA Lib Kit utilizes an optimized DNA amplification and library preparation protocol to allow the pooling of amplified DNA with a reduction in the total number of libraries. The key DNA amplification steps use QIAGEN’s multiple displacement amplification (MDA) technology with the REPLI-g enzyme to amplify gDNA directly from single cells or previously isolated genomic DNA. 

During the MDA reaction, Sample Barcodes are incorporated in the amplified DNA, allowing subsequent pooling of up to 24 samples into a single library. This greatly reduces tedious library preparation steps, reducing library preparation costs and plastic consumables. 

The kit includes all reagents required for cell lysis, whole genome amplification using REPLI-g DNA polymerase, and NGS library preparation compatible with Illumina NovaSeq and other NGS instruments. 
This kit provides comprehensive genome coverage and exceptional sequence fidelity, reducing false positives and minimizing dropouts. 

The kit contains QIAseq Unique Dual-Index Adapters and QIAseq Beads for reaction cleanup. The QIAseq UPX Single Cell DNA Lib Kit can support up to 576 samples by only multiplexing 24 libraries.

The kit delivers exceptional genome coverage from single cells, populations of cells and low quantities of genomic DNA, including regions with high GC content. Compared to PCR-based methods of whole genome amplification, the MDA technology included in the kit eliminates PCR duplicates and minimizes GC bias, ensuring high library diversity and maximum genome coverage. Additionally, the high-fidelity REPLI-g DNA polymerase introduces fewer errors than high-fidelity PCR enzymes, reducing false positives and enabling more sensitive mutation detection. Low background and comprehensive coverage make this kit highly suited for analyzing aneuploidy, copy number variations and mutations from single cells and low-input samples.

This kit relies on three key technologies to deliver high-diversity whole genome sequencing (WGS) libraries from single cells. After cell lysis, a high-fidelity MDA reaction is used to amplify to microgram amounts of gDNA using the high-fidelity REPLI-g DNA Polymerase. During the MDA reaction, Sample Barcodes are incorporated in the amplified DNA, allowing subsequent pooling of up to 24 samples into a single library. This greatly reduces tedious library preparation steps, reducing library preparation costs and plastic consumables. 

Library generation follows cDNA pooling with the directed ligation of the first sample index (BC-i5-UDI) adapter. The BC-i5-UDI ligated DNA fragments are then treated in the next step with fragmentation reagents to reduce the size of fragments and generate the second end, which is subsequently ligated to the second sample index adapter (BC-i7-UDI). The completed libraries are amplified using a HiFi amplification mix and can be automatically balanced using the QIAseq Normalizer Kits (sold separately).

The QIAseq UPX Single Cell DNA Lib Kit is a complete cell-to-library solution that includes all the reagents necessary to generate high-diversity WGS libraries from single cells or limited quantities of intact gDNA. The kit contains reagents for the effective lysis of isolated single cells or small clusters of cells. After lysis, genomic DNA is amplified using proof-reading, ultra-high fidelity REPLI-g DNA polymerase. Up to 24 MDA amplified and barcoded samples can be pooled together. The pool is purified using QIAseq Beads to remove any non-incorporated Sample Barcodes and the MDA residual reaction components.

For library construction, the pooled samples consisting of WGA–DNA strands are treated with EP facilitator to generate sticky ends and accept the BC-i5-UDI adapter. QIAseq Beads purification after the first adapter ligation will remove any non-ligated adapters. The ligation of the BC-i5-UDI adapter is directed and ensures that the read 1 will start with the Sample Barcode sequence.

In the next step, the fragments are treated with fragmentation reagents to reduce the fragment size and generate suitable sticky ends for the second BC-i7-UDI adapter.

In the following steps, the library is purified to remove non-ligated BC-i7-UDI adapters and will be amplified with the standard P7 and P5 primers. These adapters contain sequences essential for bridge amplification and sequencing on any Illumina NGS instrument.

• Surveillance studies
• Analysis of inter-cellular genome heterogeneity
• Mutation detection
• Copy number variation analysis
• Aneuploidy analysis
• Subsequent enrichment by hybrid capture*

*QIAseq Normalizer-treated libraries will not be compatible with hybrid capture