"
Template:Team:UC Berkeley/Notebook/BX notes
From 2008.igem.org
Contents |
Sixpi 04:46, 16 June 2008 (UTC)
Sunday: I finished my DNA sequence analysis:
K112000~K112017 6.14.2008 Sequence Analysis
BX001:K112000 - Sequencing data totally off.
BX002:K112001 - One possible point mutation at bp 685, T that should be a G, but chromatogram data is low, so unsure. The mutation is significant, as it changes a Gly to a stop codon.
BX003:K112002 - Parent vector with mutations.
BX004:K112003 - Perfect match.
BX005:K112004 - One possible point mutation at bp 451, changing a Tyr to a Ser. Also, read data did not cover entire part.
BX006:K112005 - Perfect match.
BX007:K112006 - Perfect match.
BX008:K112007 - Perfect match.
BX009:K112008 - Perfect match.
BX010:K112009 - Perfect match.
BX011:K112010 - Perfect match.
BX012:K112011 - Perfect match.
BX013:K112012 - Perfect match.
BX014:K112013 - Low read quality.
BX015:K112014 - Perfect match.
BX016:K112015 - Point mutation at bp 103, changing a Ile to a Thr.
BX017:K112016 - Perfect match.
BX018:K112017 - Perfect match.
Saturday: I came in to do a miniprep of the bacteria I picked yesterday using the Agencourt miniprep kit. This kit uses magnetic beads that bind dna to purify dna. The dna was sent out for sequencing analysis.
Friday: I spent a few hours waiting for our colonies to grow big enouogh to pick. When the colonies were ready, we made 2xYT media, and grew the colonies in 1 ml of media in a 96 well plate.
Sixpi 06:35, 13 June 2008 (UTC)
We had our first mini-meeting today, where we talked about what we have done for the last two weeks(somewhat), and about various subjects related to synthetic biology(more so). The meeting was interesting and not painful.
After the meeting, I went down to the lab to take out our PCR product from the machine. I then purified the product using clonewell gels, digested, cleaned up the reaction with the zymo kit, and the started the ligation. I then had to leave, so Molly will finish the transformation for me. In return, I'll do her mini-preps on Saturday.
Sixpi 22:04, 11 June 2008 (UTC)
Our oligos arrived today(yay!). We started making our basic parts. I made a mistake while making the master mix - I didn't know the dNTPs were at 10 mM instead of 2 mM, so I added 5 times as much dNTPs than needed. This means our PCR reaction has a good chance of failing, since dNTPs bind Mg, which the DNA polymerase needs in order to copy DNA. The extra dNTPs will probably outcompete the polymerase. No DNA was seen after running the eGel, so we set up the PCR reaction again, this time adding the correct amount of dNTPs.
Yesterday I poured more plates; 1 liter of Amp/Kan, 1 liter of Amp/Cam, and 1 liter of Cam/Kan.
Sixpi 23:31, 9 June 2008 (UTC)
Today I poured plates. There were 3 liters of LB/agar media, to which I added Spe. The 3 liters made 150 plates.
Sixpi 00:02, 5 June 2008 (UTC)
In our demos this morning we transformed bacteria, plated them, picked colonies, grew them up, and extracted DNA. The afternoon was taken up by designing oligos for the basic parts will start making next week(hopefully).
Sixpi 05:12, 4 June 2008 (UTC)
Today we continued our part making demo. Yesterday we set up the PCR reaction, and today we cleaned up the PCR, set up the digestion, and also ran an analytical gel of the PCR product.
