Difference between revisions of "Team:Paris Saclay/Notebook/September/19"

(→‎Monday 19th September)
(→‎Colony PCR of X clones containing GFP 1.9 in pSB1C3 (pPS16_020))
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*pPS16_018 (FKBP - GFP 10) clone 10
 
*pPS16_018 (FKBP - GFP 10) clone 10
  
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====Colony PCR of X clones containing GFP 1.9 in pSB1C3 (pPS16_020)====
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====Colony PCR of 8 clones containing GFP 1.9 in pSB1C3 (pPS16_020)====
 
''By Maxence, Mahnaz, Coline & Caroline''
 
''By Maxence, Mahnaz, Coline & Caroline''
  
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Seqencing of clones 2, 7, 8 and 12 from the 14th September was not good as empty plasmids were obtained. Another colony PCR was done for 16 clones from the 12th 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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Seqencing of clones 2, 7, 8 and 12 from the 14th September was not good as empty plasmids were obtained. Another colony PCR was done for 8 clones from the 12th September but anothers primers were used. For that purpose, 8 clones 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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|30 sec
 
|30 sec
 
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|72°C
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|48.4°C
 
|30 sec
 
|30 sec
 
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|Primers
 
|Primers
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|iPS84 and iPS140
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|iPS168 and iPS169
 
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|}
 
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GEL good
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GEL
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All PCR products were at the good size. Clones 2, 7, 8 and 12 were selected and were grown at 37°C overnight.
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====PCR of pSB1C3 with dCas9 ST - GFP 11 (pPS16_017) clone 8 to correct mutations ====
 
====PCR of pSB1C3 with dCas9 ST - GFP 11 (pPS16_017) clone 8 to correct mutations ====

Revision as of 14:08, 19 September 2016

Monday 19th September

Lab work

Visualization

Glycerol stocks of clones 7, 8, 9 and 10 containing FKBP - GFP 10 in pSB1C3 (pPS16_018)

"By Maxence, Mahnaz, Coline & Caroline"

The glycerol stock of the bacteria with the following plasmids were made.

  • pPS16_018 (FKBP - GFP 10) clone 7
  • pPS16_018 (FKBP - GFP 10) clone 8
  • pPS16_018 (FKBP - GFP 10) clone 9
  • pPS16_018 (FKBP - GFP 10) clone 10

500µL of liquid culture and 250 µL of glycerol 60% were mixed and put at -20°C.

Plasmids extraction of clones 7, 8, 9 and 10 containing GFP 1.9 in pSB1C3 (pPS16_018)

"By Maxence, Mahnaz Coline & Caroline"

The following plasmids were extracted using the "Charge Switch-Pro Plasmid Miniprep" kit:

  • pPS16_018 (FKBP - GFP 10) clone 7
  • pPS16_018 (FKBP - GFP 10) clone 8
  • pPS16_018 (FKBP - GFP 10) clone 9
  • pPS16_018 (FKBP - GFP 10) clone 10

Colony PCR of 8 clones containing GFP 1.9 in pSB1C3 (pPS16_020)

By Maxence, Mahnaz, Coline & Caroline

Seqencing of clones 2, 7, 8 and 12 from the 14th September was not good as empty plasmids were obtained. Another colony PCR was done for 8 clones from the 12th September but anothers primers were used. For that purpose, 8 clones 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
48.4°C 30 sec
72°C 30sec
Final Extension 72°C 7 min
Hold 4°C $\infty$ 
Primers used were:
Matrix Clones containing GFP 1.9 in pSB1C3 (pPS16_020)
Primers iPS168 and iPS169

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)
GFP 1.9 in pSB1C3 862

GEL

PCR of pSB1C3 with dCas9 ST - GFP 11 (pPS16_017) clone 8 to correct mutations

By Maxence, Mahnaz, Coline & Caroline

In order to correct mutations in dCas9 ST - GFP 11, PCR was performed with the following protocol.

For each 50μl of reaction, mix the following reagents :

  • 1 µL of matrix
  • 1 µL of dNTPs (10mM)
  • 2.5 µL of each primer mix (10µM)
  • 10 µL of buffer HF (5X)
  • 0,5 µL of Phusion polymerase
  • 32.5 µL of nuclease free water

Mix gently and aliquot 50 μl of the mix into the PCR tubes on ice. Perform PCR as follow:

Step Temperature Time
Initial denaturation 98°C 30sec
30 cycles 98°C 10sec
72°C 30sec
72°C t
Final Extension 72°C 5min
Hold 4°C $\infty$ 
Primers used were:
Matrix dCas9 ST - GFP 11 (pPS16_017) clone 8 dCas9 ST - GFP 11 (pPS16_017) clone 8
Primers iPS174 and iPS175 iPS173 and iPS176
Tm 72°C 72°C
t 3min 50sec

Gel of PCR products from pSB1C3 with dCas9 ST - GFP 11 (pPS16_017) clone 8

By Maxence, Mahnaz, Coline & Caroline

4 µL of each PCR products and 4 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)
Product 1 obtained by iPS174 & iPS175 5837
Product 2 obtained by iPS173 & iPS176 1599

GEL







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