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FAQ – Sequence Enrichment Assay
- What are the DNA sample requirements for the Sequence Enrichment Assay?
- Is the Sequence Enrichment Assay compatible with whole-genome amplified (WGA) DNA?
- How much target sequence can be enriched with a single primer library on the RDT 1000?
- How many droplets are created for each sample with the Sequence Enrichment Assay?
- How much genomic DNA is contained in each droplet?
- How many copies of each PCR amplicon are generated in the droplets?
- What is the size range of amplicons generated with the Sequence Enrichment Assay?
- What is the range of %GC for PCR amplicons with the Sequence Enrichment assay?
Q – What are the DNA sample requirements for the Sequence Enrichment Assay?
A – RainDance recommends using only high-quality Genomic DNA for the Sequence Enrichment Assay. The purity of each sample should be determined by evaluating the ratio of the O.D. measurement at 260 nm and 280 nm (A260/A280). Samples should have an A260/A280 >1.8. The DNA should also be of high molecular weight and should generate a single band on a 1% agarose gel that is approximately 10kb or higher.
Q – Is the Sequence Enrichment Assay compatible with whole-genome amplified (WGA) DNA?
A – RainDance now supports the use of whole-genome amplified DNA samples using as little as 50 ng of input DNA. Please contact RainDance technical support or your local RainDance representative for further information.
Q – How much target sequence can be enriched with a single primer library on the RDT 1000?
A – At present, the RDT 1000 supports custom primer libraries containing up to 20,000 unique prime pairs. The total amount of target sequence represented will vary depending on the nature of the specific target sequences. Assuming an average amplicon length of 500 bp, the total amount of target sequence per experiment can be as high as 10 Mb.
Q – How many droplets are created for each sample with the Sequence Enrichment Assay?
A – Each sample processed on the RDT 1000 using the Sequence Enrichment Assay results in up to 2 million droplets.
Q – How much genomic DNA is contained in each droplet?
A – Each template mix droplet contains on average 1.13 pg of genomic DNA, which is equivalent to approximately 34% of a haploid human genome.
Q – How many copies of each PCR amplicon are generated in the droplets?
A – Typical enrichment experiments result in a minimum of 250 ng of PCR product. This equates to an average of 2,500,000-fold amplification per droplet assuming an average amplicon length of 500 bp.
Q – What is the size range of amplicons generated with the Sequence Enrichment Assay?
A – The current range of amplicon size for the Sequence Enrichment assay is 150-1500 bp.
Q – What is the range of %GC for PCR amplicons with the Sequence Enrichment assay?
A – The RainDance primer design process limits the GC content of amplicons to 30-70%.
