Team:HokkaidoU Japan/Notebook/aggregation Week 12

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(17th~19th)
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<div class="hokkaidou-notebook-daily">
 +
==September 17th==
 +
<div>
 +
==Digestion of RBS-phaC-RBs-phaA-RBS-phaB-RBS-eYFP-dT-pSB1A2 and ptet-pSB1A2==
 +
<p>
 +
To make a construct of ptet-RBS-phaC-RBS-phaA-RBS-phaB-RBS-dT-pSB1A2, we digested RBS-phaC-RBs-phaA-RBS-phaB-RBS-eYFP-dT-pSB1A2 with XbaI & PstI, ptet-pSB1A2 with SpeI & PstI.
 +
Insert (RBS-phaC-RBs-phaA-RBS-phaB-RBS-eYFP-dT-pSB1A2)
 +
{|class="hokkaidou-table-digestion"
 +
  |-
 +
  |DNA solution ( 45=50ng/ul)
 +
  |27 ul
 +
  |-
 +
  |XbaI
 +
  |1 ul
 +
  |-
 +
  |PstI
 +
  |1 ul
 +
  |-
 +
  |10xM buffer
 +
  |4 ul
 +
  |-
 +
  |DW
 +
  |7 ul
 +
  |-
 +
  |Total
 +
  |40 ul
 +
  |}
 +
 +
 +
Vector(ptet-pSB1A2)
 +
{|class="hokkaidou-table-digestion"
 +
  |-
 +
  |DNA solution (about 20 ng/ul)
 +
  |4 ul
 +
  |-
 +
  |SpeI
 +
  |1 ul
 +
  |-
 +
  |PstI
 +
  |1 ul
 +
  |-
 +
  |10xH buffer
 +
  |2 ul
 +
  |-
 +
  |DW
 +
  |12 ul
 +
  |-
 +
  |Total
 +
  |20 ul
 +
  |}
 +
 +
 +
{|class="hokkaidou-table-digestion"
 +
|-
 +
|Number
 +
|Degree
 +
|Minute
 +
|-
 +
|1
 +
|37
 +
|120
 +
|-
 +
|2
 +
|60
 +
|15
 +
|-
 +
|3
 +
|4
 +
|HOLD
 +
|}
 +
 +
 +
{|class="hokkaidou-table-digestion"
 +
|-
 +
|Number
 +
|Degree
 +
|Minute
 +
|-
 +
|1
 +
|37
 +
|120
 +
|-
 +
|2
 +
|70
 +
|20
 +
|-
 +
|3
 +
|4
 +
|HOLD
 +
|}
 +
 +
 +
[[image:|thumb|digestion result]]
 +
 +
</p>
 +
 +
==Ethanol precipitation of RBS-phaB-RBS-eYFP-dT and RBS-phaC-RBS-phaA-pSB1A2==
 +
<p>
 +
#Added 5 ul of NaoAc, 1.5 ul of glycogen and 125 ul of 100% ethanol.
 +
#Centrifuged in 15000 rpm, 15 min at 4C.
 +
#Remove supernatant and added 220 ul of 70% ethanol.
 +
#Centrifuged in 15000 rpm, 10 min at 4C.
 +
#Remove supernatant and air drying in room temperature then added 5 ul of DW.
 +
 +
 +
[[image:|thumb|ethanol precipitation result]]
 +
We confirmed that the concentration of Insert DNA solution is 60~70 ng/ul and Vector DNA solution is about 20~30 ng/ul.
 +
</p>
 +
 +
==Ligation of RBS-phaB-RBS-eYFP-dT and RBS-phaC-RBS-phaA-pSB1A2==
 +
<p>
 +
{|class="hokkaidou-table-ligation"
 +
|-
 +
|Insert DNA (60~70 ng/ul)
 +
|4 ul
 +
|-
 +
|Vector DNA (20~30 ng/ul)
 +
|2 ul
 +
|-
 +
|Ligation Mighty Mix
 +
|6 ul
 +
|-
 +
|Total
 +
|12 ul
 +
|}
 +
 +
 +
Ligation reaction time was in detail below.
 +
 +
{|class="hokkaidou-table-ligation"
 +
|-
 +
|Degree
 +
|Minute
 +
|-
 +
|16
 +
|30
 +
|-
 +
|65
 +
|10
 +
|-
 +
|4
 +
|Hold
 +
|}
 +
 +
</p>
 +
 +
==Transformation of RBS-phaC-RBS-phaA-RBS-phaB-RBS-eYFP-dT-pSB1A2==
 +
<p>
 +
