Microsatellite Isolation and frustration with the current state of the internet

Monday I started the long process of isolating microsatellites de novo for 5 mammal species.... I'll plan on posting a step by step account of how things are going, so interested people and family can stay up to date. But in addition to this, I hope that this series of posts will serve to fill a small void that exists in the current state of the internet...

For instance, suppose, you do some DNA extraction, and run the resultant genomic DNA on a gel. What is it supposed to look like??? The size distribution of gDNA is a basic measure of the quality of an extraction.... But what is good??? Search the internet currently, and the answer is not easily encountered. This is in contrast to searching for other things (i.e. pornography) where information on the most obscure topics are readily available..

Now more specifically, suppose you are following a well cited protocol, and at each step there is a check, and this check can be run on agarose....but the author doesn't tell you how it's supposed to look.. Now that is frustrating! Why does he give you the ability to check your work, but not the ability to interpret the results of that check? You know that there are other people out there using this protocol (a web of science search shows the protocol is heavily cited), but somehow, a google search is simply no help...

Maybe this is exactly how "open science", "open lab", "open everything 2.0" is supposed to work.. I see that Bora has been a champion of this idea, but I don't see a lot of people heading his words... It seems that these basic types of information should be available... Argh.

Well I will do my part... I will write more as time permits, but for the record, I am using Travis Glenn's Microsatellite Isolation Protocol (PDF). It is a well cited protocol (Cited ~10 times this year). It uses biotinylated oligos (common msat repeat sequences) and Dynabeads for capture... The 1st step- no surprise is genomic DNA extraction. A couple of points:

1. Fresh tissue is preferred, but appropriately stored older tissue is fine.
2. You need >50uL of 100ng/uL stock DNA
3. Run a couple of uL gDNA on agarose, smearing above 2000bp is OK, but the less smearing the better...

I am using a protocol for DNA extraction that I developed myself.... Here is the PDF. Yield are very good (50uL, >400ng/uL gDNA). It is not quite as clean as using a Qiagen (or similar) kit, but I have never had a reaction not work because of that. It is safe (never have lost a sample), and CHEAP (i.e. basically free)

The gel of typical results....Most of them look pretty good... The sample in the 7th well is not great, and I bet number 8 is a pipetting error....