Difference between revisions of "Team:Cooper Union/Notebook"

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<h1>Cooper Union iGEM 2015 Notebook</h1>
 
<h1>Cooper Union iGEM 2015 Notebook</h1>
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<h2>Cooper Union iGEM 2015 Notebook</h2>
 
  
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<h4>
+
<h2>JUNE 2015</h2>
  
−
<h5>What should this page have?</h5>
+
<h4> June 3rd - 8th </h4>
 +
<li>We designed various truncated and modified TdT sequences using the SnapGene viewer. The sequences were derived from the results documented in a paper by Repasky et. all detailing the Mutational Analysis of Terminal Deoxynucleotidyltransferase-mediated N-Nucleotide Addition in V(D)J Recombination.</li>
 +
<li> The sequences can be found in the following google drive folder:
 +
https://drive.google.com/drive/folders/0ByXS6yhMrkJ7flpzTjF2cXFLTFEzUHBlUC1CTU9pd2FObmZyc0ozNTBGSnhxTnk3VGZMZzQ/0B713y2SjhYhifklQeXlvOTFSVkRTakVKREZ6dW0xTWRIVVVoWlBiM0ZZbllCdWpPTzBpVTQ/0B713y2SjhYhifldYeVRlRkZ5ZWJlRi1YUmlxOXFvZEFaa2ZBY3VMLWFLNHQyWmwzNmlPQk0/0B713y2SjhYhiflF5MU5nMnh4bExsS3h2dkx6S2JEcWxPZWRCRVNMX1lGZkp1TTc1alZad1U
 +
</li>
 +
 
 +
<h4> June 16th </h4>
 +
<li>We practiced making 1% agarose gels. We immobilized DNA to Dynabeads (following the Dynabead Prep Protocol) and then ran experiments with TdT using regular dATPs and Cleanamp dATPs (following the Dynabead Cleanamp Protocol). We ran a gel of the experiments but saw no results. It is proposed that DNA was lost when removing DNA from Dynabeads. </li>
 +
 
 +
<h4> June 17th </h4>
 +
<li>Prepared more Dynabeads with immobalized DNA (following the Dynabead Prep Protocol)</li>
 +
<li>Prepared LB Broth</li>
 +
<li>Prepared more 1% agarose gels</li>
 +
 
 +
<h4>June 18th</h4>
 +
<li>Ran gels of Cleanamp Dynabead Experiment, but saw no results.</li>
 +
 
 +
<h4>June 22nd</h4>
 +
<li>To test our polyacrimide gels (they were kind of old) we ran another polyacrimide gel with regular DNA sequences</li>
 +
 
 +
<h4>June 25th</h4>
 +
<li>Received the TdT del1-27. del26-143, and GIP subAAA variants! </li>
 +
<li>Did a double digest of TdT variants and pSB1C3 ADD PROTOCOL</li>
 +
<li>PCR purified restriction enzyme digest products and then performed a ligation with T4 DNA Ligase ADD PROTOCOL</li>
 +
 
 +
<h4>June 26th</h4>
 +
<li>Performed a Transformation of TdT variants cloned into pSB1C3 with NEB5alpha cells</li>
 +
 
 +
<h4>June 29th</h4>
 +
<li>Made two 1% agarose gels</li>
 +
<li>Observed that colonies grew on our transformation plates</li>
 +
<li>Did a colony PCR of multiple colonies</li>
 +
<li>Ran PCR products on a gel</li>
 +
<li>Made backup colonies for cells that had vector + insert</li>
 +
 
 +
<h4>June 30th</h4>
 +
<li>Sent in pSB1C3 + TdT variant colonies to be sequenced</li>
 +
 
 +
<h2> JULY 2015
 +
 
 +
<h4>July 1st</h4>
 +
 
 +
 
 +
<h5>should this page have?</h5>
 
<ul>
 
<ul>
 
<li>Chronological notes of what your team is doing.</li>
 
<li>Chronological notes of what your team is doing.</li>

Revision as of 00:00, 18 September 2015



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Cooper Union iGEM 2015 Notebook

JUNE 2015

June 3rd - 8th

  • We designed various truncated and modified TdT sequences using the SnapGene viewer. The sequences were derived from the results documented in a paper by Repasky et. all detailing the Mutational Analysis of Terminal Deoxynucleotidyltransferase-mediated N-Nucleotide Addition in V(D)J Recombination.
  • The sequences can be found in the following google drive folder: https://drive.google.com/drive/folders/0ByXS6yhMrkJ7flpzTjF2cXFLTFEzUHBlUC1CTU9pd2FObmZyc0ozNTBGSnhxTnk3VGZMZzQ/0B713y2SjhYhifklQeXlvOTFSVkRTakVKREZ6dW0xTWRIVVVoWlBiM0ZZbllCdWpPTzBpVTQ/0B713y2SjhYhifldYeVRlRkZ5ZWJlRi1YUmlxOXFvZEFaa2ZBY3VMLWFLNHQyWmwzNmlPQk0/0B713y2SjhYhiflF5MU5nMnh4bExsS3h2dkx6S2JEcWxPZWRCRVNMX1lGZkp1TTc1alZad1U

    • June 16th

  • We practiced making 1% agarose gels. We immobilized DNA to Dynabeads (following the Dynabead Prep Protocol) and then ran experiments with TdT using regular dATPs and Cleanamp dATPs (following the Dynabead Cleanamp Protocol). We ran a gel of the experiments but saw no results. It is proposed that DNA was lost when removing DNA from Dynabeads.

    • June 17th

  • Prepared more Dynabeads with immobalized DNA (following the Dynabead Prep Protocol)
  • Prepared LB Broth
  • Prepared more 1% agarose gels

    • June 18th

  • Ran gels of Cleanamp Dynabead Experiment, but saw no results.

    • June 22nd

  • To test our polyacrimide gels (they were kind of old) we ran another polyacrimide gel with regular DNA sequences

    • June 25th

  • Received the TdT del1-27. del26-143, and GIP subAAA variants!
  • Did a double digest of TdT variants and pSB1C3 ADD PROTOCOL
  • PCR purified restriction enzyme digest products and then performed a ligation with T4 DNA Ligase ADD PROTOCOL

    • June 26th

  • Performed a Transformation of TdT variants cloned into pSB1C3 with NEB5alpha cells

    • June 29th

  • Made two 1% agarose gels
  • Observed that colonies grew on our transformation plates
  • Did a colony PCR of multiple colonies
  • Ran PCR products on a gel
  • Made backup colonies for cells that had vector + insert

    • June 30th

  • Sent in pSB1C3 + TdT variant colonies to be sequenced

    • JULY 2015

    July 1st

    should this page have?
    • Chronological notes of what your team is doing.
    • Brief descriptions of daily important events.
    • Pictures of your progress.
    • Mention who participated in what task.

    Inspiration

    You can see what others teams have done to organize their notes: