I will work on microsatellite so i need to do fragment analyses. One of the company which i would like to use service use ABI DS-33 dyeset for their ABI3730xl sequencer. DS-33 Dyeset read 6-FAM, VIC, NED, PET dyes.
But these are very expensive dye sets and difficult to find service to synthese and dye the oligos. So, i found a company which give service for;
HEX instead of VIC
TAMRA instead of NED
ROX instead of PET
The oligo company is sure these dyes works on 3730xl but i couldnt get any confirmation from the fragment analyses service yet.
Do you think these dyes can be read by DS33? Would i get any problem to get fragment analyses? Any experience?
Thanks :-)
hi Turker,
there are many alternative to g5 (ds-33) dye set. The akternative you have indicated are not good, for example in g5 filter the use of HEX result in oberlap in NED (yellow channel)
These are the alternative: VIC= Yakima Yellow or ATTO532
NED: ATTO550
PET: ATTO565
these are some synthesis company which offer these dyes: http://www.microsynth.ch/; eurofingenomics.com
In some case to be accurate (but it is not so important and depend of polymer and overlap of fragment) you may need to calibrate the new dyes . It is very easy look here https://www.eurofinsgenomics.eu/media/892703/app_note_multiplex_microsatellite.pdf
Depending of the number of fragment filter D (4 color) may be a cheapest alternative. You may use FAM, HEX, ATT550 and ROX as size standard
I think that You can ask your company to calibrate their ABI for your dyeset. It is cheaper.