iGEM 2013 — Team Glendale_CC_AZ

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# Team:Glendale CC AZ/Notebook

### From 2013.igem.org

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* [Attributions](https://2013.igem.org/Team%3AGlendale_CC_AZ/Attributions "Thank you!")

Notebook

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#### Glendale Community College Arizona[![GCC](https://static.igem.org/mediawiki/2013/f/f1/Gcclogo.gif)](http://www2.gccaz.edu)

### Protocols

---

![iGEM](http://s6.postimg.org/ac6n5yrpd/Calendar.png)
[Growth Curve Assay](https://2013.igem.org/Team%3AGlendale_CC_AZ/Protocols/GrowthCurve)

[NaCl Growth Curve Assay](https://2013.igem.org/Team%3AGlendale_CC_AZ/Protocols/NaCl)
[Survival Growth Assay](https://2013.igem.org/Team%3AGlendale_CC_AZ/Protocols/SurivalGrowth)
[Alkaline Lysis Plasmid Miniprep](https://2013.igem.org/Team%3AGlendale_CC_AZ/Protocols/AlkalineLysis)
[Restriction Digest](https://2013.igem.org/Team%3AGlendale_CC_AZ/Protocols/RestrictionDigest)
[DNA Isolation](https://2013.igem.org/Team%3AGlendale_CC_AZ/Protocols/DNAIsolation)
[Bioinformatics](https://2013.igem.org/Team%3AGlendale_CC_AZ/Protocols/Bioinformatics)
[Ligation](https://2013.igem.org/Team%3AGlendale_CC_AZ/Protocols/Ligation)
[Transformation](https://2013.igem.org/Team%3AGlendale_CC_AZ/Protocols/Transformation)

---

### Daily Logs

* August 22nd 2013

  1. Performed PCR on LEA 1 and LEA 2 from D.
  hopiensis. 2. Inoculated bacteria containing single
  parts (LacI, RBS, TT, LEA-soybean, and RFP).
* August 20th 2013

  1. Performed Gel Electrophoresis on PCR products (Ran
  gel too long, had to re-run). 2. Performed Alkaline
  Lysis Plasmid Miniprep on sample B of single parts
  (LacI promoter, RBS, LEA, TT, and the RFP control).
  3. Prepared 2x 40 mL gels for mini prep products from
  8/17/13 and earlier today. 4. Read absorbance values
  for miniprep samples from today. 5. Performed PCR on
  miniprep products from 8/17/13 as well as miniprep
  products from earlier today. 6. Prepared samples for
  sequencing.
* August 17th 2013

  1. Reviewed what we've learned from gel ran on
  8/16/13. 2. Performed Alkaline Lysis Plasmid Miniprep
  on sample A of single parts(LacI promoter, RBS, LEA,
  TT, and the RFP control). 3. Read absorbance values
  of miniprep products.
* August 16th 2013

  1. Performed Gel Electrophoresis containing digest
  products from 8/15/13.
* August 15th 2013

  1. Performed control restriction digest containing
  RFP- control ONLY, but different enzymes and
  different buffers for each. (To ensure enzymes and
  buffers are performing as expected).
* August 14th 2013

  1. Discussed and planned future of GCC's 2013 iGEM
  team.
* August 13th 2013

  1. Performed PCR of LEA 1 and LEA 2 D. radiodurans
  isolates. 2. Performed Gel Electrophoresis containing
  8/12/13 PCR products. 3. Performed Gel
  Electrophoresis containing PCR products from today
  (LEA 1 & 2- D. radiodurans).
* August 12th 2013

  1. Performed PCR of LEA 1 and LEA 2 D. hopiensis
  isolates.
* August 10th 2013

  1. Team met at local public library to divide up wiki
  sections and create a complete outline of project
  section of the wiki.
* August 8th 2013

  1. Performed transformation of all ligation products
  from 8/7/13 according to iGEM's transformation
  protocol. 2. Found a few extra biobricks to order
  from iGEM for easier assembly.
* August 7th 2013

  1. Performed ligation of single and double digests
  according to iGEM's ligation protocol.
* August 6th 2013

  1. Ran out agarose gel containing PCR products from
  8/1/13 (isolates+LEA). 2. Performed Gel
  Electrophoresis (ran gel) containing Ecor1 digests,
  as well as select single/double digested parts from
  previous trials.
* August 5th 2013

  1. Debriefed team on results from all procedures
  performed 8/1/13. 2. Performed Ecor1 digest using
  miniprep products from 8/1/13. 3. Re-ran agarose gel
  of double digested parts from 8/1/13.
* August 1st 2013

  1. Performed Restriction Digest. 2. Performed
  Alkaline Lysis Plasmid Miniprep on double parts. 3.
  Read absorbance values of miniprep products. 4. Ran
  agarose gel containing digested parts (from earlier
  today). 5. Performed PCR on single and double parts
  (LacI promoter, ribosome binding site, double
  terminator, RFP, LacI+ RBS, TT+ LEA) 6. Performed PCR
  on D. hopiensis isolates and LEA. 7. Ran out 2x
  agarose gels containing (separately) PCR products
  from today.
* July 31st 2013

  1. Performed Restriction Digest according to values
  determined on 7/29/13. 2. Inoculated bacterial
  cultures from 7/25/13 plates.
* July 30th 2013

  1. Ran large agarose gel of PCR products from
  7/25/13. 2. Performed PCR on yesterday's miniprep
  products. 3. Performed PCR on LEA (D. hopiensis). 4.
  Ran agarose gel of PCR products containing miniprep
  products from 7/29/13.
* July 29th 2013

  1. Performed Alkaline Lysis Plasmid Miniprep on RFP
  Control, LacI Promoter, Double Terminator, and
  Ribosome Binding Site. 2. Read absorbance values of
  miniprep products. 3. Determined volume of miniprep
  products needed to perform Restriction Digest.
* July 25th 2013

