Template:Kyoto/Notebook/Sep 24

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Contents

Sep 24

Electrophoresis

No name

Lane- 19/20 Pcon-pT181aptamer12-1R-DT 1
29/20 Pcon-pT181aptamer12-1R-DT 2
39/20 Pcon-pT181aptamer12-1R-DT 3
49/20 Pcon-pT181aptamer12-1R-DT 4
59/20 Pcon-pT181aptamer12-1R-DT 5
69/20 Pcon-pT181aptamer12-1R-DT 6
79/20 Pcon-pT181aptamer12-1R-DT 7
89/20 Pcon-pT181aptamer12-1R-DT 8
9100bp ladder
109/22 Pcon-pT181attenuator-aptamer12-1R-DT 1
119/22 Pcon-pT181attenuator-aptamer12-1R-DT 2
129/22 Pcon-pT181attenuator-aptamer12-1R-DT 3
139/22 Pcon-pT181attenuator-aptamer12-1R-DT 4
149/20 Plac-aptamer12-1R-DT 1
159/20 Plac-aptamer12-1R-DT 2
169/20 Plac-aptamer12-1R-DT 3
179/20 Plac-aptamer12-1R-DT 4

File:Igkuxxxx.png

Transformation

No name

NameSampleCompetent CellsTotalPlate
9/23 pSB1C3-pT181attenuator 2 µL20 µL 22 µLLB (+CP)
RBS-GFP-DT+Pcon-pT181attenuator 2 µL20 µL 22 µLLB (+CP)
9/23 Plac-+spinach-DT2 µL20 µL 22 µLLB (+Amp)
9/23 Pcon-pT181attenuator-DT+Pcon-RBS-GFP-DT 2 µL20 µL 22 µLLB (+Amp)
9/23 Pcon-aptamer12-1R-DT+Pcon-RBS-GFP-DT 2 µL20 µL 22 µLLB (+Amp)
9/23 Pcon-RBS-tetR-DT+Pcon-RBS-GFP-DT 2 µL20 µL 22 µLLB (+Amp)
9/23 Pcon-pT181antisense-DT 2 µL20 µL 22 µLLB (+CP)
9/23 Pcon-pT181attenuator-RBS-GFP-DT 2 µL20 µL 22 µLLB (+CP)
9/23 Pcon-pT181attenuator-aptamer12-1R-DT 2 µL20 µL 22 µLLB (+CP)
PUC192 µL20 µL 22 µLLB (+Amp)
Ptet-RBS-lacZα-DT 2 µL20 µL 22 µLLB (+CP) pSB1C32 µL20 µL 22 µLLB (+CP)

Liquid Culture

No name

Samplemedium
aptamer12-1R-DT(Master plate) LB(+CP)

Transformation

No name

NameSampleCompetent CellsTotalPlate
9/23 Pcon-attenuator-aptamer12-1R-DT 2 µL20 µL 22 µLLB (+CP)
9/23 pT181attenuator(1C3) 2 µL20 µL 22 µLLB (+CP)
9/23 Pcon-pT181antisense-DT2 µL20 µL 22 µLLB (+CP)
9/23 Pcon-pT181attenuator-RBS--GFP-DT 2 µL20 µL 22 µLLB (+CP)

Liquid Culture

No name

Samplemedium
pSB1C3 (Master plate-1) LB(+CP)

Digestion

Kojima

8/21 pT181attenuator (330 µg/mL) XbaIPstIbuffer BSAMilliQtotal
2 cuts6.1113315.930
NC0.300117.710
9/22 Pcon-pT181attenuator (368.3 µg/mL) EcoRISpeIbuffer BSAMilliQtotal
2 cuts5.4113019.630
NC0.300108.710
9/16 pSB1C3EcoRISpeIbuffer BSAMilliQtotal
2 cuts1811307.030
NC0.900108.110

