Difference between revisions of "Team:Paris Saclay/Notebook/September/20"

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{{Team:Paris_Saclay/notebook_header}}
 
{{Team:Paris_Saclay/notebook_header}}
  
−
= Tuesday 20<sup>th</sup> September=
+
=Tuesday 20<sup>th</sup> September=
−
==Lab work==
+
 
 
===Visualization===
 
===Visualization===
  
Line 13: Line 13:
 
"By Maxence, Mahnaz & Coline"
 
"By Maxence, Mahnaz & Coline"
  
−
{| class="wikitable"
+
{| class="wikitable" style="margin: 5em;"
 
!Sample
 
!Sample
 
!Concentration (ng/µL)
 
!Concentration (ng/µL)
 
|-
 
|-
 
|FKBP - GFP 10 clone 7<div id="FKBP - GFP 10 clone 7"></div>
 
|FKBP - GFP 10 clone 7<div id="FKBP - GFP 10 clone 7"></div>
−
|X
+
|443.15
 
|-
 
|-
 
|FKBP - GFP 10 clone 8<div id="FKBP - GFP 10 clone 8"></div>
 
|FKBP - GFP 10 clone 8<div id="FKBP - GFP 10 clone 8"></div>
−
|X
+
|260.26
 
|-
 
|-
 
|FKBP - GFP 10 clone 9<div id="FKBP - GFP 10 clone 9"></div>
 
|FKBP - GFP 10 clone 9<div id="FKBP - GFP 10 clone 9"></div>
−
|X
+
|151.91
 
|-
 
|-
 
|FKBP - GFP 10 clone 10<div id="FKBP - GFP 10 clone 10"></div>
 
|FKBP - GFP 10 clone 10<div id="FKBP - GFP 10 clone 10"></div>
−
|X
+
|230.11
 
|-
 
|-
 
|PCR product 1 obtained by iPS174 & iPS175<div id="PCR product 1 obtained by iPS174 & iPS175"></div>
 
|PCR product 1 obtained by iPS174 & iPS175<div id="PCR product 1 obtained by iPS174 & iPS175"></div>
Line 89: Line 89:
 
|}
 
|}
  
−
[[Team:Paris_Saclay/Experiments#primers|Primers]] used were:
+
[[Team:Paris_Saclay/Experiments#primers|Primers]] used were:
  
 
{| class="wikitable"
 
{| class="wikitable"
Line 111: Line 111:
 
|-
 
|-
 
|GFP 1.9 in pSB1C3
 
|GFP 1.9 in pSB1C3
−
|862
+
|1135
 
|}
 
|}
  
−
GEL
+
No PCR products were obtained, plasmids were probably empty.
  
 
====Gibson of cleaned up PCR products from pSB1C3 with dCas9 ST - GFP 11 (pPS16_017) clone 8 treated by DpnI====
 
====Gibson of cleaned up PCR products from pSB1C3 with dCas9 ST - GFP 11 (pPS16_017) clone 8 treated by DpnI====
Line 137: Line 137:
 
''By Maxence, Mahnaz & Coline''
 
''By Maxence, Mahnaz & Coline''
  
−
As difficulties were faced in order to obtain GFP 1.9 in pSB1C3 with Gibson strategy, we decided to construct first pPS16_021 (FRB - GFP 10 - FKBP - GFP 11 in pSB1C3) and then clone GFP 1.9 from pUC19 in it to construct pPS16_022 (FRB - GFP 10 - FKBP - GFP 11 - GFP 1.9 in pSB1C3). For that purpose, pPS16_019 was cut by restriction enzymes EcoRI & SpeI. Before, 1/10 of the extracted plasmid was put on gel in order to assess the quantitiy of DNA left.  
+
As difficulties were faced in order to obtain GFP 1.9 in pSB1C3 with Gibson strategy, we decided to construct first pPS16_022 (FRB - GFP 11 - GFP 1.9 in pSB1C3) and then clone FKBP - GFP 10 in pSB1C3 (pPS16_018) in it to construct pPS16_023 (FRB - GFP 11 - FKBP - GFP 10 - GFP 1.9 in pSB1C3).  
  
