Difference between revisions of "Team:Paris Saclay/Notebook/September/12"
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==== Glycerol stocks of clones 4, 9, 13 and 16 containing FRB - GFP11 in pSB1C3 ==== | ==== Glycerol stocks of clones 4, 9, 13 and 16 containing FRB - GFP11 in pSB1C3 ==== | ||
| − | "By Maxence" | + | "By Maxence & Mahnaz" |
The glycerol stock of the bacteria with the following plasmids were made. | The glycerol stock of the bacteria with the following plasmids were made. | ||
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====Plasmids extraction of clones 4, 9, 13 and 16 containing FRB - GFP11 in pSB1C3==== | ====Plasmids extraction of clones 4, 9, 13 and 16 containing FRB - GFP11 in pSB1C3==== | ||
| − | "By Maxence" | + | "By Maxence & Mahnaz" |
The following plasmids were extracted using the [[Team:Paris_Saclay/Experiments#InvitrogenPlasmidExtraction|"Charge Switch-Pro Plasmid Miniprep"]] kit: | The following plasmids were extracted using the [[Team:Paris_Saclay/Experiments#InvitrogenPlasmidExtraction|"Charge Switch-Pro Plasmid Miniprep"]] kit: | ||
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====Samples preparation for sequencing==== | ====Samples preparation for sequencing==== | ||
| − | ''By Maxence'' | + | ''By Maxence & Mahnaz'' |
20 µL of plasmids pSB1C3 FRB - GFP 11 (clones 4, 9, 13 and 16) were sent to be sequenced. 20 µL of the primers iPS83 (5µM) and iPS84 (5µM) were sent for sequencing. | 20 µL of plasmids pSB1C3 FRB - GFP 11 (clones 4, 9, 13 and 16) were sent to be sequenced. 20 µL of the primers iPS83 (5µM) and iPS84 (5µM) were sent for sequencing. | ||
====NanoDrop Measurements==== | ====NanoDrop Measurements==== | ||
| − | ''By Maxence'' | + | ''By Maxence & Mahnaz'' |
{| class="wikitable" | {| class="wikitable" | ||
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====Gibson of cleaned up PCR products GFP 1.9 from 9th September x pSB1C3 treated by DpnI from 22nd August==== | ====Gibson of cleaned up PCR products GFP 1.9 from 9th September x pSB1C3 treated by DpnI from 22nd August==== | ||
| − | ''By Maxence'' | + | ''By Maxence & Mahnaz'' |
Gibson was performed with cleaned up PCR products GFP 1.9 (insert) (obtained the 9th September) x pSB1C3 treated by DpnI (plasmid) (obtained the 22nd August) with the following protocol: | Gibson was performed with cleaned up PCR products GFP 1.9 (insert) (obtained the 9th September) x pSB1C3 treated by DpnI (plasmid) (obtained the 22nd August) with the following protocol: | ||
| Line 83: | Line 83: | ||
====Transformation of DH5a cells with GFP 1.9 in pSB1C3 obtained by Gibson==== | ====Transformation of DH5a cells with GFP 1.9 in pSB1C3 obtained by Gibson==== | ||
| − | ''By Maxence'' | + | ''By Maxence & Mahnaz'' |
Dh5a cells were transformed with pSB1C3 containing GFP 1.9, or controls (no buffer mix and plasmid alone) using the usual [[Team:Paris_Saclay/Experiments#heat-shocktransformation|protocol]]. | Dh5a cells were transformed with pSB1C3 containing GFP 1.9, or controls (no buffer mix and plasmid alone) using the usual [[Team:Paris_Saclay/Experiments#heat-shocktransformation|protocol]]. | ||
====gblock 1.1 - 1.2 and gblock 2.1 - 2.2 Ligation==== | ====gblock 1.1 - 1.2 and gblock 2.1 - 2.2 Ligation==== | ||
| − | ''By Maxence'' | + | ''By Maxence & Mahnaz'' |
gBlocks pPS16_003 and pPS16_004 were ligated together as following : | gBlocks pPS16_003 and pPS16_004 were ligated together as following : | ||
| Line 111: | Line 111: | ||