Electrophoresis

No name

LaneSampleEnzyme1Enzyme2
11kb ladder--
2pT181attenuator XbaIPstI
3 pT181attenuator ----
4Pcon-pT181attenuator EcoRISpeI
5 Pcon-pT181attenuator ----
6pSB1C3 EcoRISpeI
7 pSB1C3 ----

File:Xxx

Miniprep

No name

DNAconcentration[µg/mL]260/280260/230
9/24 aptamer12-1R-DT144.71.031.21

Gel Extraction

Kojima

LaneDNAEnzyme
1100kb ladder----
2pT181attenuatorXbaIPstI
3 pT181attenuatorXbaIPstI
4 pT181attenuatorXbaIPstI
5------
6Pcon-pT181attenuatorEcoRISpeI
7 Pcon-pT181attenuatorEcoRISpeI
8 Pcon-pT181attenuatorEcoRISpeI
9------
10pSB1C3EcoRISpeI
11 pSB1C3EcoRISpeI
12 pSB1C3EcoRISpeI

File:Igkuxxx.jpg
File:Igku Axxxjpg

Nameconcentration[µg/mL]260/280260/230
pT181attenuator(XbaI&PstI)10.1 2.02 0.43
Pcon-pT181attenuator(EcoRI&SpeI)10.3 1.81 0.32
pSB1C3(EcoRI&SpeI)10.02.810.02

Colony PCR

Nakamoto

Samplebase pair
9/23 Pcon-aptamer12-1R-DT+Pcon-RBS-GFP-DT 11414
9/23 Pcon-aptamer12-1R-DT+Pcon-RBS-GFP-DT 21414
9/23 Pcon-aptamer12-1R-DT+Pcon-RBS-GFP-DT 31414
9/23 Pcon-aptamer12-1R-DT+Pcon-RBS-GFP-DT 41414
9/23 Pcon-aptamer12-1R-DT+Pcon-RBS-GFP-DT 51414
9/23 Pcon-aptamer12-1R-DT+Pcon-RBS-GFP-DT 61414
9/23 Pcon-aptamer12-1R-DT+Pcon-RBS-GFP-DT 71414
9/23 Pcon-aptamer12-1R-DT+Pcon-RBS-GFP-DT 81414
9/23 Pcon-pT181attenuator-DT+Pcon-RBS-GFP-DT 11631
9/23 Pcon-pT181attenuator-DT+Pcon-RBS-GFP-DT 21631
9/23 Pcon-pT181attenuator-DT+Pcon-RBS-GFP-DT 31631
9/23 Pcon-pT181attenuator-DT+Pcon-RBS-GFP-DT 41631
9/23 Pcon-pT181attenuator-DT+Pcon-RBS-GFP-DT 51631
9/23 Pcon-pT181attenuator-DT+Pcon-RBS-GFP-DT 61631
9/23 Pcon-pT181attenuator-DT+Pcon-RBS-GFP-DT 71631
9/23 Pcon-pT181attenuator-DT+Pcon-RBS-GFP-DT 81631
9/23 Pcon-RBS-tetR-DT+Pcon-RBS-GFP-DT 12042
9/23 Pcon-RBS-tetR-DT+Pcon-RBS-GFP-DT 22042
9/23 Pcon-RBS-tetR-DT+Pcon-RBS-GFP-DT 32042
9/23 Pcon-RBS-tetR-DT+Pcon-RBS-GFP-DT 42042
9/23 Pcon-pT181antisense-DT 1508
9/23 Pcon-pT181antisense-DT 2508
9/23 Pcon-pT181antisense-DT 3508
9/23 Pcon-pT181antisense-DT 4508
9/23 Pcon-pT181antisense-DT 5508
9/23 Pcon-pT181antisense-DT 6508
9/23 Pcon-pT181antisense-DT 7508
9/23 Pcon-pT181antisense-DT 8508
PreDenatureDenatureAnnealingExtensioncycle
94 °C94 °C55 °C68 °C--
5 min30 sec30 sec2min30 cycles
LaneSample
19/23 Pcon-aptamer12-1R-DT+Pcon-RBS-GFP-DT 1
29/23 Pcon-aptamer12-1R-DT+Pcon-RBS-GFP-DT 2
39/23 Pcon-aptamer12-1R-DT+Pcon-RBS-GFP-DT 3
49/23 Pcon-aptamer12-1R-DT+Pcon-RBS-GFP-DT 4
59/23 Pcon-aptamer12-1R-DT+Pcon-RBS-GFP-DT 5
69/23 Pcon-aptamer12-1R-DT+Pcon-RBS-GFP-DT 6
79/23 Pcon-aptamer12-1R-DT+Pcon-RBS-GFP-DT 7
89/23 Pcon-aptamer12-1R-DT+Pcon-RBS-GFP-DT 8
91kb ladder
109/23 Pcon-pT181attenuator-DT+Pcon-RBS-GFP-DT 1
119/23 Pcon-pT181attenuator-DT+Pcon-RBS-GFP-DT 2
129/23 Pcon-pT181attenuator-DT+Pcon-RBS-GFP-DT 3
139/23 Pcon-pT181attenuator-DT+Pcon-RBS-GFP-DT 4
149/23 Pcon-pT181attenuator-DT+Pcon-RBS-GFP-DT 5
159/23 Pcon-pT181attenuator-DT+Pcon-RBS-GFP-DT 6
169/23 Pcon-pT181attenuator-DT+Pcon-RBS-GFP-DT 7
179/23 Pcon-pT181attenuator-DT+Pcon-RBS-GFP-DT 8

