I apologize in advance for the science. If you are not in science, read this, and sorta think you get what I am talking about, let me know!! Or let me if there is one big confusing thing and maybe I can teach you something. :-) [I am going to assume you all know what a "gene" essentially is if you were to read that word in a newspaper. If not, you do not have to keep reading. If so, my hope is you can figure out why I am frustrated at least.]
I am trying to get some real-time reverse-transcriptase polymerase chain reaction experiments going on my project.
Anyone still with me?
That's qRT-PCR.
Essentially, I am just trying to figure out if I expose tadpoles to a chemical, which genes may change their level of expression. qRT-PCR lets me do that by magnifying any changes in gene expression after I dump the chemical on.
I have very convincing data that at least one gene in a certain class of genes is very significantly upregulated. That was using "old-fashioned" and less sensitive PCR methods that do not involve special methods. Now, because everyone wants to be so fancy, I have to use special methods. Plus, I was just accepted to the conference I REALLY REALLY REALLY want to go to. I would love new data, but also recognize that people there have not seen the other unpublished preliminary data I have, so worse comes to worse, I can ask advice at the conference.
Anyone still reading?
Here is your PCR Primer (in the teaching sense).
PCR involves changing temperatures cyclically to exponentially magnify the expression of a gene using a (c)DNA template. DNA has specific sequences of four chemical bases, and these specific sequences can be used to magnify the expression of only one gene from a pool of countless genes. You have to design "primers" (in the PCR sense) that will match the specific sequence of the gene or genes you are interested in and no other gene. The PCR primers I am using are in a scientific publication. When I checked the sequences, they do identify only the gene they are supposed to identify. (Sometimes there are typos in the published primer sequences, so you have to double check them.) The other supplies I am using are common to the machine I use that does the cycling temperatures. The different temperatures are all established, as these PCR primers are in a scientific publication.
I can not get the experiment to work.
I emailed the author of the scientific publication from which I got the PCR primer sequences and he gave me the information I requested. I have tried different PCR cycles and done all the double and triple checking I (and other grad students who use this PCR technique) can think of. I added what is called an "extension time" to the protocol that is not always used in this fancy shmancy technique. Even more curious, is that if I use these PCR primers in an old-fashioned PCR, they work BEAUTIFULLY. It is only when I try to get all fancy and stuff that they do not. I have a couple more options (increasing the amount of PCR primers, decreasing one of the temperatures in the PCR protocol) that I can try. qRT-PCR is EXPENSIVE to perform and my advisor has no grant money so I try to be conscientious.
Right now, I just need data though.
K. Sorry for the science. Have a good night.
Grrr...I hate it when I post and then am like, CRAP I forgot my main point.
MAIN POINT ------> When I was a research tech, a lot of stuff did not work and a lot of stuff got screwed up (by others, of course). Some of it was very fortuitous; other stuff was just crappy. When I started grad school, everything went pretty well. I thought maybe I had put in my time as a technician, as far as science frustration goes, for at least my tenure in grad school.
Apparently I was wrong.