====Clean-up of Ligation products ==== | ====Clean-up of Ligation products ==== | ||
| − | ''By Maxence'' | + | ''By Maxence & Mahnaz'' |
Ligation products obtained were cleaned up by using the NucleoSpin Gel and PCR Clean-up kit [[Team:Paris_Saclay/Experiments#Purification|protocol]]. | Ligation products obtained were cleaned up by using the NucleoSpin Gel and PCR Clean-up kit [[Team:Paris_Saclay/Experiments#Purification|protocol]]. | ||
====NanoDrop Measurements==== | ====NanoDrop Measurements==== | ||
| − | ''By Maxence'' | + | ''By Maxence & Mahnaz'' |
{| class="wikitable" | {| class="wikitable" | ||
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====PCR of cleaned up Ligation products (fragment 1 and fragment 2) with 3% DMSO ==== | ====PCR of cleaned up Ligation products (fragment 1 and fragment 2) with 3% DMSO ==== | ||
| − | ''By Maxence'' | + | ''By Maxence & Mahnaz'' |
As the annealing temperature (Tm) seems too high to obtain good results for fragments 1 and 2 amplification, DMSO was used in order to reduce the annealing temperature during the PCR. For that purpose, PCR was performed with the following protocol. | As the annealing temperature (Tm) seems too high to obtain good results for fragments 1 and 2 amplification, DMSO was used in order to reduce the annealing temperature during the PCR. For that purpose, PCR was performed with the following protocol. | ||
| Line 189: | Line 189: | ||
====Gel of PCR products==== | ====Gel of PCR products==== | ||
| − | ''By Maxence'' | + | ''By Maxence & Mahnaz'' |
After amplification, 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. | After amplification, 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. | ||
Revision as of 17:08, 14 September 2016
Contents
- 1 Monday 12th September
- 1.1 Lab work
- 1.1.1 Visualization
- 1.1.1.1 Glycerol stocks of clones 4, 9, 13 and 16 containing FRB - GFP11 in pSB1C3
- 1.1.1.2 Plasmids extraction of clones 4, 9, 13 and 16 containing FRB - GFP11 in pSB1C3
- 1.1.1.3 Samples preparation for sequencing
- 1.1.1.4 NanoDrop Measurements
- 1.1.1.5 Gibson of cleaned up PCR products GFP 1.9 from 9th September x pSB1C3 treated by DpnI from 22nd August
- 1.1.1.6 Transformation of DH5a cells with GFP 1.9 in pSB1C3 obtained by Gibson
- 1.1.1.7 gblock 1.1 - 1.2 and gblock 2.1 - 2.2 Ligation
- 1.1.1.8 Clean-up of Ligation products
- 1.1.1.9 NanoDrop Measurements
- 1.1.1.10 PCR of cleaned up Ligation products (fragment 1 and fragment 2) with 3% DMSO
- 1.1.1.11 Gel of PCR products
- 1.1.1 Visualization
- 1.1 Lab work
Monday 12th September
Lab work
Visualization
Glycerol stocks of clones 4, 9, 13 and 16 containing FRB - GFP11 in pSB1C3
"By Maxence & Mahnaz"
The glycerol stock of the bacteria with the following plasmids were made.
- pPS16_009 (FRB - GFP11) clone 4
- pPS16_009 (FRB - GFP11) clone 9
- pPS16_014 (FRB - GFP11) clone 13
- pPS16_014 (FRB - GFP11) clone 16
500µL of liquid culture and 250 µL of glycerol 60% were mixed and put at -20°C.
A MODIFIER
Plasmids extraction of clones 4, 9, 13 and 16 containing FRB - GFP11 in pSB1C3
"By Maxence & Mahnaz"
The following plasmids were extracted using the "Charge Switch-Pro Plasmid Miniprep" kit:
- pPS16_009 (FRB - GFP11) clone 4
- pPS16_009 (FRB - GFP11) clone 9
- pPS16_014 (FRB - GFP11) clone 13
- pPS16_014 (FRB - GFP11) clone 16
Samples preparation for sequencing
By Maxence & Mahnaz
20 µL of plasmids pSB1C3 FRB - GFP 11 (clones 4, 9, 13 and 16) were sent to be sequenced. 20 µL of the primers iPS83 (5µM) and iPS84 (5µM) were sent for sequencing.
