ETHZ/labnotes

From 2007.igem.org

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* Miniprep of #4 (J23100), #5 (J37033), #8 (Q04400), #11 (R0040), #12 (R0051), #15 (Q04510) <br> One batch is miniprepped (after step 19 in the miniprep procedure) and a second batch is frozen as a backup (which is to be miniprepped from step 3 on)
* Miniprep of #4 (J23100), #5 (J37033), #8 (Q04400), #11 (R0040), #12 (R0051), #15 (Q04510) <br> One batch is miniprepped (after step 19 in the miniprep procedure) and a second batch is frozen as a backup (which is to be miniprepped from step 3 on)
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* Transformation of #13 (Q04121) and #14 (C0053) <br> Numbers #13 and #14 are now growing in the 37°C oven (step 13 in the transformation procedure)
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* Transformation of #13 (Q04121) and #14 (C0053) <br> Numbers #13 and #14 are now growing in the 37°C incubator (step 13 in the transformation procedure)
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Markus, Christos, (Martin)
Markus, Christos, (Martin)
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| Fri, 17. Aug. 2007           
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* Miniprep of #13 and #14
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* o/n of #13 and #14
* Check whether miniprep of parts #4 #5 #8 #11 #12 (#13 #14) #15 was successful
* Check whether miniprep of parts #4 #5 #8 #11 #12 (#13 #14) #15 was successful
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* #13 and #14 didn't grow
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* # 4, 8 and 11 had the plasmid, they were streaked out new on plates, that we have them now on plates
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* New white pipette tips prepared (autoclave)
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* New bottles of Liquid LB and LB Agar prepared (autoclave)
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| Martin
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| Sat, 18. Aug. 2007           
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== Week 3 ==
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Little rearrangements of the parts. Planning of the sequences to order them.
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== Week 4 ==
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{| class="wikitable" border="1" cellspacing="0" cellpadding="2" style="text-align:left; margin: 1em 1em 1em 0; background: #f9f9f9; border: 1px #aaa solid; border-collapse: collapse;"
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! Date                       
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! TODO's             
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! Completed             
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! People
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| Mon, 27. Aug. 2007         
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| Tue, 28. Aug. 2007         
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| Wed, 29. Aug. 2007         
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| Thu, 30. Aug. 2007         
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| Fri, 31. Aug. 2007         
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| Sat, 01. Sept. 2007         
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* Transform pbr322, pcyc177 and pck01                   
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* Transform pbr322, pcyc177 and pck01 and plated them                     
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| Stefan
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| Sun, 02. Sept. 2007       
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* Prepare o/n of pbr322, pcyc177, pck01
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* o/n of pcyc177, pck01
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* the plates of pcyc177 and pck01 are in the fridge
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* transformed pbr322 because the culture didn't grow on the plate
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| Stefan
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== Week 5 ==
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{| class="wikitable" border="1" cellspacing="0" cellpadding="2" style="text-align:left; margin: 1em 1em 1em 0; background: #f9f9f9; border: 1px #aaa solid; border-collapse: collapse;"
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! Date                       
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! TODO's             
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! Completed             
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! People
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| Mon, 03. Sept. 2007         
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* Prepare new competent cells
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* Miniprep pcyc177 and pcK01
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* prepare new o/n culture of pbr322
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* Run agarose gel of Minipreped plasmids
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* New competent cells prepared, they are now in the -80° Frezzer in the basement, column #17, dark orange box (we have now 30-35 EDTs of competent cells...)
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* Minipreped pcyc177 and pck01 (in the -18° freezer, where the antibiotics are)
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* pbr322 didn't grow again, so no o/n could be prepared, but we get a culture from Andy on tuesday
 +
* new o/n of pcyc177 and pck01 prepared (3 Falcons each), because we need to have more plasmids
 +
* 2 boxes of blue pipette tips are in the autoclave
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* Stefan ran the agarose gel (?)                   
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| Martin, Stefan
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| Tue, 04. Sept. 2007         
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* Miniprep pcyc177 and pck01
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* cut the prepped plasmids to test if we've got the right ones
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* run agarose gel to test the cut and uncut ones
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* prepare new o/n of pbr322 (from Andy)                   
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| Wed, 05. Sept. 2007         
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| Thu, 06. Sept. 2007         
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| Fri, 07. Sept. 2007         
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| Sat, 08. Sept. 2007         
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| Sun, 09. Sept. 2007       
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Revision as of 10:07, 4 September 2007

