Team:UT-Tokyo/LabNote

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Parts List

Each part is represented by s number (e.g. #20 for lac promotor) in this notebook.

By pointing the mouse on the number within notebook entires, you can find out the details of the part.


Table 1. List of iGEM parts used in our project
Number Reg.ID Content Plasmid Length (bp)
#1 J23119 c.Promoter (Strong) pSB1A2 35
#2 J23118 c.Promoter (Medium) BBa_J61002 35
#3 B0032 RBS pSB1A2 13
#5 B0014 d.Ter pSB1AK3 95
#9 E0240 RBS-GFP-d.Ter pSB1A2 876
#10 E0040 GFP pSB1A2 681
#11 E1010 RFP pSB2K3 723
#14 I712019 fLuc pSB1AK8 1653
#17 J52008 rLuc pSB1AK3 936
#20 R0011 lacP pSB1A2 55
#21 C0012 LacI pSB1A2 1128
#22 I712074 pT7 pSB1AK8 46
#23 K145001 T7 RNA Pol. pSB1A2 2655
#24 J22106 recAp pSB1A2 192
#27 C0083 AspA pSB2K3 1518
#28 K112808 T4 phage lysis device (no promoter) pSB1A2 1785
#29 - CheZ pSB1AK3 728
#30 K117000 Lysis gene pSB1A2 144
#31 - LexA pSB1AK3 750
#33 - sulAp pSB1AK3 67
#34 - uvrAp pSB1AK3 96
#35 - recNp
#36 R0051 cI-repressed promoter pSB1A2 49
#37 C0051 cI repressor (LVA tagged) pSB1A2 \
#38 - RecA

Lab Diary

  • May
  • June
  • July
  • August
  • September
  • October

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May

'11/05/18 (Wed)

  • Making LB medium, 50×TAE, Tris-HCl (pH8.0)

'11/05/24 (Tue)

  • Making SOB medium, 0.5M EDTA (pH8.0)

'11/05/25(Wed)

  • Making TB(pH=6.7), LB plate

'11/05/26(Thu)

  • Making Mgaq(for SOB medium), Competent cell
  • TB filtration

'11/05/31(Tue)

  • iGEM parts resuspension + frozen stock (at -20℃)
  • Transformation
  • Overnight culture on LB plate (with 100ug/ml ampicilline)

June

'11/06/01(Wed)

  • Picking up colony and transfer to LB medium
  • Making LB medium

'11/06/02(Thu)

  • Miniprep
  • Making Glycerol(50%)(for cryopreservation)

'11/06/07(Tue)

  • Nanodrop
  • Transformation
  • Culture from frozen stock

'11/06/08(Wed)

  • Picking up colony

'11/06/09(Thu)

  • Miniprep

'11/06/13(Mon)

  • Planting Negative control
  • Making frozen stock
  • Transformation(BBa_E0240, #3, B0015, #5, #10, ,J31000, ,J44000)

'11/06/14(Tue)

  • Picking up colony
  • Making Mg reagent

'11/06/15(Wed)

  • Miniprep

'11/06/17(Fri)

  • Picking up colony(#3, B0015, B0040,#9, J31000, J44000)
  • Miniprep(#5)
  • Dissolution(#1, #2, K16500, #24)

'11/06/21(Tue)

  • Making frozen stock(#3, B0015, B0040, #9, J31000, J44000)
  • Passafe culture(#9, J31000)
  • Nanodrop again

'11/06/22(Wed)

  • Miniprep(#9, J31000)
  • Making competent cell

'11/06/24(Fri)

  • Digest (product of Miniprep 06/09 EScut)
  • Making agarose gel
  • Electrophoresis

'11/06/28(Tue)

  • Digest(product of Miniprep 06/09 EPcut)
  • Electrophoresis
  • Defrost and transformation(BBa_E0030, E0020, #14, I712052,#17）
  • Making 1×TAE, agarose gel, LB medium, LB plate(amp),

'11/06/29(Wed)

  • Picking up colony
  • Making LB broth

July

'11/07/01(Fri)

  • Digest(EPcut)
  • Miniprep(BBa_E0030, E0020, #14, I712052, #17)

'11/07/05(Tue)

  • Electrophoresis(product of digest 07/01)
  • Digest(#9, #14, #17, #3, #5)
  • Making antibiotic stock(1000×)(Km,Cm)

'11/07/06(Wed)

  • Gel extraction (pre)(BBa_I712052)
  • Picking up colony(Ba_J23119, #2, #24, #10)
  • Making agarose gel

'11/07/07(Thu)

  • Digest（BBa_E0240, #14, #17, #3, #5）
  • Defrost（BBa_E1010, K325101, #20, #21, #22, #23）
  • Transformation（BBa_K145001, #20, #21, #22）
  • Making LB plate（Cm,Km）

'11/07/08(Fri)

  • Miniprep(BBa_J23119, #2, #10, #24)

'11/07/11(Mon)

  • Gel extraction(#9 #14, #17)
  • Transformation(#1, #11, #20, #21, K325101, #22, #23)

'11/07/12(Tue)

  • Picking up colony

'11/07/13(Wed)

  • Frozen stock(#1(18A), #20(6G), #21(2O), #14(6N), #23(2F))
  • Picking up colony(#11)
  • Gel extraction(B#3, #5)
  • Digest (#2 SPcut)

'11/07/14(Thu)

  • Miniprep(#1, #11, #20, #21, #22, #23)
  • Electrophoresis(#2)
  • Gel extraction(#2, #3, #5)
  • Passafe(#11)
  • Making LB+amp

'11/07/15(Fri)