  1. Streaked plates with archived glycerol stocks. 2.
  Performed PCR.
* July 24th 2013

  1. Ran miniprep samples on agarose gels prepared
  7/22/13.
* July 23rd 2013

  1. Performed Alkaline Lysis Plasmid Miniprep on the
  rest of the transformed bacteria from 7/18/13. 2.
  Read the absorbance values for all miniprep samples.
  3. Read the absorbance values for genomic DNA
  isolated on 7/18/13. 4. Performed Restriction Digest
  on miniprep samples.
* July 22nd 2013

  1. Performed Alkaline Lysis Plasmid Miniprep on half
  of the transformed bacteria from 7/18/13. 2. Prepared
  2x 50 mL agarose gels to run all miniprep samples.
* July 19th 2013

  1. First round of wiki assignments due.
* July 18th 2013

  1. Team split up to work on transformation and DNA
  isolation.
* July 17th 2013

  1. Ran gel of digest products to ensure digest was
  successful. 2. Performed ligation according to iGEM's
  ligation protocol.
* July 16th 2013

  1. Performed Restriction Digest according to iGEM's
  restriction digest protocol. 2. Reviewed iGEM's
  ligation protocol and created table for 7/17/13.
* July 15th 2013

  1. Ran gel of of 7/9/13 and 7/10/13 Miniprep
  products. 2. Ran gel of PCR products from 7/10/13 3.
  Presentation on Restriction Digest protocol and
  created table for 7/16/13 digest.
* July 10th 2013

  1. Counted colonies on plates from yesterday's
  Survival Growth Assay. 2. Performed PCR 3. Performed
  Miniprep.
* July 9th 2013

  1. Performed NaCl Growth Curve Assay on E.coli
  containing PprA and RecA. 2. Ran gels of PCR
  products. 3. Performed Miniprep. 4. Performed
  Survival Growth Assay.
* July 8th 2013

  1. Set up bacterial growth culture of transformation
  products from 7/8/13. 2. Performed Polymerase Chain
  Reaction.
* July 3rd 2013

  1. Performed transformation on LacI promoter
  (BBa\_R0010), Ribosome Binding Site (BBa\_B0034),
  Double Terminator (BBa\_B0015), and RFP Control
  provided by iGEM.
* July 2nd 2013

  1. Team split up and performed NaCl Growth Curve
  Assay on transformed E.coli containing PprI gene or
  RecA gene (depending on group). 2. Performed Survival
  Growth Assay.
* July 1st 2013

  1. Presentation on adding information and navigating
  our wiki page. 2. First round of wiki sections
  assigned.
* June 27th 2013

  1. Performed NaCl Growth Curve Assay, working with
  higher concentration of IPTG. 2. Performed Survival
  Growth Assay.
* June 26th 2013

  1. Ran yesterday's miniprep products out on a gel. 2.
  Performed NaCl Growth Curve Assay. 3. Developed
  protocol and flowchart for Survival Growth Assay.
* June 25th 2013

  1. Performed Miniprep.
* June 20th 2013

  1. Performed Miniprep and Gel Electrophoresis.
* June 19th 2013

  1. Presentation on Gel Electrophoresis protocol.
* June 18th 2013

  1. Added prefix and suffix sequences to primers,
  reviewed entire sequence once more prior to ordering.
  2. Presentation on Alkaline Lysis Plasmid Miniprep
  protocol, drew up flowchart.
* June 17th 2013

  1. De-briefed members unable to attend ASU luncheon.
  2. Fern and Cristina debuted first clips of our team
  stop motion video!
* June 14th 2013

  1. Team went to ASU for meet-and-greet luncheon with
  ASU's 2013 iGEM team.
* June 13th 2013

  1. Performed Hydrogen Peroxide Growth Curve Assay,
  still searching working with different concentrations
  of hydrogen peroxide. 2. Presentation on iGEM's
  transformation protocol.
* June 12th 2013

  1. Team double checked primer designs for restriction
  sites Xba1, Pst1, Ecor1, and Spe1.
* June 11th 2013

  1. Performed Hydrogen Peroxide Growth Curve Assay
  with different concentrations of hydrogen peroxide.
  2. Team searched for homolog genes of interest in D.
  hopiensis.
* June 10th 2013

  1. Team presented primer designs.
* June 6th 2013

  1. Performed NaCl Growth Curve Assay to determine
  appropriate concentration of NaCl. 2. Planned next
  stages of our project.
* June 5th 2013

  1. Performed Hydrogen Peroxide Growth Curve Assay to
  determine appropriate concentration of hydrogen
  peroxide.
* June 4th 2013

  1. Reviewed protocol for DNA isolation. 2. Biotech
  student Beau came in to present his project on
  Deinococcus radiodurans.
* May 29th 2013

  1. Biobrick and gene presentations continued. 2. Team
  covered requirements for designing primers,
  determined primers for all genes of interest.
* May 28th 2013

  1. Biobrick and gene presentations continued. 2.
  Reviewed protocol for Polymerase Chain Reaction.
* May 22nd 2013

  1. Members continued biobrick and gene presentations.
  2. Team split into 5 groups and performed our first
  Growth Curve Assay.
* May 21st 2013

  1. Members began their biobrick presentations. 2. We
  covered online resources available to the team such
  as Open Wetware, iGEM Help pages, and Rstudio. 3.
  Team developed protocol for our Growth Curve Assay.
* 1st Meeting May
  20th

  1. Developed goals for the summer 2. Reviewed lab
  techniques 3. Reviewed iGEM website and registry 4.
  Assigned biobricks of interest and genes of
  interest to present