−
GEL
+
For that purpose, GFP 1.9 PCR product from the 9th September was cut by restriction enzymes EcoRI & SpeI as following:
  
−
DNA quantity was enough to run digestion as following:
+
* 4 µL of GFP 1.9 PCR product from the 9th September
 +
* 2 µL of buffer FD
 +
* 2 µL of restriction enzyme EcoRI
 +
* 2 µL of restriction enzyme SpeI
 +
* 10 µL of water
 +
 
 +
And GFP 1.9 PCR product from the 8th September was cut by restriction enzymes EcoRI & SpeI as following:
  
−
* 10 µL of pPS16_019
+
* 10 µL of GFP 1.9 PCR product from the 8th September
−
* 2 µL of buffer
+
* 2 µL of buffer FD
 
* 2 µL of restriction enzyme EcoRI
 
* 2 µL of restriction enzyme EcoRI
 
* 2 µL of restriction enzyme SpeI
 
* 2 µL of restriction enzyme SpeI
 
* 4 µL of water
 
* 4 µL of water
  
−
Furthermore, pPS16_018 was cut by restriction enzymes EcoRI & XbaI as following:
+
Furthermore, pPS16_019 was cut by restriction enzymes EcoRI & XbaI as following:
  
−
* 10 µL of pPS16_18
+
* 14 µL of pPS16_19 clone 4
−
* 2 µL of buffer
+
* 2 µL of buffer FD
−
* 1 µL of restriction enzyme EcoRI
+
* 2 µL of restriction enzyme EcoRI
 
* 2 µL of restriction enzyme XbaI
 
* 2 µL of restriction enzyme XbaI
−
* 4 µL of water
 
  
−
The mix were incubated for 1 hour at 37°C. Then restriction enzymes were inactivated by incubating the mix 20 minutes at 65°C. The digested products were cleaned up by using the NucleoSpin Gel and PCR Clean-up kit [[Team:Paris_Saclay/Experiments#Purification|protocol]]. After clean-up, 3 µL of each cleaned up PCR products and 5 µL of DNA ladder were placed in wells and migrated at 100V during 30 min.
+
The mix were incubated for 1 hour at 37°C. Then, 20 µL of each digestion products and 5 µL of DNA ladder were placed in wells and migrated at 100V during 30 min.
  
−
PCR products expected were :
+
Migration products expected were :
  
 
{| class="wikitable"
 
{| class="wikitable"
 
|-
 
|-
−
!PCR products
+
!Migration products
 
!Expected band size (bp)
 
!Expected band size (bp)
 
|-
 
|-
−
|Template digested (pPS16_019 treated by EcoRI & SpeI)
+
|Template digested (GFP 1.9 PCR product treated by EcoRI & SpeI)
−
|X
+
|900
 
|-
 
|-
−
|Vector digested (pPS16_018 treated by EcoRI & XbaI)
+
|Vector digested (pPS16_019 treated by EcoRI & XbaI)
−
|X
+
|2900
 
|-
 
|-
 
|}
 
|}
  
−
GEL
+
[[File:T--Paris Saclay--Gel1121.png|400px|thumb|center|Result of the migration]]
  
−
Once template and vector were cut, DNA ligase was used to join the sticky ends of the template and vector together. For that purpose, two protocols were used:  
+
The digestion products were cleaned up from the gel by using the NucleoSpin Gel and PCR Clean-up kit [[Team:Paris_Saclay/Experiments#Purification|protocol]]. Their concentrations were assessed by NanoDrop:
  
−
* 7 µL of template (pPS16_019 treated by EcoRI & SpeI)
+
{| class="wikitable"
−
* 1 µL of vector (pPS16_018 treated by EcoRI & XbaI)
+
!Sample
−
* 1 µL of Buffer T4 10X
+
!Concentration (ng/µL)
 +
|-
 +
|GFP 1.9 digested from the 8th<div id="GFP 1.9 digested from the 8th"></div>
 +
|23
 +
|-
 +
|GFP 1.9 digested from the 9th (DMSO)<div id="GFP 1.9 digested from the 9th (DMSO)"></div>
 +
|103.5
 +
|-
 +
|FRB - GFP 11 digested<div id="FRB - GFP 11 digested"></div>
 +
|18.67
 +
|-
 +
|}
 +
 
 +
Once template and vector were cut, DNA ligase was used to join the sticky ends of the template and vector together. Two protocols were used as template concentration was not the same between the two GFP 1.9:
 +
 
 +
* 5 µL of template (pPS16_009 treated by EcoRI & SpeI) from the 8th
 +
* 7 µL of vector (pPS16_019 treated by EcoRI & XbaI)
 +
* 2 µL of Buffer T4 10X
 
