On my first day in the lab, a
couple weeks ago, Adam had leave early to go to the airport, and I ended up
loosely following two other grad students in the lab that day, Alan and Tim.
Well Tim had the pleasure of taking me out to lunch that day, and I thought we
would go to restaurant. Instead, there was a truck outside the Stern School of
business called Sidewalk Tacos that sold Mexican food. Well we got our food and
walked to Washington Square Park and ate our lunch while watching some student
performers. Well now, with or without Adam, Alan, or Tim, I will usually bring
whatever lunch I have, Tacos and the like, to the park to eat. The reason I
tell you guys this anecdote is because I actually found this funny myself; I
remember when Arnob gave his powerpoint presentation during one of those
Wednesday lunches he talked about how he ate at some taco truck everyday. I
remember finding that pretty funny because of all the other food options in New
York; Well turns out Arnob was onto something because Sidewalk Tacos and the
Halal guys on the street make quick, cheap, and good food. Just a fun story I
thought I’d share.
I
had my first lab meeting on Tuesday of this week (6-28) and though I thought I
was going to get a minute or two to talk about the results of the buffer
experiment I had performed for my first week and a half in my lab, low and
behold, we ran out of time for the meeting. Anyways, now Adam and I have just
set about creating primers for PCR of the human 45S rRNA gene (check my last
post for why the 45S gene is relevant), for our DASH project. So basically Adam
helped me find the FASTA (the bare bones DNA sequence on ncbi) for the 45S
gene. From there we isolated the actual coding portion of those sequences, the
18S, 5.8S, and 28S, genes. Once we had located those genes within the whole 45S
gene we used an online tool called ‘Benchling’ that develops primers based off
of a certain set of parameters. In short, Benchling looks for regions of DNA
flanking the sequences we are looking to run PCR on that have a GC content
between 40-60%, are unique across all genomic DNA, and are not ‘symmetrical’
meaning that they cannot bind with themselves (primer dimers). So after
modifying the parameters to specifically fit what we want, we developed some 10
different primer pairs that we ordered. Since both the project as a whole and
ordering primers is expensive, Adam had to talk to the PI to see if there’s any
type of grant money that is available to help us out before we ordered. So last
Friday(7-1) Adam informed me that there was enough grant money for the primers
and that the order has been placed. So until they arrive sometime next week,
most likely Thursday(7-7), Adam has given me some tips about how to better use
my computer through Windows Powershell. Basically, Powershell lets you navigate
your computer without ever needing a mouse. The only complication is that it is
very confusing and I don’t really know how to do much more than access text
files and move between folders. Also waiting for these primers to arrive has
given me substantial time to write this blog in the lab!
Using Benchling to Design Primers
Learning how to use Windows PowerShell
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