Template:Kyoto/Notebook/Sep 14

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==Sep 14==
==Sep 14==
-
===shuiaf===
+
===Restriction Enzyme Digestion===
 +
<div class="experiment">
 +
<span class="author">Hirano</span>
 +
{| class="wikitable"
 +
! ||9/14 pSB4K5S||EcoRI||XbaI||SpeI||PstI||BufferB||BufferD||BSA||MilliQ||total
 +
|-
 +
|2cuts||10&micro;L||1&micro;L||0&micro;L||1&micro;L||0&micro;L||3&micro;L||0&micro;L||3&micro;L||12&micro;L||30&micro;L
 +
|-
 +
|NC||0.5&micro;L||0&micro;L||0&micro;L||0&micro;L||0&micro;L||1&micro;L||0&micro;L||1&micro;L||7.5&micro;L||10&micro;L
 +
|}
 +
{| class="wikitable"
 +
! ||9/13 Plac||XbaI||PstI||BufferH||BSA||MilliQ||total
 +
|-
 +
|1 cut||9&micro;L||0&micro;L||1&micro;L||3&micro;L||3&micro;L||14&micro;L||30&micro;L
 +
|-
 +
|NC||1&micro;L||0&micro;L||0&micro;L||1&micro;L||1&micro;L||7&micro;L||10&micro;L
 +
|}
 +
{| class="wikitable"
 +
! ||9/14 PKaiBC||EcoRI||XbaI||SpeI||PstI||BufferB||BSA||MilliQ||total
 +
|-
 +
|2cuts||11&micro;L||1&micro;L||0&micro;L||1&micro;L||0&micro;L||3&micro;L||3&micro;L||11&micro;L||30&micro;L
 +
|-
 +
|NC||4&micro;L||0&micro;L||0&micro;L||0&micro;L||0&micro;L||1&micro;L||1&micro;L||4&micro;L||10&micro;L
 +
|}
 +
{| class="wikitable"
 +
! ||9/14 RpaB||EcoRI||XbaI||SpeI||PstI||BufferD||BSA||MilliQ||total
 +
|-
 +
|2cuts||13&micro;L||0&micro;L||1&micro;L||0&micro;L||1&micro;L||3&micro;L||3&micro;L||9&micro;L||30&micro;L
 +
|-
 +
|NC||2&micro;L||0&micro;L||0&micro;L||0&micro;L||0&micro;L||1&micro;L||1&micro;L||5&micro;L||10&micro;L
 +
|}
 +
{| class="wikitable"
 +
! ||8/17 RBS-GFP-DT||EcoRI||XbaI||SpeI||PstI||BufferD||BSA||MilliQ||total
 +
|-
 +
|1cut||9&micro;L||0&micro;L||1&micro;L||0&micro;L||0&micro;L||3&micro;L||3&micro;L||14&micro;L||30&micro;L
 +
|-
 +
|NC||0.5&micro;L||0&micro;L||0&micro;L||0&micro;L||0&micro;L||1&micro;L||1&micro;L||7.5&micro;L||10&micro;L
 +
|}
 +
*incubated 37&deg;C 1hour
 +
</div>
 +
 
 +
===Liquid Culture===
 +
<div class="experiment">
 +
<span class="author">Hirano</span>
 +
{| class="wikitable"
 +
!Sample||medium
 +
|-
 +
|9/11 Plac(BBa-R0011)-(3)||Plusgrow medium(+Amp)
 +
|}
 +
</div>
 +
 
