[Azazel]

I came from a lab in industry that trialed the BioA, TapeStation, Caliper system and Advanced Analytical fragment analyzer. While other groups in the company chose the BioA for the sake of "it's the standard," we chose the Advanced Analytical as it outperformed in almost every way, including running fragment analysis of dirty digests, without getting clogged.

Is this published anywhere? Data showing Fragment Analyzer outperforming Bioanalyzer? If published, would be thankful for a pointer. I'm interested in alternatives to BA as well especially if there is data showing that/how the alternative is better.

[northpaw]

Illumina R&D has transitioned away from chip-based systems and is now releasing new sample prep kits recommending the Fragment Analyzer:

http://res.illumina.com/documents/products/technotes/technote-truseq-rna-access.pdf

Illumina recently announced Advanced Analytical as an automation partner for their Fragment Analyzer system:

http://applications.illumina.com/applications/sequencing/ngs-library-prep/automation.html

[batpat]

We recently installed a Qiaxcel in our lab, but the training was horrible. Could you tell me what run parameters, marker, etc. you use for running NGS libraries for sizing etc.? I can't seem to find any references for using the system for this purpose. --Thanks!

I am also interested in using the QIAxcell for this purpose, could you share some expertize with us?

[bilyl]

We have a fragment analyzer and a labchip GX. I haven't seen the former being used very much in our facility but the GX gets a lot of play. Personally I like it a lot because the assays are very similar to the Bioanalyzer.

[knp]

Can Qiaxcel be used instead of Bioanalyzer for Library QC?

I use the Qiaxcel system. It works for me as well as the Bioanalyzer but the sample cost is about 4 times lower. It does use gel capillaries and the array lasts for only 6 months at a time so if you are not a high volume user, it might not be as cost effective as it is for me.

I'm hoping to purchase a MiSEQ in the next few months and wondering whether I need a Bioanalzyer as I already have a Qiaxcel - can you use the Qiaxcel for library QC? Do you have any SOPs for doing this?

Thanks,
k

[seqdx]

I believe the Qiaxcell injects markers independently of sample, so it will deliver size data, but you will need a fluorometer (Qubit) to get accurate concentration measurements. Ionic strength differences between samples and standards impact injection efficiency. Normalization is required to measure concentration.

The Fragment Analyzer offers qualitative kits that inject markers independently of sample like the Qiaxcel. These kits are inexpensive and useful for sizing applications like PCR screening, genotyping, RFLP, microsatellites, etc. They are also useful for relative concentration measurements of peaks within a sample. IDT just published a CRISPER/Cas9 cleavage assay for their gene block products using these kits on the Fragment Analyzer:

http://genengnews.com/gen-articles/simplifying-crispr/5533/

The Fragment Analyzer also has quantitative kits that mix markers with samples like the BioAnalyzer. This enables use of the marker molecules as a normalization factor with reference to the molecules in the ladder as concentration standards. The system is easy to use and reliable with automated gel cycling and parallel analysis (not rapid serial injection). The different Fragment Analyzer quantitative kits work for small Illumina type NGS libraries as well as larger PacBio and nanopore type libraries and genomic DNA that exceed the size range of the BioAnalyzer. Resolution and sensitivity are excellent. Its a solid analytical platform for all kinds of DNA and RNA applications.