Transformation of JM109.
 +
#Mixed 2 ul RBS-phaC-RBS-phaA-RBS-phaB-RBS-eYFP-dT-pSB1A2 ligation product to 50 ul of thawed competent cells on ice.
 +
#Incubated on ice for 30 min.
 +
#Mixed 350 ul of LB. 
 +
#Prepared and Labeled two plastic plates with LB plate medium which contained appropriate antibiotics (LBA).
 +
#Plated 300 ul of the culture onto first dish and spread.
 +
#Mixed 450 ul of LB to 50 ul of the culture and plated 300 ul of it onto second dish and spread.
 +
#Incubated the plates at 37C for 17 hours.
 +
</p>
 +
</div></div>
 +
 +
==September 18th==
 +
<div>
 +
==Colony PCR of pBAD-RBS-eCFP-RBS-Ag43-dI-pSB1C3==
 +
<p>
 +
 +
We did colony PCR two times.
 +
 +
{|class="hokkaidou-table-pcr-reagent"
 +
|-
 +
|DNA solution
 +
|4 ul
 +
|-
 +
|Kapa-Taq(Taq polymerase)
 +
|10 ul
 +
|-
 +
|Forward Primer(200bp down primer)
 +
|0.8 ul
 +
|-
 +
|Reverse Primer(ag43-f4 primer)
 +
|0.8 ul
 +
|-
 +
|DW
 +
|4.4 ul
 +
|-
 +
|Total
 +
|20 ul
 +
|}
 +
 +
 +
{|class="hokkaidou-table-pcr-time"
 +
|-
 +
|Number
 +
|Degree
 +
|Second
 +
|-
 +
|1
 +
|95
 +
|120
 +
|-
 +
|2
 +
|95
 +
|30
 +
|-
 +
|3
 +
|53.0
 +
|30
 +
|-
 +
|4
 +
|72
 +
|60
 +
|-
 +
|5
 +
|72
 +
|60
 +
|-
 +
|6
 +
|4
 +
|HOLD
 +
|}
 +
Cycle:2~4 x 35
 +
 +
 +
We used N1 (DW only) and N2(pBAD-RBS-Ag43-dT-pSB1A2)as controls.
 +
Desired product is about 702bp.
 +
 +
[[image:|thumb|Colony PCR result]]
 +
 +
 +
Target products didn't exist in all samples. We noticed the reason why such results shown is that we used incorrect pSB1C3 DNA solution which isn't confirmed the sequence. We'll try the synthesis once again in today. 
 +
</p>
 +
 +
==Digestion of pBAD-RBS-eCFP-RBS-Ag43-dT-pSTV28 and pSB1C3==
 +
<p>
 +
To make a construct of pBAD-RBS-eCFP-RBS-Ag43-dT-pSB1C3, we digested pBAD-RBS-eCFP-RBS-Ag43-dT-pSTV28 with EcoRI & SpeI and pSB1C3 with EcoRI & SpeI.
 +
 +
Insert (pBAD-RBS-eCFP-RBS-Ag43-dT-pSTV28)
 +
{|class="hokkaidou-table-digestion"
 +
  |-
 +
  |DNA solution (about 35ng/ul)
 +
  |41 ul
 +
  |-
 +
  |EcoRI
 +
  |2 ul
 +
  |-
 +
  |SpeI
 +
  |2 ul
 +
  |-
 +
  |10xH buffer
 +
  |5 ul
 +
  |-
 +
  |Total
 +
  |50 ul
 +
  |}
 +
 +
 +
Vector(pSB1C3)
 +
{|class="hokkaidou-table-digestion"
 +
  |-
 +
  |DNA solution (about 30~40 ng/ul)
 +
  |2 ul
 +
  |-
 +
  |EcoRI
 +
  |1 ul
 +
  |-
 +
  |SpeI
 +
  |1 ul
 +
  |-
 +
  |10xH buffer
 +
  |2 ul
 +
  |-
 +
  |DW
 +
  |14 ul
 +
  |-
 +
  |Total
 +
  |20 ul
 +
  |}
 +
 +
 +
{|class="hokkaidou-table-digestion"
 +
|-
 +
|Number
 +
|Degree
 +
|Minute
 +
|-
 +
|1
 +
|37
 +
|120
 +
|-
 +
|2
 +
|60
 +
|15
 +
|-
 +
|3
 +
|4
 +
|HOLD
 +
|}
 +
 +
 +
[[image:|thumb|digestion result]]
 +
 +
</p>
 +