 +
===Electrophoresis===
 +
 +
<div class="experiment">
 +
<span class="author">Hirano</span>
 +
{| class="wikitable"
 +
!Lane||Sample||Enzyme1||Enzyme2
 +
|-
 +
|1||1kb ladder||--||--
 +
|-
 +
|2||pSB4K5(1)||EcoRI||SpeI
 +
|-
 +
|3|| pSB4K5(1)||--||--
 +
|-
 +
|4||Plac(1A2)||PstI||--
 +
|-
 +
|5||Plac(1A2)||--||--
 +
|-
 +
|6||PKaiBC||EcoRI||SpeI
 +
|-
 +
|7||PKaiBC||--||--
 +
|-
 +
|8||RpaB(1)||XbaI||PstI
 +
|-
 +
|9||RpaB(1)||--||--
 +
|-
 +
|10||RBS-GFP-DT||XbaI||--
 +
|-
 +
|11||RBS-GFP-DT||--||--
 +
|-
 +
|12||1kb ladder||--||--
 +
|}
 +
[[File:igku_0914_E1.jpg]]<br>
 +
</div>
 +
{| class="wikitable"
 +
!Lane||Sample||Enzyme
 +
|-
 +
|1||1kb ladder||--
 +
|-
 +
|2||Plac(pSB1A2)||PstI
 +
|-
 +
|3||Plac(pSB1A2)||--
 +
|}
 +
[[File:igku_0914_E2.jpg]]<br>
 +
 
 +
===Sequence PCR===
 +
<div class="experiment">
 +
<span class="author">No name</span>
 +
{| class="wikitable"
 +
!genome DNA||Big Dye||5x buffer||temp(400mg)||primer||milliQ
 +
|-
 +
|Pcon-RBS-luxR-DT||0.5||1.75||0.9||0.5||6.85
 +
|-
 +
|Pcon-RBS-luxR-DT||0.5||1.75||0.4||0.5||7.35
 +
|-
 +
|Pcon-RBS-tetR-DT||0.5||1.75||3||0.5||5.25
 +
|-
 +
|Pcon-RBS-tetR-DT||0.5||1.75||3||0.5||5.25
 +
|-
 +
|Plux||0.5||1.75||2.4||0.5||5.35
 +
|-
 +
|Plux-RBS-GFP-DT||0.5||1.75||1.9||0.5||5.85
 +
|-
 +
|Plux-RBS-GFP-DT||0.5||0.5||1.9||0.5||5.85
 +
|-
 +
|Pcon-RBS-GFP-DT||0.5||0.5||1.2||0.5||6.55
 +
|-
 +
|Pcon-RBS-GFP-DT||0.5||0.5||1.2||0.5||6.55
 +
|-
 +
|RBS-lysis3-DT||0.5||0.5||1.0||0.5||6.75
 +
|-
 +
|Pcon-antisense-Spinach-DT||0.5||0.5||1.4||0.5||6.35
 +
|-
 +
|Pcon-RBS lacZ&alpha;-DT||0.5||0.5||1.4||0.5||6.35
 +
|-
 +
|Ptet-RBS lacZ&alpha;-DT||0.5||0.5||0.59||0.5||1.85
 +
|}
 +
{| class="wikitable"
 +
!PreDenature||Denature||Annealing||Extension||cycle
 +
|-
 +
|96&deg;C||96&deg;C||50&deg;C||60&deg;C||--
 +
|-
 +
|2min||10sec||5sec||4min||30cycle
 +
|}
 +
</div>
 +
 
 +
===Gel Extraction===
 +
<div class="experiment">
 +
<span class="author">Tatsui</span>
 +
{| class="wikitable"
 +
!Lane||DNA||Enzyme
 +
|-
 +
|1||1kb ladder||--
 +
|-
 +
|2||pSB4K5||EcoRI&SpeI
 +
|-
 +
|3||pSB4K5||EcoRI&SpeI
 +
|-
 +
|4||pSB4K5||EcoRI&SpeI
 +
|}
 +
[[File:igku_0914_G8.jpg]]<br>
 +
[[File:igku_0914_G9.jpg]]<br>
 +
 
 +
===Restriction Enzyme Digestion===
 +
<div class="experiment">
 +
<span class="author">No name</span>
 +
{| class="wikitable"
 +
! ||9/14 Plac(1A2)||EcoRI||XbaI||SpeI||PstI||BufferB||BSA||MilliQ||total
 +
|-
 +
|2cuts||23&micro;L||0&micro;L||0&micro;L||0.3&micro;L||0&micro;L||3&micro;L||3&micro;L||0&micro;L||30&micro;L
 +
|}
 +
{| class="wikitable"
 +
! ||9/14 RBS-GFP-DT||EcoRI||XbaI||SpeI||PstI||BufferH||BSA||MilliQ||total
 +
|-
 +
|2 cuts||23&micro;L||1&micro;L||0&micro;L||0&micro;L||0&micro;L||3&micro;L||3&micro;L||0&micro;L||30&micro;L
 +
|}
 +
</div>
 +
 