File:Igkuxxxx.png
</div>

LaneSample
19/23 Pcon-RBS-tetR-DT+Pcon-RBS-GFP-DT 1
29/23 Pcon-RBS-tetR-DT+Pcon-RBS-GFP-DT 2
39/23 Pcon-RBS-tetR-DT+Pcon-RBS-GFP-DT 3
49/23 Pcon-RBS-tetR-DT+Pcon-RBS-GFP-DT 4
59/23 Pcon-pT181antisense-DT 1
69/23 Pcon-pT181antisense-DT 2
71kb ladder
89/23 Pcon-pT181antisense-DT 3
99/23 Pcon-pT181antisense-DT 4
109/23 Pcon-pT181antisense-DT 5
119/23 Pcon-pT181antisense-DT 6
129/23 Pcon-pT181antisense-DT 7
139/23 Pcon-pT181antisense-DT 8
14--

File:Igkuxxxx.png
</div>

Restriction Enzyme Digestion

Nakamoto

9/24 aptamer12-1R-DT EcoRIXbaI bufferBSAMilliQtotal
2cuts17.5µL1.0µL 1.0µL 3.0µL 3.0µL 4.5µL 30µL
NC0.9µL 0µL 0µL 1.0µL 1.0µL 7.1µL 10µL
9/20 PtetSpeIPstI bufferBSAMilliQtotal
2cuts9.5µL1.0µL 1.0µL 3.0µL 0µL 15.5µL 30µL
NC0.5µL 0µL 0µL 1.0µL 0µL 8.5µL 10µL
9/22 RBS-GFP-DTEcoRI SpeI bufferBSAMilliQtotal
2cuts3.8µL1.0µL 1.0µL 3.0µL 0µL 21.2µL 30µL
NC0.2µL 0µL 0µL 1.0µL 0µL 8.8µL 10µL
9/22 Pcon-RBS-GFP-DTEcoRI XbaI bufferBSAMilliQtotal
2cuts2.4µL1.0µL 1.0µL 3.0µL 3.0µL 19.6µL 30µL
NC0.1µL 0µL 0µL 1.0µL 1.0µL 7.9µL 10µL
9/22 Pcon-pT181attenuator 1 EcoRI XbaI bufferBSAMilliQtotal
2cuts5.4µL1.0µL 1.0µL 3.0µL 3.0µL 16.6µL 30µL
NC0.3µL 0µL 0µL 1.0µL 1.0µL 7.7µL 10µL
9/22 RBS-GFP-DTXbaI PstI bufferBSAMilliQtotal
2cuts3.8µL1.0µL 1.0µL 3.0µL 3.0µL 18.2µL 30µL
NC0.2µL 0µL 0µL 1.0µL 1.0µL 7.8µL 10µL