==Ethanol precipitation of pBAD-RBS-eCFP-RBS-Ag43-dT--pSB1C3==
 +
<p>
 +
#Added 5 ul of NaoAc, 1.5 ul of glycogen and 125 ul of 100% ethanol.
 +
#Centrifuged in 15000 rpm, 15 min at 4C.
 +
#Remove supernatant and added 220 ul of 70% ethanol.
 +
#Centrifuged in 15000 rpm, 10 min at 4C.
 +
#Remove supernatant and air drying in room temperature then added 5 ul of DW.
 +
 +
 +
[[image:|thumb|ethanol precipitation result]]
 +
 +
</p>
 +
 +
==Ligation of pBAD-RBS-eCFP-RBS-Ag43-dT and pSB1C3==
 +
<p>
 +
{|class="hokkaidou-table-ligation"
 +
|-
 +
|Insert DNA
 +
|4 ul
 +
|-
 +
|Vector DNA
 +
|2 ul
 +
|-
 +
|Ligation Mighty Mix
 +
|6 ul
 +
|-
 +
|Total
 +
|12 ul
 +
|}
 +
 +
 +
Ligation reaction time was in detail below.
 +
 +
{|class="hokkaidou-table-ligation"
 +
|-
 +
|Degree
 +
|Minute
 +
|-
 +
|16
 +
|30
 +
|-
 +
|65
 +
|10
 +
|-
 +
|4
 +
|Hold
 +
|}
 +
 +
</p>
 +
 +
==Transformation of pBAD-RBS-eCFP-RBS-Ag43-dT-pSB1C3==
 +
<p>
 +
Transformation of JM109.
 +
#Mixed 2 ul pBAD-RBS-eCFP-RBS-Ag43-dT--pSB1C3 ligation product to 50 ul of thawed competent cells on ice.
 +
#Incubated on ice for 30 min.
 +
#Mixed 350 ul of LB. 
 +
#Incubated for 2 hrs to get the resistance to Chloramphenicol.
 +
#Prepared and Labeled two plastic plates with LB plate medium which contained appropriate antibiotics (LBC).
 +
#Plated 300 ul of the culture onto first dish and spread.
 +
#Mixed 450 ul of LB to 50 ul of the culture and plated 300 ul of it onto second dish and spread.
 +
#Incubated the plates at 37C for 15 hours.
 +
</p>
 +
 +
==Colony PCR of pBAD-RBS-eCFP-RBS-Ag43-dI-pSB1C3==
 +
<p>
 +
 +
We did colony PCR two times.
 +
 +
{|class="hokkaidou-table-pcr-reagent"
 +
|-
 +
|DNA solution
 +
|4 ul
 +
|-
 +
|Kapa-Taq(Taq polymerase)
 +
|10 ul
 +
|-
 +
|Forward Primer(200bp down primer)
 +
|0.8 ul
 +
|-
 +
|Reverse Primer(ag43-f4 primer)
 +
|0.8 ul
 +
|-
 +
|DW
 +
|4.4 ul
 +
|-
 +
|Total
 +
|20 ul
 +
|}
 +
 +
 +
{|class="hokkaidou-table-pcr-time"
 +
|-
 +
|Number
 +
|Degree
 +
|Second
 +
|-
 +
|1
 +
|95
 +
|120
 +
|-
 +
|2
 +
|95
 +
|30
 +
|-
 +
|3
 +
|53.0
 +
|30
 +
|-
 +
|4
 +
|72
 +
|60
 +
|-
 +
|5
 +
|72
 +
|60
 +
|-
 +
|6
 +
|4
 +
|HOLD
 +
|}
 +
Cycle:2~4 x 35
 +
 +
 +
We used N1 (DW only) and N2(pBAD-RBS-Ag43-dT-pSB1A2)as controls.
 +
Desired product is about 702bp.
 +
 +
[[image:|thumb|Colony PCR result]]
 +
 +
There are some desired products exist in plated colonies. We selected No.5,6 for Incubation for mini-prep and No.10,11 for stock at 4C.
 +
</p>
 +
 +
</div></div>
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{{Team:HokkaidoU_Japan/footer}}
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Revision as of 03:10, 22 September 2012