 +
===Ligation===
 +
<div class="experiment">
 +
<span class="author">Nakamoto and Hirano</span>
 +
{| class="wikitable"
 +
!state||colspan="2"|Vector||colspan="2"|Inserter||Ligation High ver.2
 +
|-
 +
|experiment||9/13 Pcon-PT181attenuator(SpeI&PstI)||1.7||9/13 RBS-lacZα-DT (XbaI & PstI)||12.5||5
 +
|-
 +
|experiment||9/13 pSB2C3 (XbaI & PstI)||1.9||9/14 RpaB (XbaI & PstI)||16.3||10.5
 +
|-
 +
|experiment||9/13 pSB2C3 (XbaI & PstI)||4.7||9/14 PkaiBC (EcoRI & SpeI)||6.7||5.7
 +
|-
 +
|experiment||9/14 RBS-GFP-DT (PstI&XbaI)||0.7||9/14 PkaiBC (EcoRI & SpeI)||2.6||1.6
 +
|-
 +
|experiment||9/14 Plac (SpeI&PstI)||2.4||9/14 RBS-lysis1-DT (XbaI & PstI)||4.9||3.6
 +
|-
 +
|experiment||9/14 Plac (SpeI&PstI)||2.4||9/14 RBS-lysis2-DT (XbaI & PstI)||7.0||4.7
 +
|-
 +
|experiment||9/14 Plac (SpeI&PstI)||2.4||9/14 RBS-lysis3-DT (XbaI & PstI)||9.2||5.8
 +
|}
 +
 
 +
Samples were evaporeted used evaporator into about 7 µL
 +
</div>
 +
 
 +
===Colony PCR===
 +
<div class="experiment">
 +
<span class="author">No name</span>
 +
{| class="wikitable"
 +
!Sample||base pair
 +
|-
 +
|9/13 Plux＋RBS-lysis1-DT (1)~(3)||--
 +
|-
 +
|9/13 Plux＋RBS-lysis2-DT (1)~(3)||-
 +
|-
 +
|9/13 Plux＋RBS-lysis3-DT (1)~(2)||-
 +
|}
 +
{| class="wikitable"
 +
!Sample||base pair
 +
|-
 +
|9/13 Pcon-RBS-luxR-DT＋Plux-RBS-GFP-DT (1)~(4)||--
 +
|-
 +
|9/13 Pcon-PT181attenuator＋aptamer121R-DT (1)~(2)||-
 +
|-
 +
|9/13 Plac＋PT181attenuator (1)||-
 +
|}
 +
{| class="wikitable"
 +
!Sample||base pair
 +
|-
 +
|Dλ-lux(1) (1)~(2)||--
 +
|-
 +
|NC ||--
 +
|}
 +
</div>
 +
 