  • Ligation(#2-#9, #2-#3, #14-#5, #17-#5)
  • Transformation(#2-#9, #2-#3, #14-#5, #17-#5)
  • Dispensing Ligation Buffer
  • Frozen stock(#11)

'11/07/19(Tue)

  • Digest
  • Gel extraction
  • Making competent cell

'11/07/20(Wed)

  • Picking up colony
  • Making Master plate
  • Testing product of Miniprep
  • Transformation (#2, #27, #28)

'11/07/21(Thu)

  • Miniprep(#2-3, #2-9, #14-5, #17-5, #11, #20)
  • Testing product
  • Digest
    • SPcut : #20, #2-3
    • XPcut : #10, #11, #14-5, #17-5
  • Making TB

'11/07/22(Fri)

  • Frozen stock(#2, #2-3, #2-9, #14-5, #17-5）
  • Electrophoresis(#20_SP, #2-3_SP, #10_XP, #11_XP, #14-5_XP, #17-5_XP）
  • Digest
    • SPcut : #20
    • XPcut : #10, #11, #14-5, #17-5
  • Transformation(#27, #28, product of Miniprep 07/20)

'11/07/25(Mon)

  • Colony check(#2, #2-9)
  • Gel Extraction(#20_SP, #10_XP, #11_XP, #14-5_XP, #17-5_XP)
  • Ligation and Transformation(#20-#9, #3-#11, #3-#14-5, #3-#17-5)
  • Defrost Primer(200×, 10×)
  • Dispensing PCR Mix

'11/07/26(Tue)

  • Picking up colony and making master plate(#20-9, #3-11, #3-14-5, #3-17-5)
  • Colony PCR(#20-9, #3-11, #3-14-5, #3-17-5)
  • Digest(#14-5 XPcut,Ecut, #22 SPcut, #23 XPcut)
  • Ligation(#3-#14-5(Re), #3(Negative control))
  • Transformation(#15, #27, #28, #30, #3-14-5(Re), #3(Negative control))
  • Making reagent for TB(KOH, CaCl2, KCl, MnCl2)

'11/07/27(Wed)

  • Miniprep(#1, #2, #3, #10, #22, #24, #20-9, #3-11, #3-17-5)
  • Electrophoresis

'11/07/28(Thu)

  • Gel extraction(#14-5_XP, #22_SP, #23_XP)
  • Digest
    • SPcut : #1,#2, #3, #24
    • EScut : #3-11
    • XPcut : #3-17-5
  • Ligation(#3-#14-5)
  • Making TB bugger, LB plate, 0.3% LB plate

'11/07/29(Fri)

  • Cloning(lexA, cheZ)
  • Colony PCR(#3-#14-5)
  • Gel extraction(#1_SP, #2_SP, #3_SP, #24_SP, #3-11_ES, #3-17-5_XP, lexA, cheZ PCR product）
  • Miniprep(#30)
  • Digest(lexA, cheZ PCR product XP cut)

August

'11/08/01(Mon)

  • Nanodrop(#3-11(1), #1, #3, #24, #2, #3-17-5(4)M#30)
  • Digest(#3 SPcut, #5 EXcut, #9 XPcut, #30 XP cut)
  • Cloning(lexA, cheZ)
  • Gel extraction(#3, #9, #30, pSB1A2)
  • Ligation(#2-#3-17-5, #3-11-#5, #14-#5, #3-#23, #22-#9, #3-#30)
  • Transformation(#2-#3-17-5, #3-11-#5, #14-#5, #3-#23, #22-#9, #3-#30, #27(IPTG), #28)

'11/08/02(Tue)

  • Colony PCR(#2-#3-17-5, #3-11-#5, #14-#5, #3-#23, #22-#9)
  • Cloning(PCR)(#27, #28)
  • Gel extraction
  • PCR_2nd(lexA, cheZ, #27, #28)
  • Digest (#30 again)
  • Making competent cell(cheZ-, Wild Type)
  • Miniprep

'11/08/04(Thu)

  • Electrophoresis(product of ligation #2-3-17-5(2), #3-11-5(1,2), #14-5(2), #22-9(1,2,3))
  • Frozen stock(#2-3-17-5(2), #3-11-5(1,2), #14-5(2), #22-9(1,2))
  • Making Gel
  • Digest(#23 XPcut)
  • IPTG induct(#20-9)

'11/08/05(Fri)

  • Digest(#14-5(2) XPcut, #3-11-5(1) XPcut)
  • Cloning(PCR)(#27, #28, lexA, cheZ)

'11/08/08(Mon)

  • Defrost Frozen stock, Miniprep, Nanodrop and Electrophoresis(#5, #20, #23, #30)
  • Making Gel
  • Digest
    • XPcut : #27, #28, cheZ, lexA, #3-11-5(1), #23,#30
    • EScut : #6
    • EXcut : #7
    • SPcut : #7,#20
  • Defrost Frozen stock(#5, #14-5(2), #3-11-5(1))

'11/08/09(Tue)

  • Miniprep, Electrophoresis and Digest(#5, #14-5(2), #3-11-5(1))
  • Gel extraction and Nanodrop(#6, #27, #8, cheZ, lexA③, #3-11-5(1), #23, #7_EX, #20, #7_SP)
  • Ligation(#27-psB1A2, #3-27, #20-28, #28-psB1A2, #3-29, #29-psB1A2, #31-psB1A2, #3-#23, #1-#3-11-5(1), #2-#3-11-5(1), #24-#3-11-5(1), #3-#30)
  • Making LB plate

'11/08/10(Wed)

  • Colony PCR(#27-pSB1A2, #3-27, #20-28, #28-psB1A2, #3-
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