Ligation

Nakamoto

stateVectorInserterLigation High ver.2
9/22 aptamer12-1R-DT(EcoRI&XbaI) 1.4 µL9/24 Pcon-pT181attenuator(EcoRI&SpeI)26 µL3.5 µL
9/4 Ptet(SpeI&PstI)2.0 µL9/21 RBS-GFP-DT(XbaI&PstI)9.0 µL3.5 µL
  • incubated at 37 °C for 1 hour.

colony PCR

Kojima

Samplebase pair
9/23 Pcon-RBS-tetR-DT-Pcon-RBS-GFP-DT 52042bp
9/23 Pcon-RBS-tetR-DT-Pcon-RBS-GFP-DT 62042bp
9/23 Pcon-RBS-tetR-DT-Pcon-RBS-GFP-DT 72042bp
9/23 Pcon-RBS-tetR-DT-Pcon-RBS-GFP-DT 82042bp
9/23 Pcon-RBS-tetR-DT-Pcon-RBS-GFP-DT 92042bp
9/23 Pcon-RBS-tetR-DT-Pcon-RBS-GFP-DT 102042bp
9/23 Pcon-RBS-tetR-DT-Pcon-RBS-GFP-DT 112042bp
9/23 Pcon-RBS-tetR-DT-Pcon-RBS-GFP-DT 122042bp
9/23 Pcon-pT181antisense-DT 9508bp
9/23 Pcon-pT181antisense-DT 10508bp
9/23 Pcon-pT181antisense-DT 11508bp
9/23 Pcon-pT181antisense-DT 12508bp
9/23 Pcon-pT181antisense-DT 13508bp
9/24 Pcon-pT181attenuator-RBS-GFP-DT 11527bp
9/24 Pcon-pT181attenuator-RBS-GFP-DT 21527bp
9/24 Pcon-pT181attenuator-RBS-GFP-DT 31527bp
9/24 Pcon-pT181attenuator-RBS-GFP-DT 41527bp
9/24 Pcon-pT181attenuator-aptamer12-1R-DT 1859bp
9/24 Pcon-pT181attenuator-aptamer12-1R-DT 2859bp
9/24 Pcon-pT181attenuator-aptamer12-1R-DT 3859bp
9/24 Pcon-pT181attenuator-aptamer12-1R-DT 4859bp
9/24 pT181attenuator(pSB1C3) 1390bp
9/24 pT181attenuator(pSB1C3) 2390bp
9/24 pT181attenuator(pSB1C3) 3390bp
9/24 pT181attenuator(pSB1C3) 4390bp

Tatsui

PreDenatureDenatureAnnealingExtensioncycle
 94°C 94°C 55°C 68°C--
5min30s 30s 2min30cycle

Miniprep

No name

DNAconcentration[µg/mL]260/280260/230
pSB1C3183.9 1.91 1.59
Pcon-pT181attenuator-aptamer12-1R-DT231.71.822.35
Plac-aptamer12-1R-DT208.91.981.79

