Difference between revisions of "Team:Paris Saclay/Notebook/August/19"
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{{Team:Paris_Saclay/notebook_header}} | {{Team:Paris_Saclay/notebook_header}} | ||
= Friday 19<sup>th</sup> August= | = Friday 19<sup>th</sup> August= | ||
| − | + | ||
===Visualization=== | ===Visualization=== | ||
| + | ====Q5 PCR on fragments 3 and 4==== | ||
| + | "By Charlène" | ||
| − | ==== | + | A Q5 PCR was made on fragments 3 and 4 for a gel extraction. |
| + | Tm = 72°C. Elongation time = 1 minute. | ||
| + | Problem : 25 cycles at the place of 30. | ||
| + | |||
| + | |||
| + | [[File:T--Paris Saclay--20160819 3 and 4 Q5 PCR.JPG|500px|thumb|right|Q5 PCR of fragments 3 and 4]] | ||
| + | |||
| + | There is not enough product for the extraction gel : a second PCR was done with 30 cycles. It will be run on gel next Monday. | ||
| + | |||
| + | ==== Glycerol stocks ==== | ||
"By Terrence, Alice and Mahnaz" | "By Terrence, Alice and Mahnaz" | ||
| + | |||
| + | Glycerol stocks of bacteria transformed with the following plasmids were made. | ||
| + | * pPS16_009 (GFP1-9) clone 4 | ||
| + | * pPS16_009 (GFP1-9) clone 5 | ||
| + | * pPS16_014 (sgRNA Nm) clone 1 | ||
| + | * pPS16_014 (sgRNA Nm) clone 2 | ||
| + | * pPS16_013 (FKBP) clone 3 | ||
| + | * pPS16_013 (FKBP) clone 4 | ||
| + | * pPS16_013 (FKBP) clone 5 | ||
| + | * pPS16_010 (FRB) clone 2 | ||
| + | * pPS16_010 (FRB) clone 3 | ||
| + | * pPS16_010 (FRB) clone 5 | ||
| + | * pPS16_002 (1.2) clone 1 | ||
| + | * pPS16_002 (1.2) clone 11 | ||
| + | |||
| + | 500µL of liquid culture and 250 µL of glycerol 60% were mixed and put at -20°C. | ||
| + | |||
| + | ====Plasmid extractions==== | ||
| + | "By Terrence, Alice and Mahnaz" | ||
| + | |||
| + | The following plasmids were extracted using the [[Team:Paris_Saclay/Experiments#InvitrogenPlasmidExtraction|"Charge Switch-Pro Plasmid Miniprep"]] kit: | ||
| + | * pPS16_009 (GFP1-9) clone 4 | ||
| + | * pPS16_009 (GFP1-9) clone 5 | ||
| + | * pPS16_014 (sgRNA Nm) clone 1 | ||
| + | * pPS16_014 (sgRNA Nm) clone 2 | ||
| + | * pPS16_013 (FKBP) clone 3 | ||
| + | * pPS16_013 (FKBP) clone 4 | ||
| + | * pPS16_013 (FKBP) clone 5 | ||
| + | * pPS16_010 (FRB) clone 2 | ||
| + | * pPS16_010 (FRB) clone 3 | ||
| + | * pPS16_010 (FRB) clone 5 | ||
| + | * pPS16_002 (1.2) clone 1 | ||
| + | * pPS16_002 (1.2) clone 11 | ||
| + | |||
Nano drop : | Nano drop : | ||
| Line 36: | Line 81: | ||
|1.05 | |1.05 | ||
|- | |- | ||
| − | |pPS16_013 (FKBP | + | |pPS16_013 (FKBP) clone 3 |
|272.37 | |272.37 | ||
|2.32 | |2.32 | ||
|1.93 | |1.93 | ||
|- | |- | ||
| − | |pPS16_013 (FKBP | + | |pPS16_013 (FKBP) clone 4 |
|404.65 | |404.65 | ||
|2.34 | |2.34 | ||
|1.94 | |1.94 | ||
|- | |- | ||
| − | |pPS16_013 (FKBP | + | |pPS16_013 (FKBP) clone 5 |
|204.87 | |204.87 | ||
|2.32 | |2.32 | ||
| Line 77: | Line 122: | ||
|- | |- | ||
|} | |} | ||
| + | |||
| + | The extracted plasmids were also put on agarose gel for confirmation. | ||
==== Colony and Extraction product DreamTaq PCR==== | ==== Colony and Extraction product DreamTaq PCR==== | ||
"By Léa and Naiane" | "By Léa and Naiane" | ||
| − | A | + | A colony PCR was performed on DH5a transformed with pJet containing sgRNA Nm or 1.2 gBlocks. |
| − | sgRNA Nm clones 6, 7, 8, 10, 11 and 12 were screened, and 1.2 clones 13 to 18 were screened and | + | sgRNA Nm clones 6, 7, 8, 10, 11 and 12 were screened, and 1.2 clones 13 to 18 were screened and spread on Petri dish containing solid LB and Ampicilin. |
In the meantime, a DreamTaq PCR was performed on plasmids extractions listed above, using the same PCR mix. | In the meantime, a DreamTaq PCR was performed on plasmids extractions listed above, using the same PCR mix. | ||
| − | The PCR mix was made following the usual [[Team:Paris_Saclay/Experiments##Polymerase_chain_reaction|protocol]]. Universal primers for | + | The PCR mix was made following the usual [[Team:Paris_Saclay/Experiments##Polymerase_chain_reaction|protocol]]. Universal primers for pJET were used (Tm= 51.9°). |
| + | |||
| + | |||
| + | For 1.2 gBlock, only the sample from the clone number 14 seems to have an appropriate size (expected at 1073 bp). This clone will be grown and the plasmid will be extracted to be sequenced. | ||
| + | For FRB (492bp), plasmid extractions from clones 5 and 2 seem to have an appropriate size and will be send for sequencing. | ||
| + | For FKBP12 (537bp), the 3 plasmids extraction will be sent. For 1.2 (1073bp), only plasmid extraction from clone 11 will be sent, and no plasmid extraction will be sent for sgRNA Nm (480bp). | ||
| + | No significative stripe is observed for sgRNA Nm gBlock. There is no clone carrying the plasmid of interrest. | ||
| + | |||
| + | [[File:T--Paris Saclay--190826 visualization PCR1.jpeg|500px|thumb|right|Gel electrophoresis of colony PCR products 1.2 gBlock.]] | ||
| + | |||
| + | |||
| + | [[File:T--Paris_Saclay--190826_visualization_PCR2.JPG|500px|thumb|right|Gel electrophoresis of PCR products FRB, FKBP and sgRNA Nm gBlocks.]] | ||
| + | |||
| + | |||
| + | [[File:T--Paris Saclay--190826 visualization PCR3.jpeg|500px|thumb|right|Gel electrophoresis of colony PCR products, gBlock sg RNA Nm.]] | ||
| − | |||
{{Team:Paris_Saclay/notebook_footer}} | {{Team:Paris_Saclay/notebook_footer}} | ||
Latest revision as of 16:55, 9 October 2016
