Team:Baltimore/Notebook

From 2011.igem.org

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<!--- The Mission, Experiments --->
<!--- The Mission, Experiments --->
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{| style="color:#1b2c8a;background-color:#0c6;" cellpadding="3" cellspacing="1" border="1" bordercolor="#fff" width="62%" align="center"
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==Notebook==  
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!align="center"|[[Team:Baltimore|Home]]
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For more information about the project click [[Dr. Tom's Notes]]
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!align="center"|[[Team:Baltimore/Team|Team]]
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!align="center"|[https://igem.org/Team.cgi?year=2010&team_name=Baltimore Official Team Profile]
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!align="center"|[[Team:Baltimore/Project|Project]]
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!align="center"|[[Team:Baltimore/Parts|Parts Submitted to the Registry]]
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!align="center"|[[Team:Baltimore/Modeling|Modeling]]
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!align="center"|[[Team:Baltimore/Notebook|Notebook]]
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!align="center"|[[Team:Baltimore/Safety|Safety]]
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!align="center"|[[Team:Baltimore/Attributions|Attributions]]
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|}
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==Notebook==
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Run through for abstract and scheduling:
Run through for abstract and scheduling:
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Start with plasmid with taq gene and pst1 gene
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Start with plasmid with taq gene and pst1 site
Remove pst1 site from taq coding sequence
Remove pst1 site from taq coding sequence
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* PCR   
* PCR   
* Digestion
* Digestion
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* Transformation
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* [[Team:Baltimore/Notebook/Transformation | Transformation]]
* Screening (1day)
* Screening (1day)
** Dilute DNA
** Dilute DNA
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* Ligation with vector (could be vector with the terminator sequence, promoter and RBS)  
* Ligation with vector (could be vector with the terminator sequence, promoter and RBS)  
* Transformation
* Transformation
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Add a promoter, transcriptional terminator, ribosome binding site (RBS)
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[[Team:Baltimore/Notebook/bb_assemblies| Add a promoter, transcriptional terminator, ribosome binding site (RBS)]]
* Screen colonies (1 day)
* Screen colonies (1 day)
** Colony PCR
** Colony PCR
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===Calendar===
===Calendar===
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----
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====July====
====July====
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'''Week 1:'''  [[Thursday, July 7]];
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'''Week 2:'''  [[Tuesday, July 12]];  [[Wednesday, July 13]];  [[Thursday, July 14]];  [[Friday, July 15]];  [[Saturday, July 16]];  [[Sunday, July 17]];
'''Week 2:'''  [[Tuesday, July 12]];  [[Wednesday, July 13]];  [[Thursday, July 14]];  [[Friday, July 15]];  [[Saturday, July 16]];  [[Sunday, July 17]];
'''Week 3:'''  [[Tuesday, July 19]];  [[Wednesday, July 20]];  [[Thursday, July 21]];  [[Friday, July 22]];  [[Saturday, July 23]];  [[Sunday, July 24]];
'''Week 3:'''  [[Tuesday, July 19]];  [[Wednesday, July 20]];  [[Thursday, July 21]];  [[Friday, July 22]];  [[Saturday, July 23]];  [[Sunday, July 24]];
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===July, Week 2===
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'''Week 4:'''  [[Tuesday, July 26]];  [[Wednesday, July 27]];  [[Thursday, July 28]];  [[Friday, July 29]];  [[Saturday, July 30]];  [[Sunday, July 31]];
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====7-12-11====
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Made one agarose gel 1%
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Used 0.5g Agarose and 50 mLs x TAE
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Poured the gel in the cold room and covered with a papre towel labled iGEM
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--[[User:Mduley|Mduley]] 19:19, 12 July 2011 (CDT)
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====7-13-2011====
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Retrieved gel from cold room and covered with 1x TAE in gel box and heated it (by running the gel with nothing in it)
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Prepared Mutagenesis PCR products from last Thursday to be run on Gel
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The tubes I made up came from the following:
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A = Green/ Blue tubes conatained Dr. Burkett's dNTP's
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====August====
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B = Orange tubes contain Dr. Goode's dNTP's 
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'''Week 1:'''   [[Tuesday, August 2]];  [[Wednesday, August 3]];  [[Thursday, August 4]];  [[Friday, August 5]];  [[Saturday, August 6]];  [[Sunday, August 7]];
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I prepared 8 tubes as follows:
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'''Week 2:'''    Week Off
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CA  = Pink tube contains 10 microliters of the Control A sample and 2 microliters of loading dye
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CB  = Blue tube contains 10 microliters of the Control B sample and 2 microliters of loading dye
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'''Week 3:'''    [[Tuesday, August 16]];  [[Wednesday, August 17]];  [[Thursday, August 18]];  [[Friday, August 19]];  [[Saturday, August 20]];  [[Sunday, August 21]];
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Rxn 1 A & B = Pink A tube contains 10 microliters of the RXN 1 A sample and 2 microliters of loading dye
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Beginning in Week 4, we will be tightening up our iGEM ship for a multitude of reasons. READ the [[New Rules]].
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              Blue B tube contains 10 microliters of the RXN 1 B sample and 2 microliters of loading dye
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'''Week 4:'''    [[Tuesday, August 23]];  [[Wednesday, August 24]];  [[Thursday, August 25]];  [[Friday, August 26]];  [[Saturday, August 27]];  [[Sunday, August 28]];
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Rxn 4 A & B = Pink A tube contains 10 microliters of the RXN 4 A sample and 2 microliters of loading dye
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'''Week 5:'''    [[Tuesday, August 30]];  [[Wednesday, August 31]];
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              Blue B tube contains 10 microliters of the RXN 4 B sample and 2 microliters of loading dye
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Rxn 5 A & B = Pink A tube contains 10 microliters of the RXN 5 A sample and 2 microliters of loading dye
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====September====
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              Blue B tube contains 10 microliters of the RXN 5 B sample and 2 microliters of loading dye
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These 8 tubs are located in the freezer and are ready to be run on the gel. They are in a yellow rack with a pink taped labeled with todays date and iGEM, mutagenesis PCR for gel.
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'''Week 1:'''    [[Thursday, September 1]];  [[Friday, September 2]];  [[Saturday, September 3]];  [[Sunday, September 4]];
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'''Week 2:''' [[Tuesday, September 6]]; [[Thursday, September 8]]; [[Friday, September 9]];  [[Saturday, September 10]];  [[Sunday, September 11]];
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Dr. Goode requested that the gel lanes be filled as follows
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'''Week 3:''' [[Tuesday, September 13]]; [[Thursday, September 15]]; [[Friday, September 16]];  [[Saturday, September 17]];  [[Sunday, September 18]];
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1.  Ladder
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'''Week 4:''' [[Tuesday, September 20]]; [[Thursday, September 22]]; [[Friday, September 23]];  [[Saturday, September 24]];  [[Sunday, September 25]];
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2.  CA
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3.  CB
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4.  R1A
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5.  R1B
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6.  Ladder
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7.  R4A
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8.  R4B
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9.  R5A
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10. R5B
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--[[User:Mduley|Mduley]] 18:00, 13 July 2011 (CDT)
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'''Week 5:''' [[Tuesday, September 27]]; [[Wednesday, September 28]]; [[ Thursday, September 29 - DEADLINE FOR EVERYTHING]];