Contents

Part/Plasmid Numberings

The following are the numbering of the parts/plasmids that we use in the lab. Please use the same numberings if you label something when working in the lab. Extend the list for new concatenated parts.

  1. [http://partsregistry.org/Part:BBa_B0034 B0034]
  2. [http://partsregistry.org/Part:BBa_R0062 R0062]
  3. [http://partsregistry.org/Part:BBa_R0053 R0053]
  4. [http://partsregistry.org/Part:BBa_J23100 J23100]
  5. [http://partsregistry.org/Part:BBa_J37033 J37033]
  6. [http://partsregistry.org/Part:BBa_E0434 E0434]
  7. [http://partsregistry.org/Part:BBa_B0015 B0015]
  8. [http://partsregistry.org/Part:BBa_Q04400 Q04400]
  9. [http://partsregistry.org/Part:BBa_R0010 R0010]
  10. [http://partsregistry.org/Part:BBa_E0422 E0422]
  11. [http://partsregistry.org/Part:BBa_R0040 R0040]
  12. [http://partsregistry.org/Part:BBa_R0051 R0051]
  13. [http://partsregistry.org/Part:BBa_Q04121 Q04121]
  14. [http://partsregistry.org/Part:BBa_C0053 C0053]
  15. [http://partsregistry.org/Part:BBa_Q04510 Q4510]

Week 1

Date TODO's Completed People
Mon, 06. Aug. 2007
  • Preparing the Solutions
Sylke, Raphael, Stefan, Markus, Martin, Christos, Joe
Tue, 07. Aug. 2007
  • Prepare competent cells for all parts
  • Transformation of all the parts
Sylke, Raphael, Stefan, Markus, Martin, Christos, Joe
Wed, 08. Aug. 2007
  • Preparing the grown cultures (12) for the MINIPREP
    (o/n cultures)
Raphael, Stefan
Thu, 09. Aug. 2007
  • MINIPREP of the grown (10) o/n cultures
  • Gelelectrophoresis of the grown cultures (step: 0.8% Agarose)
Raphael, Stefan, Martin, Christos, Joe
Fri, 10. Aug. 2007
  • 7 working parts/plasmids (step after "DIGESTS"):
    (B0034, R0062, R0053, E0434, B0015, R0010, E0422)
  • 4 parts/plasmids minipreped:
    (R0040, R0051, Q04121, C0053)

Christos
Markus
Stefan

Sat, 11. Aug. 2007 no labwork
Sun, 12. Aug. 2007 labwork cancelled

Week 2

Date TODO's Completed People
Mon, 13. Aug. 2007
start at 3 pm
  • Prepare competent cells
  • Transformations of J23100, J37033, Q04400, Q04510
  • Control Restrictions (step after "MINIPREP")
    R0040, R0051, Q04121, C0053
  • o/n culture (E.Coli Top10)
  • Control Restrictions (didn't work)
Martin
Markus
Christos
Tim
Tue, 14. Aug. 2007 Morning Shift:
  • Start Preparing competent cells (for J23100, J37033, Q04400, Q04510)

Evening Shift:

  • Transformations of J23100, J37033, Q04400, Q04510
Morning Shift:
  • Prepared competent cells (stored in the -80°C freezer in the basement)

Evening Shift:

  • Transformation of J23100, J37033, Q04400, Q04510 and R0040, R0051, Q04121, C0053 (in the 37°C incubator until Wednesday)
  • Prepared new Liquid LB, LB Agar (both in the autoclave), Agarose Gel with concentrations of 0.8% and 2.4%
Morning Shift (9am-1pm?):
Markus, Tim

Evening Shift (5pm-...):
Martin, Christos
Wed, 15. Aug. 2007
  • Ligation (step: "LINK ASSEMBLY"):
    R0053 + E0422
    R0010 + E0422
    R0010 + E0434
    S/P: R0053, R0010
    X/P: E0422, E0434
  • Ligation didn't work due to bad quality of enzymes (probably)
From 12:
Martin, Markus

Thu, 16. Aug. 2007
  • Miniprep (J23100, J37033, Q04400, Q04510, R0040, R0051, Q04121, C0053)
  • Transformation of #13 and #14
  • Miniprep of #4 (J23100), #5 (J37033), #8 (Q04400), #11 (R0040), #12 (R0051), #15 (Q04510)
    One batch is miniprepped (after step 19 in the miniprep procedure) and a second batch is frozen as a backup (which is to be miniprepped from step 3 on)
  • Transformation of #13 (Q04121) and #14 (C0053)
    Numbers #13 and #14 are now growing in the 37°C incubator (step 13 in the transformation procedure)

Markus, Christos, (Martin)

Fri, 17. Aug. 2007
  • o/n of #13 and #14
  • Check whether miniprep of parts #4 #5 #8 #11 #12 (#13 #14) #15 was successful
  • #13 and #14 didn't grow
  • # 4, 8 and 11 had the plasmid, they were streaked out new on plates, that we have them now on plates
  • New white pipette tips prepared (autoclave)
  • New bottles of Liquid LB and LB Agar prepared (autoclave)
Martin
Sat, 18. Aug. 2007
Sun, 19. Aug. 2007

Week 3

Little rearrangements of the parts. Planning of the sequences to order them.


Week 4

Date TODO's Completed People
Mon, 27. Aug. 2007
Tue, 28. Aug. 2007
Wed, 29. Aug. 2007
Thu, 30. Aug. 2007
Fri, 31. Aug. 2007
Sat, 01. Sept. 2007
  • Transform pbr322, pcyc177 and pck01
  • Transform pbr322, pcyc177 and pck01 and plated them
Stefan
Sun, 02. Sept. 2007
  • Prepare o/n of pbr322, pcyc177, pck01
  • o/n of pcyc177, pck01
  • the plates of pcyc177 and pck01 are in the fridge
  • transformed pbr322 because the culture didn't grow on the plate
Stefan

Week 5

Date TODO's Completed People
Mon, 03. Sept. 2007
  • Prepare new competent cells
  • Miniprep pcyc177 and pcK01
  • prepare new o/n culture of pbr322
  • Run agarose gel of Minipreped plasmids
  • New competent cells prepared, they are now in the -80° Frezzer in the basement, column #17, dark orange box (we have now 30-35 EDTs of competent cells...)
  • Minipreped pcyc177 and pck01 (in the -18° freezer, where the antibiotics are)
  • pbr322 didn't grow again, so no o/n could be prepared, but we get a culture from Andy on tuesday
  • new o/n of pcyc177 and pck01 prepared (3 Falcons each), because we need to have more plasmids
  • 2 boxes of blue pipette tips are in the autoclave
  • Stefan ran the agarose gel (?)
Martin, Stefan
Tue, 04. Sept. 2007
  • Miniprep pcyc177 and pck01
  • cut the prepped plasmids to test if we've got the right ones
  • run agarose gel to test the cut and uncut ones
  • prepare new o/n of pbr322 (from Andy)
Wed, 05. Sept. 2007
Thu, 06. Sept. 2007
Fri, 07. Sept. 2007
Sat, 08. Sept. 2007
Sun, 09. Sept. 2007
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