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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Compare it to other enzymes and make sure it works
Compare it to other enzymes and make sure it works
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===Calendar===
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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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====July====
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'''Week 1:'''  [[Thursday, July 7]];
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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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'''Week 2:'''  [[Tuesday, July 12]];  [[Wednesday, July 13]];  [[Thursday, July 14]];  [[Friday, July 15]];  [[Saturday, July 16]];  [[Sunday, July 17]];
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Prepared Mutagenesis PCR products from last Thursday to be run on Gel
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'''Week 3:'''  [[Tuesday, July 19]];  [[Wednesday, July 20]];  [[Thursday, July 21]];  [[Friday, July 22]];  [[Saturday, July 23]];  [[Sunday, July 24]];
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The tubes I made up came from the following:
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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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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'
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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 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;