Contents

September 17th

Digestion of RBS-phaC-RBs-phaA-RBS-phaB-RBS-eYFP-dT-pSB1A2 and ptet-pSB1A2

To make a construct of ptet-RBS-phaC-RBS-phaA-RBS-phaB-RBS-dT-pSB1A2, we digested RBS-phaC-RBs-phaA-RBS-phaB-RBS-eYFP-dT-pSB1A2 with XbaI & PstI, ptet-pSB1A2 with SpeI & PstI. Insert (RBS-phaC-RBs-phaA-RBS-phaB-RBS-eYFP-dT-pSB1A2)

DNA solution ( 45=50ng/ul) 27 ul
XbaI 1 ul
PstI 1 ul
10xM buffer 4 ul
DW 7 ul
Total 40 ul


Vector(ptet-pSB1A2)

DNA solution (about 20 ng/ul) 4 ul
SpeI 1 ul
PstI 1 ul
10xH buffer 2 ul
DW 12 ul
Total 20 ul


Number Degree Minute
1 37 120
2 60 15
3 4 HOLD


Number Degree Minute
1 37 120
2 70 20
3 4 HOLD


[[image:|thumb|digestion result]]

Ethanol precipitation of RBS-phaB-RBS-eYFP-dT and RBS-phaC-RBS-phaA-pSB1A2

  1. Added 5 ul of NaoAc, 1.5 ul of glycogen and 125 ul of 100% ethanol.
  2. Centrifuged in 15000 rpm, 15 min at 4C.
  3. Remove supernatant and added 220 ul of 70% ethanol.
  4. Centrifuged in 15000 rpm, 10 min at 4C.
  5. Remove supernatant and air drying in room temperature then added 5 ul of DW.
[[image:|thumb|ethanol precipitation result]] We confirmed that the concentration of Insert DNA solution is 60~70 ng/ul and Vector DNA solution is about 20~30 ng/ul.

Ligation of RBS-phaB-RBS-eYFP-dT and RBS-phaC-RBS-phaA-pSB1A2

Insert DNA (60~70 ng/ul) 4 ul
Vector DNA (20~30 ng/ul) 2 ul
Ligation Mighty Mix 6 ul
Total 12 ul


Ligation reaction time was in detail below.

Degree Minute
16 30
65 10
4 Hold

Transformation of RBS-phaC-RBS-phaA-RBS-phaB-RBS-eYFP-dT-pSB1A2

Transformation of JM109.

  1. Mixed 2 ul RBS-phaC-RBS-phaA-RBS-phaB-RBS-eYFP-dT-pSB1A2 ligation product to 50 ul of thawed competent cells on ice.
  2. Incubated on ice for 30 min.
  3. Mixed 350 ul of LB.
  4. Prepared and Labeled two plastic plates with LB plate medium which contained appropriate antibiotics (LBA).
  5. Plated 300 ul of the culture onto first dish and spread.
  6. Mixed 450 ul of LB to 50 ul of the culture and plated 300 ul of it onto second dish and spread.
  7. Incubated the plates at 37C for 17 hours.

September 18th

Colony PCR of pBAD-RBS-eCFP-RBS-Ag43-dI-pSB1C3

We did colony PCR two times.