 +
===Electrophoresis===
 +
 +
<div class="experiment">
 +
<span class="author">No name</span>
 +
{| class="wikitable"
 +
!Lane||Sample
 +
|-
 +
|1||1kbp ladder
 +
|-
 +
|2||9/13 Plux+RBS-lysis1-DT1
 +
|-
 +
|3||9/13 Plux+RBS-lysis1-DT2
 +
|-
 +
|4||9/13 Plux+RBS-lysis1-DT3
 +
|-
 +
|5||9/13 Plux+RBS-lysis2-DT1
 +
|-
 +
|6||9/13 Plux+RBS-lysis2-DT2
 +
|-
 +
|7||9/13 Plux+RBS-lysis2-DT3
 +
|-
 +
|8||9/13 Plux+RBS-lysis3-DT1
 +
|-
 +
|9||9/13 Plux+RBS-lysis3-DT2
 +
|-
 +
|10||9/13 Pcon-RBS-luxR-DT+Plux-RBS-GFP-DT1
 +
|-
 +
|11||9/13 Pcon-RBS-luxR-DT+Plux-RBS-GFP-DT2
 +
|-
 +
|12||9/13 Pcon-RBS-luxR-DT+Plux-RBS-GFP-DT3
 +
|-
 +
|13||9/13 Pcon-RBS-luxR-DT+Plux-RBS-GFP-DT4
 +
|-
 +
|14||9/13 Ptet-pT181 antisense+Spinach-DT1
 +
|-
 +
|15||9/13 Pcon-pT181 attenuator+aptamer12-1R-PT1
 +
|-
 +
|16||9/13 Pcon-pT181 attenuator+aptamer12-1R-PT1
 +
|-
 +
|17||9/13 Plac+pT181 attenuator
 +
|}
 +
[[File:Igku_0914_E5.jpg]]<br>
 +
</div>
 +
 
 +
{| class="wikitable"
 +
!Lane||Sample
 +
|-
 +
|1||1kbp ladder
 +
|-
 +
|2||P&lambda;-lux(1)1
 +
|-
 +
|3|| P&lambda;-lux(1)1
 +
|-
 +
|4||NC
 +
|}
 +
[[File:Igku_0914_E6.jpg]]<br>
 +
 
 +
===Liquid Culture===
 +
<div class="experiment">
 +
<span class="author">No name</span>
 +
{| class="wikitable"
 +
!Sample||medium
 +
|-
 +
|9/13 Pλ-luxI(1)-1||Plusgrow medium(+Amp)
 +
|}
 +
</div>
 +
 
 +
===Transformation===
 +
<div class="experiment">
 +
<span class="author">Nakamoto</span>
 +
{| class="wikitable"
 +
!Name||Sample||Competent Cells||Total||Plate
 +
|-
 +
|9/13 RBS-lysisZα-DT(XbaI&PstI)＋9/13 Pcon-PT181 attenuator(SpeI&PstI)||2&micro;L||20&micro;L||22&micro;L||Amp
 +
|-
 +
|9/13 SB2C3＋9/14 PzαB||2&micro;L||20&micro;L||22&micro;L||CP
 +
|-
 +
|9/13 pSB2C3＋9/14 PkaiBC||2&micro;L||20&micro;L||22&micro;L||CP
 +
|-
 +
|9/13 RBS-GFP-DT＋9/14 PkaiBC||2&micro;L||20&micro;L||22&micro;L||CP
 +
|-
 +
|Plac＋RBS-lysis1-DT||2&micro;L||20&micro;L||22&micro;L||Amp
 +
|-
 +
|Plac＋RBS-lysis2-DT||2&micro;L||20&micro;L||22&micro;L||Amp
 +
|-
 +
|Plac＋RBS-lysis2-DT||2&micro;L||20&micro;L||22&micro;L||Amp
 +
|}
 +
</div>
 +
 
 +
===Sequence PCR===
 +
<div class="experiment">
 +
<span class="author">Tatsui</span>
 +
{| class="wikitable"
 +
!genome DNA||temp||Big Dye||5x buffer||primer||MilliQ
 +
|-
 +
|9/6 PT181 attenuator(VR)||3.9||0.5||1.75||0.5||3.85
 +
|-
 +
|8/17 RBS lacZα-DT||2.1||0.5||1.75||0.5||5.65
 +
|-
 +
|9/6 PT181 attenuator(VR)||3.9||0.5||1.75||0.5||3.85
 +
|}
 +
{| class="wikitable"
 +
!PreDenature||Denature||Annealing||Extension||cycle
 +
|-
 +
|96&deg;C||50&deg;C||60&deg;C||4&deg;C||--
 +
|-
 +
|10sec||5sec||4min||1min||30cycle
 +
|}
 +
</div>

