Fragment Analysis

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

FA

Please note: Fragment Analysis is included for all samples submitted for Illumina or PacBio sequencing. If you are submitting a sequencing sample and you are not in need of additional services, there is no need to request this service!

The Fragment Analyzer is an automated capillary electrophoresis instrument that provides the same sort of data as an Agilent Bioanalyzer. It can resolve a broad range of DNA fragment sizes: Samples with fragment sizes between 1 and 6000 bp are characterized using NGS runs, or Small Fragment runs for higher resolution of small fragments under 1500bp. Larger genomic-sized DNA can be accurately sized on Large Fragment runs (up to 200 kb).

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 DNA samples or 10 RNA samples, plus a ladder in the 12th well.  For all analysis types, pricing is $50 per run, even if you submit fewer than 10 or 11, 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 drop off a minimum of 3 µL of each sample in the labeled box in the GC3F freezer (located in 288 Klamath). Only 2 µL is used for the assay, but please provide at least 3 µL to account for pipetting loss. Please also be sure to fill out the Sample Submission sheet taped to the drop-off freezer!

ANALYSIS TYPE FRAGMENT SIZES IN RANGE REQUIRED CONCENTRATION 
NGS, cDNA, any other dsDNA  1 – 6,000 bp 0.1 – 10 ng/µL
Large Fragments (DNA) 75 – 200,000 bp  0.005 – 1 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