Dear Colleagues, I posted my question about selecting Microsatellite electrophoresis few weeks ago. Thank you very for your suggestions. We silver stain microsatellite loci, and have been doing this for a number of years. The gel rigs we use are from Biorad, we have two sizes of gel but the most user friendly are the short fat gels (38 x 30 cm) onto which you can load 96 samples plus controls. The gels are very easy to use. The power packs are also Biorad, but this is probably because we got a good deal on them. Then we use pre-measured silver staining reagents from Promega, which probably isn't the cheapest way of doing things but having everything pre-measured is a huge time saver. Hope this helps Jo I used a Hoefer SE660 vertical gel for analysing human derived tetranucleotide loci in baboons (see http://www.hoeferinc.com/product.asp?ProdID=32). This system allows you to run four gels simultaneously and up to 100 lanes. I got very clean results using 1mm thick 8% non-denaturing acrylamide (29:1 acrylamide:bisacrylamide) gels which were then stained with silver. I’ve attached a picture as an example – the alleles closest together differ by 1 repeat unit. I also tried to look at dinucleotide loci (this time from gazelles), but I found these more difficult to resolve because the alleles were closer together and there were more stutter bands than with the tetranucleotide loci. An alternative might be to consider a ‘Spreadex gel’. These are preformed gels and run on a horizontal system and can be stained with SYBR green. Never used them myself but other people say they are very good. They are probably significantly more expensive than acrylamide. The Elchrom site is found at http://www.elchrom.com/public/index.php?article=144. Good luck and I hope that this helps. Please feel free to contact me again if you need any more info. Cheers Rob. During my phd I used big slab gels (the old sequencing rigs) I would attach the gel to one of the plates using some sigma product which i could find in an old lab note book if you need it. Anyways the protocal for this method at least the actual silver staining part is in Morgan et al 2003 J heredity which is attached. This protocol worked very well for my needs, but given the cheapness of dye labeled primers I might do a cost benifit analysis before you spend tons of money on silver staining chemicals. I guess that all hinges on you having access to a sequencer or gel scanner. Hope this helps. Ted I am working with microsatellites in Mexico on seagrasses. I am using the electrophoresis set of Biorad (Sequigen GT) it is a bit expensive, but it works fine. I am using the 38 x 50 cm gels, and load them 2 times. this gives me (if lucky), results of 120 samples. To estimate size I use 10 bp ladder of invirtogen! Hope this will help. Yours, Kor-jent Hi I use the OWL Scientific vertical rigs. The S3S model. 18002425560. When you order it you get two sets of plates. I these rigs more than BWR because the buffer tends to leak from top to bottom on those. If you are using silver staining they plates work pretty well with the promega silver sequence staining reagents... I never seem to have much trouble with it. Lee Dear Binh, I'm using Biorad Sequigen. It's just wonderful :-) It uses large amount of buffer but thanks to it there are almost no smiles on gel. In my opinion the best set is 30x38 with 0,4mm spacers (thinner gels have problems with reaching the desired temperature in prerun). If you're going to analyse large sets of samples I advise you to buy 100 Shark Tooth Comb. I'm silver staining on longer plate as it's easier to manipulate - don't forget to change the picture form the camera as the samples are in reverse order. You could also load it in reverse order :) Good luck! Maciek Binh Thai PhD Research Student School of Ecology and Environment Deakin University P.O. Box 423 Warrnambool, Victoria, 3280 AUSTRALIA Phone: +61 3 5563 3569, +61 431 745 873 Fax: +61 3 5563 3462 e-mail: tbt@deakin.edu.au Binh Thai