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Fragment Analyzer Service

The MBCL operates a Fragment Analyzer Service using the Advanced Analytical capillary electrophoresis system. Samples are analyzed for concentration and molecular weight/size. Results are presented in a graphic format similar to a Bioanalyzer including size, concentration, molarity, and RIN values.

Download our introductory flyer here!
Here is an information sheet on how to assess RNA quality.
Here are some FAQs about the Fragment Analyzer service.

Available Assays:

  • small RNA
  • mRNA
  • total RNA
  • DNA
  • large fragment DNA
  • genomic DNA
  • No minimum or maximum number of samples required!
  • Only 3 µl per sample required!
  • Resolution as low as 3 bp (assay dependent)
  • DNA Fragment Sizing: 25 bp to 48 Kb (assay dependent)

Please email for a ticket or more information: MBCL@umassmed.edu

Sample Drop Off Locations:

1. LRB - 6th floor copy room
2. ASC - 8th floor room 2058
3. Biotech 2 - fridge or freezer in the hall outside of room 207.
4. 222 Maple Ave. Shrewsbury, MA, 01545 - Rose Gordon Building, 1st floor. Available weekdays from 8AM to 5PM  (Email us if you leave samples here).

Samples get picked up at 11:00 AM every Monday through Friday, and assay types are run on scheduled days (see below).

Helpful Tips:

1.  Plan for your results to be ready by the end of the next business day after your assay type is scheduled to run. Guaranteed same-day service is not available. While pick-up occurs every day, DNA assays will run Mondays, Wednesdays, and Fridays, while RNA assays will be run Tuesdays and Thursdays. Samples turned in ahead of time will be stored appropriately until they are processed.

2.  Samples should be suspended in water. Contaminants can create problems with the run, including a less intense signal.

3.  RNA, dsDNA, and ssDNA can be detected by the machine, and will be visible if they are in your sample no matter which assay you select.

4.  The main reason the concentration column is on the form is to ensure your chosen assay matches your sample concentrations. If your sample is limited you can write “low”, or give your best estimate for the concentration if it is not low.

5.  The High Sensitivity DNA Assays are designed to give the best results at about 1 ng/μl. As a rule, if you are expecting a broad peak(s), hundreds of bp wide, submit higher concentrations (up to 5 ng/μl). If you are expecting a narrow peak(s), 10-50 bp wide, submit at concentrations between 0.5 and 1 ng/μl. For best results on RNA assays, submit samples with concentrations in the upper end of the concentration range.

6.  The NanoDrop frequently reads concentrations higher (sometimes ten-fold more than what the Fragment Analyzer shows). This is because the NanoDrop detects everything, including contaminants, in the sample. The Fragment Analyzer detects RNA and DNA only. If you use a NanoDrop to measure the concentration of your samples, remember to check the 260/230 ratio, and consider submitting samples at a higher concentration than the recommended 1-5 ng/μl and choosing “Do not dilute” on your ticket.

NOTE:  These results are intended for research use only, and are not appropriate for use in clinical diagnosis nor for forensic purposes.