Latest revision as of 17:41, 27 September 2013

Contents

Sep 14

Restriction Enzyme Digestion

Hirano

9/14 pSB4K5SEcoRIXbaISpeIPstIBufferBBufferDBSAMilliQtotal
2cuts10µL1µL0µL1µL0µL3µL0µL3µL12µL30µL
NC0.5µL0µL0µL0µL0µL1µL0µL1µL7.5µL10µL
9/13 PlacXbaIPstIBufferHBSAMilliQtotal
1 cut9µL0µL1µL3µL3µL14µL30µL
NC1µL0µL0µL1µL1µL7µL10µL
9/14 PKaiBCEcoRIXbaISpeIPstIBufferBBSAMilliQtotal
2cuts11µL1µL0µL1µL0µL3µL3µL11µL30µL
NC4µL0µL0µL0µL0µL1µL1µL4µL10µL
9/14 RpaBEcoRIXbaISpeIPstIBufferDBSAMilliQtotal
2cuts13µL0µL1µL0µL1µL3µL3µL9µL30µL
NC2µL0µL0µL0µL0µL1µL1µL5µL10µL
8/17 RBS-GFP-DTEcoRIXbaISpeIPstIBufferDBSAMilliQtotal
1cut9µL0µL1µL0µL0µL3µL3µL14µL30µL
NC0.5µL0µL0µL0µL0µL1µL1µL7.5µL10µL
  • incubated 37°C 1hour

Liquid Culture

Hirano

Samplemedium
9/11 Plac(BBa-R0011)-(3)Plusgrow medium(+Amp)

Electrophoresis

Hirano

LaneSampleEnzyme1Enzyme2
11kb ladder----
2pSB4K5(1)EcoRISpeI
3 pSB4K5(1)----
4Plac(1A2)PstI--
5Plac(1A2)----
6PKaiBCEcoRISpeI
7PKaiBC----
8RpaB(1)XbaIPstI
9RpaB(1)----
10RBS-GFP-DTXbaI--
11RBS-GFP-DT----
121kb ladder----

Igku 0914 E1.jpg

LaneSampleEnzyme
11kb ladder--
2Plac(pSB1A2)PstI
3Plac(pSB1A2)--

Igku 0914 E2.jpg

Sequence PCR

No name

genome DNABig Dye5x buffertemp(400mg)primermilliQ
Pcon-RBS-luxR-DT0.51.750.90.56.85
Pcon-RBS-luxR-DT0.51.750.40.57.35
Pcon-RBS-tetR-DT0.51.7530.55.25
Pcon-RBS-tetR-DT0.51.7530.55.25
Plux0.51.752.40.55.35
Plux-RBS-GFP-DT0.51.751.90.55.85
Plux-RBS-GFP-DT0.50.51.90.55.85
Pcon-RBS-GFP-DT0.50.51.20.56.55
Pcon-RBS-GFP-DT0.50.51.20.56.55
RBS-lysis3-DT0.50.51.00.56.75
Pcon-antisense-Spinach-DT0.50.51.40.56.35
Pcon-RBS lacZα-DT0.50.51.40.56.35
Ptet-RBS lacZα-DT0.50.50.590.51.85
PreDenatureDenatureAnnealingExtensioncycle
96°C96°C50°C60°C--
2min10sec5sec4min30cycle

Gel Extraction

Tatsui

LaneDNAEnzyme
11kb ladder--
2pSB4K5EcoRI&SpeI
3pSB4K5EcoRI&SpeI
4pSB4K5EcoRI&SpeI

Igku 0914 G8.jpg
Igku 0914 G9.jpg

Restriction Enzyme Digestion

No name

9/14 Plac(1A2)EcoRIXbaISpeIPstIBufferBBSAMilliQtotal
2cuts23µL0µL0µL0.3µL0µL3µL3µL0µL30µL
9/14 RBS-GFP-DTEcoRIXbaISpeIPstIBufferHBSAMilliQtotal
2 cuts23µL1µL0µL0µL0µL3µL3µL0µL30µL

