Off topic
If this is supposed to be my column about the exciting aspects of labelling cells with antibodies against various potential components inside and then again with colored fluorochromes that will single out certain kinds of those antibodies from others, making your cells glow in wonderful colors under a fluorescent microscope, you’ve come to the wrong place.
Looking at the results is the best part, but making them is actually pretty boring.
I’ve been also trying to teach myself a software that will allow me to align millions of short sequence reads with the reference human genome, and see where more of them pile up. Such peaks will allow us to believe that the precipitation of those bits of DNA by locking on the bound proteins, then dragging them out of solution, are the normal sequence-specific targets of those proteins.
The technique is called chromatin immunoprecipitation or ChIP; my Paris student Ms. DQ is getting to be an ace at it, but we’re all learning fast on the fly. Here in Toulouse, we’re trying out writing a new protocol that includes microscopic bits of iron that will allow us to separate out the protein-DNA complexes from the rest of the cell lysate with a super-powerful magnet. I had invested in products from one company that I had used before, and then chose another in the end. Brand loyalty isn’t everything.
I’m trying to tie up loose ends in the next 1/2 hour because it’s a four-day long weekend coming up, so I need to feed my live cells, rinse my dead cells and put coverslips on, and leave!
Have a great weekend, everyone. Oh yes, here’s a delightful link for Obama fans out there.
Posted on Friday, November 7th, 2008 at 10:00 am Categorized as:General You can leave a response, or trackback from your own site.
November 9th, 2008 at 11:05 pm
What software’s that? I’m looking at RNA ChIP…
November 11th, 2008 at 4:47 pm
It’s called CisGenome, and it appeared in Nature Biotechnology recently – it’s pretty much everything I need, but formatting the input files is proving to be a hassle. I believe this is my fault and not theirs.