DNA solution 4 ul
Kapa-Taq(Taq polymerase) 10 ul
Forward Primer(200bp down primer) 0.8 ul
Reverse Primer(ag43-f4 primer) 0.8 ul
DW 4.4 ul
Total 20 ul


Number Degree Second
1 95 120
2 95 30
3 53.0 30
4 72 60
5 72 60
6 4 HOLD

Cycle:2~4 x 35


We used N1 (DW only) and N2(pBAD-RBS-Ag43-dT-pSB1A2)as controls. Desired product is about 702bp.

[[image:|thumb|Colony PCR result]]


Target products didn't exist in all samples. We noticed the reason why such results shown is that we used incorrect pSB1C3 DNA solution which isn't confirmed the sequence. We'll try the synthesis once again in today.

Digestion of pBAD-RBS-eCFP-RBS-Ag43-dT-pSTV28 and pSB1C3

To make a construct of pBAD-RBS-eCFP-RBS-Ag43-dT-pSB1C3, we digested pBAD-RBS-eCFP-RBS-Ag43-dT-pSTV28 with EcoRI & SpeI and pSB1C3 with EcoRI & SpeI. Insert (pBAD-RBS-eCFP-RBS-Ag43-dT-pSTV28)

DNA solution (about 35ng/ul) 41 ul
EcoRI 2 ul
SpeI 2 ul
10xH buffer 5 ul
Total 50 ul


Vector(pSB1C3)

DNA solution (about 30~40 ng/ul) 2 ul
EcoRI 1 ul
SpeI 1 ul
10xH buffer 2 ul
DW 14 ul
Total 20 ul


Number Degree Minute
1 37 120
2 60 15
3 4 HOLD


[[image:|thumb|digestion result]]

Ethanol precipitation of pBAD-RBS-eCFP-RBS-Ag43-dT--pSB1C3

  1. Added 5 ul of NaoAc, 1.5 ul of glycogen and 125 ul of 100% ethanol.
  2. Centrifuged in 15000 rpm, 15 min at 4C.
  3. Remove supernatant and added 220 ul of 70% ethanol.
  4. Centrifuged in 15000 rpm, 10 min at 4C.
  5. Remove supernatant and air drying in room temperature then added 5 ul of DW.
[[image:|thumb|ethanol precipitation result]]

Ligation of pBAD-RBS-eCFP-RBS-Ag43-dT and pSB1C3

Insert DNA 4 ul
Vector DNA 2 ul
Ligation Mighty Mix 6 ul
Total 12 ul


Ligation reaction time was in detail below.

Degree Minute
16 30
65 10
4 Hold

Transformation of pBAD-RBS-eCFP-RBS-Ag43-dT-pSB1C3

Transformation of JM109.

  1. Mixed 2 ul pBAD-RBS-eCFP-RBS-Ag43-dT--pSB1C3 ligation product to 50 ul of thawed competent cells on ice.
  2. Incubated on ice for 30 min.
  3. Mixed 350 ul of LB.
  4. Incubated for 2 hrs to get the resistance to Chloramphenicol.
  5. Prepared and Labeled two plastic plates with LB plate medium which contained appropriate antibiotics (LBC).
  6. Plated 300 ul of the culture onto first dish and spread.
  7. Mixed 450 ul of LB to 50 ul of the culture and plated 300 ul of it onto second dish and spread.
  8. Incubated the plates at 37C for 15 hours.

Colony PCR of pBAD-RBS-eCFP-RBS-Ag43-dI-pSB1C3

We did colony PCR two times.

DNA solution 4 ul
Kapa-Taq(Taq polymerase) 10 ul
Forward Primer(200bp down primer) 0.8 ul
Reverse Primer(ag43-f4 primer) 0.8 ul
DW 4.4 ul
Total 20 ul


Number Degree Second
1 95 120
2 95 30
3 53.0 30
4 72 60
5 72 60
6 4 HOLD

Cycle:2~4 x 35


We used N1 (DW only) and N2(pBAD-RBS-Ag43-dT-pSB1A2)as controls. Desired product is about 702bp.

[[image:|thumb|Colony PCR result]]

There are some desired products exist in plated colonies. We selected No.5,6 for Incubation for mini-prep and No.10,11 for stock at 4C.


</div>

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