Ligation

Nakamoto and Hirano

stateVectorInserterLigation High ver.2
experiment9/13 Pcon-PT181attenuator(SpeI&PstI)1.79/13 RBS-lacZα-DT (XbaI & PstI)12.55
experiment9/13 pSB2C3 (XbaI & PstI)1.99/14 RpaB (XbaI & PstI)16.310.5
experiment9/13 pSB2C3 (XbaI & PstI)4.79/14 PkaiBC (EcoRI & SpeI)6.75.7
experiment9/14 RBS-GFP-DT (PstI&XbaI)0.79/14 PkaiBC (EcoRI & SpeI)2.61.6
experiment9/14 Plac (SpeI&PstI)2.49/14 RBS-lysis1-DT (XbaI & PstI)4.93.6
experiment9/14 Plac (SpeI&PstI)2.49/14 RBS-lysis2-DT (XbaI & PstI)7.04.7
experiment9/14 Plac (SpeI&PstI)2.49/14 RBS-lysis3-DT (XbaI & PstI)9.25.8

Samples were evaporeted used evaporator into about 7 µL

Colony PCR

No name

Samplebase pair
9/13 Plux＋RBS-lysis1-DT (1)~(3)--
9/13 Plux＋RBS-lysis2-DT (1)~(3)-
9/13 Plux＋RBS-lysis3-DT (1)~(2)-
Samplebase pair
9/13 Pcon-RBS-luxR-DT＋Plux-RBS-GFP-DT (1)~(4)--
9/13 Pcon-PT181attenuator＋aptamer121R-DT (1)~(2)-
9/13 Plac＋PT181attenuator (1)-
Samplebase pair
Dλ-lux(1) (1)~(2)--
NC --

Electrophoresis

No name

LaneSample
11kbp ladder
29/13 Plux+RBS-lysis1-DT1
39/13 Plux+RBS-lysis1-DT2
49/13 Plux+RBS-lysis1-DT3
59/13 Plux+RBS-lysis2-DT1
69/13 Plux+RBS-lysis2-DT2
79/13 Plux+RBS-lysis2-DT3
89/13 Plux+RBS-lysis3-DT1
99/13 Plux+RBS-lysis3-DT2
109/13 Pcon-RBS-luxR-DT+Plux-RBS-GFP-DT1
119/13 Pcon-RBS-luxR-DT+Plux-RBS-GFP-DT2
129/13 Pcon-RBS-luxR-DT+Plux-RBS-GFP-DT3
139/13 Pcon-RBS-luxR-DT+Plux-RBS-GFP-DT4
149/13 Ptet-pT181 antisense+Spinach-DT1
159/13 Pcon-pT181 attenuator+aptamer12-1R-PT1
169/13 Pcon-pT181 attenuator+aptamer12-1R-PT1
179/13 Plac+pT181 attenuator

Igku 0914 E5.jpg

LaneSample
11kbp ladder
2Pλ-lux(1)1
3 Pλ-lux(1)1
4NC

Igku 0914 E6.jpg

Liquid Culture

No name

Samplemedium
9/13 Pλ-luxI(1)-1Plusgrow medium(+Amp)

Transformation

Nakamoto

NameSampleCompetent CellsTotalPlate
9/13 RBS-lysisZα-DT(XbaI&PstI)＋9/13 Pcon-PT181 attenuator(SpeI&PstI)2µL20µL22µLAmp
9/13 SB2C3＋9/14 PzαB2µL20µL22µLCP
9/13 pSB2C3＋9/14 PkaiBC2µL20µL22µLCP
9/13 RBS-GFP-DT＋9/14 PkaiBC2µL20µL22µLCP
Plac＋RBS-lysis1-DT2µL20µL22µLAmp
Plac＋RBS-lysis2-DT2µL20µL22µLAmp
Plac＋RBS-lysis2-DT2µL20µL22µLAmp

Sequence PCR

Tatsui

genome DNAtempBig Dye5x bufferprimerMilliQ
9/6 PT181 attenuator(VR)3.90.51.750.53.85
8/17 RBS lacZα-DT2.10.51.750.55.65
9/6 PT181 attenuator(VR)3.90.51.750.53.85
PreDenatureDenatureAnnealingExtensioncycle
96°C50°C60°C4°C--
10sec5sec4min1min30cycle
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