Black stuff in my DNA? - (Dec/08/2008 )
I have a DNA sample that was sent to our lab by a lab in Germany and the blood was from a Saudi Arabia patient, so it's possible that our lab didn't do anything wrong, but I just want to know what this might be...
The DNA PCR'd and sequenced fine for about 3 months, but then it stopped working well. The absorbance spectrum looked nasty (it was more of a line with a kink in it than a nice bump like it should have). I put that project on hold until I had time to work at getting the DNA to look better so I put the DNA in the refrigerator just like all of my other DNA samples. Now that I have some extra time, I started to work on that DNA again, but I've noticed that it has little black stuff at the bottom of the tube! when I vortex the tube, they go away but come back when I centrifuge it-it's almost like there were a lot of them and they were just slightly denser than the rest of the solution so they sank over time (or are centrifuged out). They don't appear to affect a Qiagen whole genome application or PCR (we'll see about sequencing). Has anyone had an experience like this? It's almost like there's something growing in my DNA!!!
The DNA PCR'd and sequenced fine for about 3 months, but then it stopped working well. The absorbance spectrum looked nasty (it was more of a line with a kink in it than a nice bump like it should have). I put that project on hold until I had time to work at getting the DNA to look better so I put the DNA in the refrigerator just like all of my other DNA samples. Now that I have some extra time, I started to work on that DNA again, but I've noticed that it has little black stuff at the bottom of the tube! when I vortex the tube, they go away but come back when I centrifuge it-it's almost like there were a lot of them and they were just slightly denser than the rest of the solution so they sank over time (or are centrifuged out). They don't appear to affect a Qiagen whole genome application or PCR (we'll see about sequencing). Has anyone had an experience like this? It's almost like there's something growing in my DNA!!!
Why not spin it down and use the upper sup? Perhaps you should investigate the pellet by microscopy, and if you have connections, send to microbiology lab for various cultures! Let us know.
I have never had an experience like this, but sometimes with flies I've noticed that the tiniest bits of cuticle (wings and stuff) sometimes get pressed into the pellet if I'm not being careful. Over time they can detach and bump around. It's gross, but it doesn't really affect anything. And people don't have those little chitinous bits. I think it's more likely that there are little particles of something in your sample rather than something growing.
Maybe extraction techniques are different in Saudi Arabia? 
If you can spare a bit of it, perhaps spin it down and aliquot a little bit of it out, and borrow a Qiagen cleanup column from somebody. (You might already use them to purify PCR products for sequencing.) Then if you look at the filter after the cleanup, and see black specks, you'll know that they're out. Then set aside the cleaned DNA and see if it produces any more specks.