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Team:Glendale CC AZ/Notebook
From 2013.igem.org
Glendale Community College Arizona
Protocols
Growth Curve Assay
NaCl Growth Curve Assay
Survival Growth Assay
Alkaline Lysis Plasmid Miniprep
Restriction Digest
DNA Isolation
Bioinformatics
Ligation
Transformation
Timeline & 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
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
