Fragment Analysis

Fragment Analysis

The GC3F offers nucleic acid fragment size analysis using an Advanced Analytical Fragment Analyzer.


The Fragment Analyzer is an automated capillary electrophoresis instrument that provides the same sort of data as an Agilent Bioanalyzer. 

The Fragment Analyzer can resolve a broad range of DNA fragment sizes.  Samples with fragment sizes between 1 and 6000 bp are characterized using “NGS” runs.  Larger DNA fragments (up to 40 kb) can be accurately sized using “Genomic” runs.

RNA samples can also be analyzed, and the instrument provides an “RNA Quality Number (RQN)” that is mathematically equivalent to the “RIN” values generated by Agilent Bioanalyzer instruments.

Pricing and Sample Submission

The Fragment Analyzer can run up to 11 samples, plus a ladder in the 12th well.  For all analysis types, pricing is $50 per run, even if you submit fewer than 11 samples since all wells must be filled with reagents. If you have a small run and would like to save on cost, we suggest coordinating with another user prior to submission and we can then split the cost for you!

Please dilute your samples as indicated below and submit a minimum of 3 µL of each sample in the designated box in the GC3F freezer (located in 288 Klamath). Please also fill out the requested info on the form taped to the freezer.

NGS, cDNA, any other dsDNA  1 – 6,000 bp 0.1 – 10 ng/µL
gDNA 50 – 20,000 bp 0.05 – 10 ng/µL
Large Fragments (DNA) 75 – 200,000 bp  0.005 – 5 ng/µL
Small Fragments (DNA) 1 – 1,500 bp 0.2 – 5 ng/µL
RNA - High sensitivity 15 – 6,000 nt 0.1 – 10 ng/µL
RNA - Standard sensitivity 15 – 6,000 nt 5 – 500 ng/µL

Fragment Anayzer capillary array