Electrophoresis

Nakamoto

LaneSampleEnzyme1Enzyme2
1kb ladder----
29/24 aptamer12-1R-DTEcoRIXbaI
3 9/24 aptamer12-1R-DT -- --
49/24 Ptet SpeI PstI
59/24 Ptet ----
69/24 RBS-GFP-DT EcoRISpeI
9/24 RBS-GFP-DT -- --
89/24 Pcon-RBS-GFP-DT EcoRIXbaI
89/24 Pcon-RBS-GFP-DT ----
99/24 Pcon-RBS-GFP-DT ----
109/24 Pcon-pT181attenuator 1 EcoRIXbaI
119/24 Pcon-pT181attenuator 1 ----
129/24 RBS-GFP-DT XbaIPstI
139/24 RBS-GFP-DT ----
141kb ladder

File:Igkuxxxx.jpg

Gel Extraction

No name 1

LaneDNAEnzyme1Enzyme2
11kb ladder----
2aptamer12-1R-DTEcoRIXbaI
3aptamer12-1R-DTEcoRIXbaI
4aptamer12-1R-DTEcoRIXbaI
5-- -- --
6PtetSpeIPstI
7PtetSpeIPstI
8PtetSpeIPstI
9------
10RBS-GFP-DTEcoRISpeI
11RBS-GFP-DTEcoRISpeI
12RBS-GFP-DTEcoRISpeI

File:Igku xxxbefore.jpg
File:Igkuxxx1-2.jpg

LaneDNAEnzyme1Enzyme2
11kb ladder----
2Pcon-RBS-GFP-DTEcoRIXbaI
3Pcon-RBS-GFP-DTEcoRIXbaI
4Pcon-RBS-GFP-DTEcoRIXbaI
5------
6Pcon-pT181attenuatorEcoRIXbaI
7Pcon-pT181attenuatorEcoRIXbaI
8Pcon-pT181attenuatorEcoRIXbaI
9------
10RBS-GFP-DTXbaIPstI
11RBS-GFP-DTXbaIPstI
12RBS-GFP-DTXbaIPstI

File:Igkuxxxxpg
File:Igkuxxxx2.jpg

Electrophoresis

No name
1

LaneSample
11kb ladder
2Pcon-RBS-tetR-DT-Pcon-RBS-GFP-DT 5
3Pcon-RBS-tetR-DT-Pcon-RBS-GFP-DT 6
4Pcon-RBS-tetR-DT-Pcon-RBS-GFP-DT 7
5Pcon-RBS-tetR-DT-Pcon-RBS-GFP-DT 8
6Pcon-RBS-tetR-DT-Pcon-RBS-GFP-DT 9
7Pcon-RBS-tetR-DT-Pcon-RBS-GFP-DT 10
81kb ladder

File:Igkuxxxx.jpg


2

LaneSample
11kb ladder
2Pcon-RBS-tetR-DT-Pcon-RBS-GFP-DT 11
3Pcon-RBS-tetR-DT-Pcon-RBS-GFP-DT 12
4Pcon-pT181attenuator-RBS-GFP-DT 1
5Pcon-pT181attenuator-RBS-GFP-DT 2
6Pcon-pT181attenuator-RBS-GFP-DT 3
7Pcon-pT181attenuator-RBS-GFP-DT 4
81kb ladder

File:Igkuxxxx.jpg


3

LaneSample
1Pcon-pT181antisense-DT 9
2 Pcon-pT181antisense-DT 10
3 Pcon-pT181antisense-DT 11
4 Pcon-pT181antisense-DT 12
5 Pcon-pT181antisense-DT 13
6100bp ladder
7Pcon-pT181attenuator-aptamer12-1R-DT 1
8 Pcon-pT181attenuator-aptamer12-1R-DT 2

File:Igkuxxxx.jpg


4

LaneSample
1Pcon-pT181attenuator-aptamer12-1R-DT 3
2 Pcon-pT181attenuator-aptamer12-1R-DT 4
3 100bp ladder
4 pT181attenuator(pSB1C3) 1
5 pT181attenuator(pSB1C3) 2
6 pT181attenuator(pSB1C3) 3
7 pT181attenuator(pSB1C3) 4
File:Igkuxxxx.jpg