* 1 µL of ligase T4 enzyme
 
* 1 µL of ligase T4 enzyme
  
−
And:  
+
And:
  
−
* 1 µL of template (pPS16_019 treated by EcoRI & SpeI)
+
* 1 µL of template (pPS16_009 treated by EcoRI & SpeI) from the 9th (DMSO)
−
* 1 µL of vector (pPS16_018 treated by EcoRI & XbaI)
+
* 7 µL of vector (pPS16_019 treated by EcoRI & XbaI)
−
* 1 µL of Buffer T4 10X
+
* 2 µL of Buffer T4 10X
 
* 1 µL of ligase T4 enzyme
 
* 1 µL of ligase T4 enzyme
−
* 6 µL of water
 
  
 
The mix were incubated for 1 hour at rooming temperature.
 
The mix were incubated for 1 hour at rooming temperature.
  
−
Two controls were done for further transformation application: one open plasmid and one ligated plasmid (without template).
+
====Transformation of DH5a cells with FRB - GFP 11 - GFP 1.9 in pSB1C3 (pPS16_022) obtained by Digestion-Ligation====
−
 
+
−
====Clean-up of FRB - GFP 11 - FKBP - GFP 10 in pSB1C3 (pPS16_021) obtained by Digestion-Ligation ====
+
 
''By Maxence, Mahnaz & Coline''
 
''By Maxence, Mahnaz & Coline''
  
−
GFP 1.9 in pSB1C3 (pPS16_020) obtained by Digestion-Ligation was cleaned up by using the NucleoSpin Gel and PCR Clean-up kit [[Team:Paris_Saclay/Experiments#Purification|protocol]].
+
Dh5a cells were transformed with pSB1C3 containing FRB - GFP 11 - GFP 1.9 (pPS16_022), or controls (digested plasmid and water) using the usual [[Team:Paris_Saclay/Experiments#heat-shocktransformation|protocol]].
−
 
+
−
====Transformation of DH5a cells with FRB - GFP 11 - FKBP - GFP 10 in pSB1C3 (pPS16_021) obtained by Digestion-Ligation====
+
−
''By Maxence, Mahnaz & Coline''
+
−
 
+
−
Dh5a cells were transformed with pSB1C3 containing FRB - GFP 11 - FKBP - GFP 10 in pSB1C3 (pPS16_021), or controls (open plasmid and ligated plasmid) using the usual [[Team:Paris_Saclay/Experiments#heat-shocktransformation|protocol]].
+
−
 
+
  
 
{{Team:Paris_Saclay/notebook_footer}}
 
{{Team:Paris_Saclay/notebook_footer}}

Latest revision as of 14:35, 18 October 2016

Tuesday 20th September

Visualization

Samples preparation for sequencing

"By Maxence, Mahnaz & Coline"

20 µL of plasmids pSB1C3 FKBP - GFP 10 (clones 7, 8, 9 and 10) were sent to be sequenced. 20 µL of the primers iPS84 (5µM) and iPS140 (5µM) were sent for sequencing.

NanoDrop Measurements

"By Maxence, Mahnaz & Coline"

Sample Concentration (ng/µL)
FKBP - GFP 10 clone 7
 443.15
FKBP - GFP 10 clone 8
 260.26
FKBP - GFP 10 clone 9
 151.91
FKBP - GFP 10 clone 10
 230.11
PCR product 1 obtained by iPS174 & iPS175
 108.17
PCR product 2 obtained by iPS173 & iPS176
 136.91
GFP 1.9 PCR product from 9th September (with DMSO)
 420
GFP 1.9 PCR product from 8th September
 133
FRB - GFP 11 - pSBI1C3 (pPS16_019) clone 4
 98

Colony PCR of the 4 clones containing GFP 1.9 in pSB1C3 (pPS16_020) from the 12th September

By Maxence, Mahnaz & Coline

As results from sequencing were not good, clones sent previously and stocked in glycerol (2, 7, 8 and 12) were put on plate the 19th September, as each colony may not not be homogenous enough. Another colony PCR was done and anothers primers were used.

For that purpose, the 4 clones were 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 1135

No PCR products were obtained, plasmids were probably empty.

