Team:Kyoto/Notebook

From 2013.igem.org

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Revision as of 05:16, 3 September 2013

Home Team Official Team Profile Project Parts Submitted to the Registry Modeling Notebook Material and method Safety Attributions

Contents

template

Transformation

じっけんしゃ

NameWellSampleCompetent CellsTotalPlate
いでんしぱーつのうぇるなんちゃらµLごにょごにょµLほにゃららµLこーせーぶっしつ
いかどうよう

Restriction digestion and Electrophoresis

じっけんしゃ

DNABufferrestricion enzymeµLrestriction enzyme µLMilliQ µLtotal
(´・ω・)

Restriction enzyme processing

じっけんしゃ

DNABufferrestricion enzymeµLrestriction enzyme µLMilliQ µLtotal
(°°)

Electrophoresis

じっけんしゃ

DNABufferrestricion enzymeµLrestriction enzyme µLMilliQ µLtotal
(°Д°)

Ligation

じっけんしゃ

Vecter(name & concentration)quantity µL
(>o<)

Gel Extraction

じっけんしゃ

LaneDNAEnzyme
(>ω・)b


Colony PCR

No name

Samplebase pair
(`・ω・´)
PreDenatureDenatureAnnealingExtensioncycle
 °C °C °C °C-
(◎Д◎)    

Liquid culture

No name

Samplemedium
(・ω・)
(・X・)  

Miniprep

No name

DNAconcentrationµg/µL260/280260/230
(・▽・)   

Extracted gel?

No name

Namequantityconcentration280/260260/230
(´ω`)
(ΦωΦ^)

Aug 19

Colony PCR

Kojima

numbarSamplebase pair
18/18 J23100 control -(1)1142
28/18 J23100-RBS-GFP-DT -(1)1156
38/18 J23100-RBS-GFP-DT -(2)1156
48/18 J23100-RBS-luxR-DT -(1)1271
58/18 J23100-RBS-luxR-DT -(2)1271
68/18 J23100-RBS-lacZα-DT -(1)670
78/18 J23100-RBS-lacZα-DT -(2)670
88/18 RBS-lysis3 -(1)997
98/18 RBS-lysis3 -(2)997
108/18 P0440(RBS-tetR-DT) -(1)1154
118/18 P0440(RBS-tetR-DT) -(2)1154
12negative control-
PreDenatureDenatureAnnealingExtensioncycle
94°C94°C55°C68°C-
5min30s30s1min30cycles

File:Igku Aug19electrophoresis1.png

numbarSamplebase pair
178/18 RBS control -(1)-
188/18 R0040(Ptet) -(1)686
198/18 R0040(Ptet) -(2)686
20negative control-
PreDenatureDenatureAnnealingExtensioncycle
94°C94°C55°C68°C-
5min30s30s30s30cycles

File:Igku Aug19electrophoresis2.png

Gel Extraction

Ashida

LaneDNAEnzyme
1100bp ladder-
38/18 K117000(lysis1) -1XbaI & PstI
58/18 K117000(lysis2) -1XbaI & PstI

File:Igku Aug19electrophoresis3
File:Igku Aug19electrophoresis4

LB Liquid Mideum Culture

Restriction Enzyme Proccessing

Transformation

Gel Extraction

Master Plate

Miniprep

Aug 20

Miniprep

Kojima

DNAconcentration[µg/µL]260/280260/230
8/18 Ptet -12201.691.87
8/18 Ptet -22101.691.71
8/18 RBS-tetR-DT -12361.631.69
8/18 RBS-tetR-DT -21821.651.98
8/18 J23100-RBS-GFP-DT -13341.712.12
8/18 J23100-RBS-luxR-DT -14401.671.60
8/18 J23100-RBS-luxR-DT -23441.681.83
8/18 J23100-RBS-lacZα-DT -12801.701.81
8/18 RBS-lysis3 -12821.671.76
8/18 RBS-lysis3 -22121.301.35

