Fragment analysis
dnaseq@yale.edu
9:00 AM - 5:00 PM, Monday - Friday
300 George Street, floor 2, room 2127
Fragment analysis service
We will add the size standard of your choosing and perform electrophoresis on the samples. We will return .fsa data files through Box.com. Please select an appropriate software to view your results; you can find some on our Freeware Page.
Available to Yale researchers & external researchers
Core website
Fragment analysis
Cutoff time for Friday processing is 4PM! Turnaround time for fragment analysis is 1 business day. Yale users receive priority over non-Yale users. If you have RUSH samples, please make us aware before we receive your samples.
Sample submission Sample sheet template (optional)Submission protocols
- Yale users: 1-2 µl of each fluorescently labeled PCR product brought to a final volume of 10 µl with water or HiDi formamide.
- External users: 1-2 µl of each fluorescently labeled PCR product brought to a final volume of 10 µl with water.
We will add the size standard of your choosing to your submission.
Before pooling multiplex PCR products
- We recommend running a mini-gel to verify that your PCR product works.
- Determine optimal PCR concentration by serial dilution.
- Example of possible microsatellite optimized concentration: pre-PCR = 50 ng/µl, post amplification 25 ng/µl
- To avoid Plus A problem, order primer with tails. See User Bulletin: Plus A Artifacts for more information.
Plus A artifacts
To avoid a Plus A problem, order primer with tails. See the User Bulletin: Plus A Artifacts.
Plate setup
All samples must be submitted in a (non-fully-skirted) 96-well optical plate with clear 2 mL wells. For thicker plastic plates, the angled corner must be in A12. (See the Plasticware specifications page.)
Please fill your plate by column; i.e: A1-H1, A2-H2, and so on.
You may fill out the Sample Sheet Template form if you wish to have specific names for your samples.
It must be sealed properly with strip caps or sealing film to avoid spillage/cross-contamination. If using stop caps, we recommend wrapping the plate with parafilm.
The submission is light sensitive, and should be wrapped in aluminum foil.
If you are shipping your samples, be sure to protect your wells with packing paper, bubble wrap, plate holders, etc. to avoid any breakage.
Specifications
These are the current size standard sets we offer:
| GelCo ROX500 | Thermo LIZ500 | Thermo LIZ600 | Thermo ROX500 |
Dye sets and compatibility
| Applied Biosystems standard dye sets for genotyping applications | ||
| Dye set | DS-30 | DS-33 |
| Filter set | D | G5 |
| Dye set components | 6-FAM, HEX, NED, ROX | 6-FAM, VIC, NED, PET, LIZ |
| Applied Biosystems kits and other products for genotyping | Custom oligos | AmpFLSTR Identifiler kits, AmpFLSTR Yfiler amplification kits, custom oligos, LMS v2.5, Mouse Mapping Primers, Stockmark kits |
Please check the compatibility of your dyes and filter sets with our offerings.
AmpFLSTR 4- and 5-dye kits are not supported on the Applied Biosystems 3730/3730xl instruments.
Sample submission
If including a sample sheet, please email it to DNAseq@Yale.edu.
Fragment analysis applications
- Fact sheet Fragment analysis applications
- BAC Fingerprinting on 3730/3730xl BAC Fingerprinting on 3730/3730xl
- Screen for Loss of Heterozygosity Screen for Loss of Heterozygosity
Tutorials & user guides
- Microsatellite analysis software user guide User guides
- GeneMapper user guide
-
GeneMarker Tutorial.pdf (1.42 MB)GeneMarker user guide
Rates
The minimum number of samples for a fragment analysis submission is 24 samples. You may submit fewer, but you will still be charged for 24 wells.
If samples are submitted in an incorrect plate type, the user will be charged a re-plate fee.
As of 7/1/2024
| Service | Yale user | For-profit user | Non-profit user |
|---|---|---|---|
Fragment analysis, 96-well plate, per well (Minimum charge is 24 wells) | $1.40 | $2.00 | $1.75 |
| Re-plate samples, incorrect plasticware | $10.00 | $15.00 | $15.00 |