Latest revision as of 17:47, 25 September 2011

Home Team Project Parts Submitted to the Registry Modeling Notebook Solutions Safety Attributions Hardware Material Safety Data Sheets [http://partsregistry.org/assembly/libraries.cgi?id=35|MIT Parts Registry]

Contents

Notebook

For more information about the project click Dr. Tom's Notes

Run through for abstract and scheduling:

Start with plasmid with taq gene and pst1 site

Remove pst1 site from taq coding sequence

  • In order to remove the restriction site, do site directed mutagenesis (1day)
  • PCR
  • Digestion
  • Transformation
  • Screening (1day)
    • Dilute DNA
    • Colony PCR individually
    • Digestion of PCR product with pst1
    • Run gel ~2500bp

Add biobrick prefix/suffix to taq coding sequence

  • PCR and add the prefix and suffix as primers (one prefix has an extra AG-make sure to use the correct one) (1-2 days)
    • Run gel
    • Cut out of gel
  • Cut with restriction enzyme
  • Clean up DNA
  • Ligation with vector (could be vector with the terminator sequence, promoter and RBS)
  • Transformation

Add a promoter, transcriptional terminator, ribosome binding site (RBS)

  • Screen colonies (1 day)
    • Colony PCR
    • Restriction Digestion
    • Clean up DNA
  • Sequence (1 day)

Make taq protein

Compare it to other enzymes and make sure it works

Calendar

July

Week 1: Thursday, July 7;

Week 2: Tuesday, July 12; Wednesday, July 13; Thursday, July 14; Friday, July 15; Saturday, July 16; Sunday, July 17;

Week 3: Tuesday, July 19; Wednesday, July 20; Thursday, July 21; Friday, July 22; Saturday, July 23; Sunday, July 24;

Week 4: Tuesday, July 26; Wednesday, July 27; Thursday, July 28; Friday, July 29; Saturday, July 30; Sunday, July 31;

August

Week 1: Tuesday, August 2; Wednesday, August 3; Thursday, August 4; Friday, August 5; Saturday, August 6; Sunday, August 7;

Week 2: Week Off

Week 3: Tuesday, August 16; Wednesday, August 17; Thursday, August 18; Friday, August 19; Saturday, August 20; Sunday, August 21;

Beginning in Week 4, we will be tightening up our iGEM ship for a multitude of reasons. READ the New Rules.

Week 4: Tuesday, August 23; Wednesday, August 24; Thursday, August 25; Friday, August 26; Saturday, August 27; Sunday, August 28;

Week 5: Tuesday, August 30; Wednesday, August 31;

September

Week 1: Thursday, September 1; Friday, September 2; Saturday, September 3; Sunday, September 4;

Week 2: Tuesday, September 6; Thursday, September 8; Friday, September 9; Saturday, September 10; Sunday, September 11;

Week 3: Tuesday, September 13; Thursday, September 15; Friday, September 16; Saturday, September 17; Sunday, September 18;

Week 4: Tuesday, September 20; Thursday, September 22; Friday, September 23; Saturday, September 24; Sunday, September 25;

Week 5: Tuesday, September 27; Wednesday, September 28; Thursday, September 29 - DEADLINE FOR EVERYTHING;

Retrieved from "http://2011.igem.org/Team:Baltimore/Notebook"