LB Culture Medium

Okazaki

volume200mL
Bacto Trypton2g
Bacto yeast extract1g
Nacl1g
Agar Powder2g
Amp40µl

1.Measuring reagents and put they in the Erlenmeyer flask
2.diluting in measuring cylinder to 200ml total
3.autoclaving
4.adding ampicirine 40ml


not written yet

Ristriction Enzyme Proccessing

Kojima and Ashida

8/20 Ptet -1(220µg/mL)EcoRIXbaI10x BSA10x buffer MMilliQtotal
4.5113317.530
0.50.20117.310
0.500.2117.310
0.500117.510
8/20 RBS-tetR-DT -2(182µg/mL)EcoRISpeI10x buffer HMilliQtotal
5.511319.530
0.60.2018.210
0.600.218.210
0.60018.410
8/20 J23100-RBS-GFP-DT(334µg/ml)EcoRISpeI10x buffer HMilliQtotal
3.01132230
0.30.2018.510
0.300.218.510
0.30018.710
8/20 J23100-RBS-luxR-DT -2(344µg/mL)EcoRIXbaIBSA10x buffer MMilliQtotal
2.9113319.130
0.30.20117.510
0.300.2117.510
0.300117.710
8/20 RBS-lysis3 -1(282µg/mL)EcoRISpeI10x buffer HMilliQtotal
3.511321.530
0.40.2018.410
0.400.218.410
0.40018.610
8/17 DT -1(188µg/mL)EcoRIXbaI10x BSA10x buffer MMilliQtotal
5.3113316.730
0.30.20117.510
0.300.2117.510
0.300117.710

incubate ~20:00

Transformation

Nakamoto

NameSampleCompetent Cells(XL10-gold)TotalPlate
tRNA-Spinach-tRNA1µL10µL11µL8/19 LB+Amp
tetR-aptamer 12_PC(076)1µL10µL11µL8/19 LB+Amp
tetR-aptamer 12_1R(113)1µL10µL11µL8/19 LB+Amp
tetR-aptamer 12_1M(105)1µL10µL11µL8/19 LB+Amp
pT181 attenuator1µL10µL11µL8/19 LB+Amp
Fusin1 attenuator1µL10µL11µL8/19 LB+Amp
Fusion3m2 attenuator1µL10µL11µL8/19 LB+Amp
pT181 antisense1µL10µL11µL8/19 LB+Amp
Fusion1 antisense1µL10µL11µL8/19 LB+Amp
Fusion6 antisense1µL10µL11µL8/19 LB+Amp

incubate 37°C overnight 20:34~

Electrophoresis

Kojima

LaneSampleEnzyme1Enzyme2
18/20 Ptet -1EcoRIXbaI
28/20 Ptet -1EcoRI-
38/20 Ptet -1-XbaI
48/20 Ptet -1--
58/20 RBS-tetR-DT -2EcoRISpeI
68/20 RBS-tetR-DT -2EcoRI-
78/20 RBS-tetR-DT -2-SpeI
88/20 RBS-tetR-DT -2--
91kbp ladder--
108/20 J23100-RBS-GFP-DT -1EcoRISpeI
118/20 J23100-RBS-GFP-DT -1EcoRI-
128/20 J23100-RBS-GFP-DT -1-SpeI
138/20 J23100-RBS-GFP-DT -1--
148/20 J23100-RBS-luxR-DT -1EcoRIXbaI
158/20 J23100-RBS-luxR-DT -1EcoRI-
168/20 J23100-RBS-luxR-DT -1-XbaI
178/20 J23100-RBS-luxR-DT -1--
181kbp ladder--
198/20 RBS-lysis3 -1EcoRISpeI
208/20 RBS-lysis3 -1EcoRI-
218/20 RBS-lysis3 -1-SpeI
228/20 RBS-lysis3 -1--
231kbp ladder--
248/17 DTEcoRIXbaI
258/17 DTEcoRI-
268/17 DT-XbaI
278/17 DT--

Aug 21

Plusgrow medium(+Amp)