Gibson of cleaned up PCR products from pSB1C3 with dCas9 ST - GFP 11 (pPS16_017) clone 8 treated by DpnI

By Maxence, Mahnaz & Coline

Gibson was performed with cleaned up PCR products from pSB1C3 with dCas9 ST - GFP 11 (pPS16_017) clone 8 treated by DpnI, more precisely PCR product 1 obtained by iPS174 & iPS175 (plasmid) and PCR product 2 obtained by iPS173 & iPS176 (insert) with the following protocol:

For each 20μl of reaction, mix the following reagents :

  • 0.63 µL of insert
  • 1.2 µL of plasmid
  • 8.17 µL of water
  • 10 µL of buffer mix

Two controls were done: one without insert and one without buffer (water was added in order to have a total of 20 µL). The PCR was performed as follow : 1 hour at 50°C.

Transformation of DH5a cells with correct dCas9 ST - GFP 11 in pSB1C3 (pPS16_017) obtained by Gibson

By Maxence, Mahnaz & Coline

Dh5a cells were transformed with corrected pSB1C3 containing dCas9 ST - GFP 11 (pPS16_017), or controls (no buffer mix and plasmid alone) using the usual protocol.

Cloning of GFP 1.9 from pUC19 (pPS16_009) in FRB - GFP 11 - pSB1C3 (pPS16_019) by digestion-ligation

By Maxence, Mahnaz & Coline

As difficulties were faced in order to obtain GFP 1.9 in pSB1C3 with Gibson strategy, we decided to construct first pPS16_022 (FRB - GFP 11 - GFP 1.9 in pSB1C3) and then clone FKBP - GFP 10 in pSB1C3 (pPS16_018) in it to construct pPS16_023 (FRB - GFP 11 - FKBP - GFP 10 - GFP 1.9 in pSB1C3).

For that purpose, GFP 1.9 PCR product from the 9th September was cut by restriction enzymes EcoRI & SpeI as following:

  • 4 µL of GFP 1.9 PCR product from the 9th September
  • 2 µL of buffer FD
  • 2 µL of restriction enzyme EcoRI
  • 2 µL of restriction enzyme SpeI
  • 10 µL of water

And GFP 1.9 PCR product from the 8th September was cut by restriction enzymes EcoRI & SpeI as following:

  • 10 µL of GFP 1.9 PCR product from the 8th September
  • 2 µL of buffer FD
  • 2 µL of restriction enzyme EcoRI
  • 2 µL of restriction enzyme SpeI
  • 4 µL of water

Furthermore, pPS16_019 was cut by restriction enzymes EcoRI & XbaI as following:

  • 14 µL of pPS16_19 clone 4
  • 2 µL of buffer FD
  • 2 µL of restriction enzyme EcoRI
  • 2 µL of restriction enzyme XbaI

The mix were incubated for 1 hour at 37°C. Then, 20 µL of each digestion products and 5 µL of DNA ladder were placed in wells and migrated at 100V during 30 min.

Migration products expected were :

Migration products Expected band size (bp)
Template digested (GFP 1.9 PCR product treated by EcoRI & SpeI) 900
Vector digested (pPS16_019 treated by EcoRI & XbaI) 2900
Result of the migration

The digestion products were cleaned up from the gel by using the NucleoSpin Gel and PCR Clean-up kit protocol. Their concentrations were assessed by NanoDrop:

Sample Concentration (ng/µL)
GFP 1.9 digested from the 8th
 23
GFP 1.9 digested from the 9th (DMSO)
 103.5
FRB - GFP 11 digested
 18.67

Once template and vector were cut, DNA ligase was used to join the sticky ends of the template and vector together. Two protocols were used as template concentration was not the same between the two GFP 1.9:

  • 5 µL of template (pPS16_009 treated by EcoRI & SpeI) from the 8th
  • 7 µL of vector (pPS16_019 treated by EcoRI & XbaI)
  • 2 µL of Buffer T4 10X
  • 1 µL of ligase T4 enzyme

And:

  • 1 µL of template (pPS16_009 treated by EcoRI & SpeI) from the 9th (DMSO)
  • 7 µL of vector (pPS16_019 treated by EcoRI & XbaI)
  • 2 µL of Buffer T4 10X
  • 1 µL of ligase T4 enzyme

The mix were incubated for 1 hour at rooming temperature.

Transformation of DH5a cells with FRB - GFP 11 - GFP 1.9 in pSB1C3 (pPS16_022) obtained by Digestion-Ligation

By Maxence, Mahnaz & Coline

Dh5a cells were transformed with pSB1C3 containing FRB - GFP 11 - GFP 1.9 (pPS16_022), or controls (digested plasmid and water) using the usual protocol.





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