Difference between revisions of "Team:Paris Saclay/Notebook/September/16"

(→‎Colony PCR of 16 clones containing FRB - GFP 11 in pSB1C3)
(→‎Lab work)
 
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{{Team:Paris_Saclay/notebook_header}}
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= Friday 16<sup>th</sup> September=
 
= Friday 16<sup>th</sup> September=
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==Lab work==
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===Visualization===
 
===Visualization===
  
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====Colony PCR of 16 clones containing FRB - GFP 11 in pSB1C3====
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====Colony PCR of 16 clones containing FKBP - GFP 10 in pSB1C3 (pPS16_019)====
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''By Maxence & Mahnaz''
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''By Mahnaz''
  
 
Colonies were obtained for the Gibson done the 15th September. A colony PCR was done for 16 clones from the 15th September. For that purpose, 16 were screened and used for the usual [[Team:Paris_Saclay/Experiments##Polymerase_chain_reaction|protocol]] of Colony PCR. The same colonies were also plated on Petri dish containing solid LB + 30 µg/mL Cm and liquid cultures (LB + 30 µg/mL Cm) were made from these clones. Both petri dishes and liquid cultures were grown at 37°C.
 
Colonies were obtained for the Gibson done the 15th September. A colony PCR was done for 16 clones from the 15th September. For that purpose, 16 were screened and used for the usual [[Team:Paris_Saclay/Experiments##Polymerase_chain_reaction|protocol]] of Colony PCR. The same colonies were also plated on Petri dish containing solid LB + 30 µg/mL Cm and liquid cultures (LB + 30 µg/mL Cm) were made from these clones. Both petri dishes and liquid cultures were grown at 37°C.
  
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For each clones contained in 20 μl water, 4.13 μL of the following mix were added :
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For each clones contained in 20 μl water, 5.13 μL of the following mix were added :
 
* 2.5 µL DreamTaq Buffer
 
* 2.5 µL DreamTaq Buffer
 
* 0.5 µL of dNTPs (10mM)
 
* 0.5 µL of dNTPs (10mM)
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|-
 
|-
 
|72°C
 
|72°C
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|1 min 30 sec
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|30 sec
 
|-
 
|-
 
|Final Extension
 
|Final Extension
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|}
 
|}
  
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[[Team:Paris_Saclay/Experiments#primers|Primers]] used were:
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[[Team:Paris_Saclay/Experiments#primers|Primers]] used were:
  
 
{| class="wikitable"
 
{| class="wikitable"
 
|-
 
|-
 
!Matrix
 
!Matrix
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!Clones containing FKBP - GFP 10 in pSB1C3
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!Clones containing FKBP - GFP 10 in pSB1C3 (pPS16_19)
 
|-
 
|-
 
|Primers
 
|Primers
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!Expected band size (bp)
 
!Expected band size (bp)
 
|-
 
|-
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|FKBP - GFP 10 in pSB1C3
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|FKBP - GFP 10 in pSB1C3 (pPS16_019)
 
|757
 
|757
 
|}
 
|}
  
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GEL
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[[File:T--Paris Saclay--Gel1118.png|400px|thumb|center|Result of the migration]]
  
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====PCR of pSB1C3 from dCas9 ST - GFP 11 clone 8 to correct mutations ====
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Some PCR products were at the good size. Clones 7, 8, 9 and 10 were selected and were grown at 37°C overnight.
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''By Maxence''
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In order to correct mutations in dCas9 ST - GFP 11, PCR was performed with the following protocol.
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{{Team:Paris_Saclay/notebook_footer}}
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For each 50μl of reaction, mix the following reagents :
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* 1 µL of matrix
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* 1 µL of dNTPs (10mM)
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* 2.5 µL of each primer mix (10µM)
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* 10 µL of buffer HF (5X)
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* 0,5 µL of Phusion polymerase
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* 32.5 µL of nuclease free water
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Mix gently and aliquot 50 μl of the mix into the PCR tubes on ice.
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Perform PCR as follow:
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{| class="wikitable"
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|-
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!Step
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!Temperature
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!Time
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|-
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|Initial denaturation
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|98°C
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|30sec
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|-
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|rowspan="3"|30 cycles
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|98°C
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|10sec
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|-
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|72°C
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|30sec
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|-
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|72°C
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|t
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−
|-
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|Final Extension
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|72°C
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|5min
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|-
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|Hold
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|4°C
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|$\infty$
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−
|}
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−
 
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[[Team:Paris_Saclay/Experiments#primers|Primers]] used were:
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−
 
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{| class="wikitable"
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−
|-
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!Matrix
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!dCas9 ST - GFP 11 clone 8
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!dCas9 ST - GFP 11 clone 8
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|-
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|Primers
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|iPS174 and iPS175
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|iPS173 and iPS176
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|-
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|Tm
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|72°C
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|72°C
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|-
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|t
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|3min
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|50sec
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|-
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−
|}
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Latest revision as of 17:06, 9 October 2016

Friday 16th September

Visualization

Colony PCR of 16 clones containing FKBP - GFP 10 in pSB1C3 (pPS16_019)

By Mahnaz

Colonies were obtained for the Gibson done the 15th September. A colony PCR was done for 16 clones from the 15th September. For that purpose, 16 were screened and used for the usual protocol of Colony PCR. The same colonies were also plated on Petri dish containing solid LB + 30 µg/mL Cm and liquid cultures (LB + 30 µg/mL Cm) were made from these clones. Both petri dishes and liquid cultures were grown at 37°C.

For each clones contained in 20 μl water, 5.13 μL of the following mix were added :

  • 2.5 µL DreamTaq Buffer
  • 0.5 µL of dNTPs (10mM)
  • 1 µL of each primer mix (10µM)
  • 0.13 μl of DreamTaq Pol

PCR was performed as follow:

Step Temperature Time
Initial denaturation 95°C 3 min
30 cycles 95°C 30 sec
61°C 30 sec
72°C 30 sec
Final Extension 72°C 7 min
Hold 4°C $\infinity\$

Primers used were:

Matrix Clones containing FKBP - GFP 10 in pSB1C3 (pPS16_19)
Primers iPS83 and iPS84

After amplification, 3 µL of each PCR products and 5 µL of DNA ladder were placed in wells and migrated at 100V during 30 min.

PCR products expected were :

PCR products Expected band size (bp)
FKBP - GFP 10 in pSB1C3 (pPS16_019) 757
Result of the migration

Some PCR products were at the good size. Clones 7, 8, 9 and 10 were selected and were grown at 37°C overnight.





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