Tatsui

  • material
  • 8/17 Plusgrow medium 50ml
  • 7/22 5000x Ampicillin 10µl


  1. Measuring materials and putting them in a 50ml tube

Liquid culture

Tatsui

Samplemedium
8/20 tRNA-spinach8/21 Plusgrow medium(+Amp)
8/20 TetR-aptamer 12_P(1076)8/21 Plusgrow medium(+Amp)
8/20 TetR-aptamer 12_1R(113)8/21 Plusgrow medium(+Amp)
8/20 TetR-aptamer 12_1M(105) 8/21 Plusgrow medium(+Amp)
8/20 PT181 attenuator8/21 Plusgrow medium(+Amp)
8/20 Fusion1 attenuator 8/21 Plusgrow medium(+Amp)
8/20 Fusion3m2 attenuator 8/21 Plusgrow medium(+Amp)
8/20 PT181 antisense 8/21 Plusgrow medium(+Amp)
8/20 Fusion1 antisense 8/21 Plusgrow medium(+Amp)
8/20 Fusion6 antisense 8/21 Plusgrow medium(+Amp)

incubate 37°C 10hour

Ristriction Enzyme Proccessing

Kojima and Nakamoto

8/20 Ptet-(1) EcoRIXbaI10x BSA10x buffer MMilliQtotal
4.5113317.530
0.50.20117.310
0.500.2117.310
0.500117.510
8/20 Pconst-RBS-luxR-DT-(2) EcoRIXbaI10x BSA10x buffer MMilliQtotal
2.9113319.130
0.30.20117.510
0.300.2117.510
0.300117.710
8/17 DTEcoRIXbaI10x BSA10x buffer MMilliQtotal
5.3113316.730
0.50.20117.310
0.500.2117.310
0.500117.510


incubate 37°C 1h

Electrophoresis

Aug 22

Liquid culture

Nakamoto

SampleMedium
8/21 Pcon-RBS-GFP-DT-Pcon-RBS-luxR-DT (1)8/21 Plusgrow medium(+Amp)
8/21 Pcon-RBS-GFP-DT-Pcon-RBS-luxR-DT (2)8/21 Plusgrow medium(+Amp)
8/21 Pcon-RBS-GFP-DT control (1)8/21 Plusgrow medium(+Amp)
8/21 Pcon-RBS-GFP-DT control (2)8/21 Plusgrow medium(+Amp)
8/21 RBS-lysis1 (1)8/21 Plusgrow medium(+Amp)
8/21 RBS-lysis1 (2)8/21 Plusgrow medium(+Amp)
8/21 RBS control (1)8/21 Plusgrow medium(+Amp)
8/21 RBS control (2)8/21 Plusgrow medium(+Amp)
8/21 Ptet(pm)-RBS-tetR-DT (1)8/21 Plusgrow medium(+Amp)
8/21 Ptet(pm)-RBS-tetR-DT (2)8/21 Plusgrow medium(+Amp)
8/21 Ptet(pm) control (1)8/21 Plusgrow medium(+Amp)
8/21 Ptet(pm) control (2)8/21 Plusgrow medium(+Amp)
8/21 Plux-RBS-GFP-DT (1)8/21 Plusgrow medium(+Amp)
8/21 pSB1C3(BBa_J04450) (1)8/21 Plusgrow medium(+Amp)
8/21 pSB1C3(BBa_J04450) (2)8/21 Plusgrow medium(+Amp)

incubate 37°C 10hour

Colony PCR

Kojima

Samplebase pair
8/21 RBS-lysis1(1)400
8/21 RBS-lysis1(2)400
8/21 RBS control(1)
8/21 RBS control(2)
negative control
PreDenatureDenatureAnnealingExtensioncycle
94°C94°C55°C68°C-
5min30s30s30s30cycles
Samplebase pair
8/21 Pcon-GFP-DT-Pcon-RBS-luxR-DT (1)2143
8/21 Pcon-GFP-DT-Pcon-RBS-luxR-DT (2)2143
8/21 Pcon-RBS-luxR control(1)
8/21 Pcon-RBS-luxR control(2)
negative control
PreDenatureDenatureAnnealingExtensioncycle
94°C94°C55°C68°C-
5min30s30s30s30cycles
Samplebase pair
8/21 Ptet(pm)-RBS-tetR-DT (1)
8/21 Ptet(pm)-RBS-tetR-DT (2)
8/21 Ptet(pm) control (1)
8/21 Ptet(pm) control (2)
8/21 Plux-RBS-GFP-DT (1)
8/21 pSB1C3(BBa_J04450) (1)
8/21 pSB1C3(BBa_J04450) (2)
negative control
PreDenatureDenatureAnnealingExtensioncycle
94°C94°C55°C68°C-
5min30s30s30s30cycles