NanoDrop Measurements
By Maxence & Mahnaz
| Sample | Concentration (ng/µL) |
|---|---|
| FRB - GFP 11 clone 4 | 96.29 |
| FRB - GFP 11 clone 9 | 35.51 |
| FRB - GFP 11 clone 13 | 79.91 |
| FRB - GFP 11 clone 16 | 50.58 |
| PCR product GFP 1.9 from 9th September | 438.11 |
| pSB1C3 from 22nd August | 31.61 |
| PCR fragment gblock 1.1 from 9th September | 239.41 |
| PCR fragment gblock 1.2 from 9th September | 195.92 |
| PCR fragment gblock 2.1 from 9th September | 165.99 |
| PCR fragment gblock 2.2 from 9th September | 143.45 |
Gibson of cleaned up PCR products GFP 1.9 from 9th September x pSB1C3 treated by DpnI from 22nd August
By Maxence & Mahnaz
Gibson was performed with cleaned up PCR products GFP 1.9 (insert) (obtained the 9th September) x pSB1C3 treated by DpnI (plasmid) (obtained the 22nd August) with the following protocol:
For each 20μl of reaction, mix the following reagents :
- 0.2 µL of insert
- 3.16 µL of plasmid
- 6.64 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 GFP 1.9 in pSB1C3 obtained by Gibson
By Maxence & Mahnaz
Dh5a cells were transformed with pSB1C3 containing GFP 1.9, or controls (no buffer mix and plasmid alone) using the usual protocol.
gblock 1.1 - 1.2 and gblock 2.1 - 2.2 Ligation
By Maxence & Mahnaz
gBlocks pPS16_003 and pPS16_004 were ligated together as following :
- 8 µL of pPS16_00 PCR product from 9th September
- 8 µL of pPS16_004 PCR product from 9th September
- 2 µL of Buffer T4 10X
- 2 µL of ligase T4 enzyme
This strategy aims to obtain fragment 1.
gBlocks pPS16_003 and pPS16_004 were ligated together as following :
- 8 µL of pPS16_00 PCR product from 9th September
- 8 µL of pPS16_004 PCR product from 9th September
- 2 µL of Buffer T4 10X
- 2 µL of ligase T4 enzyme
This strategy aims to obtain fragment 2.
The ligation product was put at rooming temperature for 2 hours.
A MODIFIER
Clean-up of Ligation products
By Maxence & Mahnaz
Ligation products obtained were cleaned up by using the NucleoSpin Gel and PCR Clean-up kit protocol.
NanoDrop Measurements
By Maxence & Mahnaz
| Sample | Concentration (ng/µL) |
|---|---|
| gblock 1.1 and gblock 1.2 cleaned-up Ligation product | 194 |
| gblock 2.1 and gblock 2.2 cleaned-up Ligation product | 157 |
PCR of cleaned up Ligation products (fragment 1 and fragment 2) with 3% DMSO
By Maxence & Mahnaz
As the annealing temperature (Tm) seems too high to obtain good results for fragments 1 and 2 amplification, DMSO was used in order to reduce the annealing temperature during the PCR. For that purpose, 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 (5X)
- 0,5 µL of Phusion polymerase
- 31 µL of nuclease free water
- 1.5 µL of DMSO
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 |
| 60°C | 30sec | |
| 72°C | 1 min | |
| Final Extension | 72°C | 2min |
| Hold | 4°C | $\infty$ |
Primers used were:
| Matrix | Products from Ligation of gblock 1.1 and gblock 1.2 (fragment 1) | Products from Ligation of gblock 1.1 and gblock 1.2 (fragment 2) |
|---|---|---|
| Primers | iPS140 and iPS122 | iPS 123 and iPS84 |
Gel of PCR products
By Maxence & Mahnaz
After amplification, 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.
PCR products expected were :
| PCR products | Expected band size (bp) |
|---|---|
| Fragment 1 | 1920 |
| Fragment 2 | 1831 |
GEL bizare 1
A large smearing in agarose gel of PCR products was obtained. As this result was not usable, a new PCR was run by diluting the Ligations products : 1/100, 1/10,000 and 1/1,000,000.
GEL bizare 2
A large smearing in agarose gel of PCR products was also obtained, but the smears were seemed to decrease with the dilution rate.
