Team:Paris Bettencourt/Notebook/Phage Sensor/Thursday 3rd October.html

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Electrocompetent cells (delta PyrF, parental, NEB)
+
<b>Electrocompetent cells (delta PyrF, parental, NEB)</b>
-
 
+
<br>
1) Start Culture
1) Start Culture
-
 
+
<br>
2) When the cells reach an OD600 of 0.2.
2) When the cells reach an OD600 of 0.2.
-
 
+
<br>
3) Harvest the cells.
3) Harvest the cells.
-
 
+
<br>
           When the cells reach an OD600 of between 0.6 and 0.8 (OD: 0,683)
           When the cells reach an OD600 of between 0.6 and 0.8 (OD: 0,683)
-
 
+
<br>
           Centrifuge at 4 °C for 10 min at 4000 rpm.
           Centrifuge at 4 °C for 10 min at 4000 rpm.
-
 
+
<br>
4) Wash and combine the cells.
4) Wash and combine the cells.
-
 
+
<br>
           Remove the supernatant.
           Remove the supernatant.
-
 
+
<br>
           Resuspend the cells in 25 ml of ice cold water
           Resuspend the cells in 25 ml of ice cold water
-
 
+
<br>
5) Wash the cells 2 more times.
5) Wash the cells 2 more times.
-
 
+
<br>
           Centrifuge at 4 °C for 10 min at 4000 rpm.
           Centrifuge at 4 °C for 10 min at 4000 rpm.
-
 
+
<br>
           Resuspend in 50 ml of ice cold water.
           Resuspend in 50 ml of ice cold water.
-
 
+
<br>
           Repeat.
           Repeat.
-
 
+
<br>
6) Wash and concentrate the cells for electroporation.
6) Wash and concentrate the cells for electroporation.
-
 
+
<br>
           Centrifuge at 4 °C for 10 min at 4000 rpm.
           Centrifuge at 4 °C for 10 min at 4000 rpm.
-
 
+
<br>
           Resuspend in 1-2 ml of ice cold water.
           Resuspend in 1-2 ml of ice cold water.
-
 
+
<br>
           We will use 200 ul of washed cells per transformation.
           We will use 200 ul of washed cells per transformation.
-
 
+
<br>
-
 
+
<br>
-
Transformation
+
<b>Transformation </b>
-
 
+
<br>
1) Prepare BD tubes with a pipette filled with LB at the interior of each tube (pipette supplied with the electroporation cuvette)
1) Prepare BD tubes with a pipette filled with LB at the interior of each tube (pipette supplied with the electroporation cuvette)
-
 
+
<br>
2) Test the purity of the electrocompetent cells.
2) Test the purity of the electrocompetent cells.
-
 
+
<br>
           Add 200 ul of washed cells to a cuvette.
           Add 200 ul of washed cells to a cuvette.
-
 
+
<br>
3) Mix the cells and DNA in a cuvette.
3) Mix the cells and DNA in a cuvette.
-
 
+
<br>
           200 ul of washed cells with 200 ng of PCR product.
           200 ul of washed cells with 200 ng of PCR product.
-
 
+
<br>
           Keep the cuvette on ice until just before the electroporation.
           Keep the cuvette on ice until just before the electroporation.
-
 
+
<br>
4) Preload a pipette with 1 ml of LB.
4) Preload a pipette with 1 ml of LB.
-
 
+
<br>
5) Pulse the cuvette with voltage.
5) Pulse the cuvette with voltage.
-
 
+
<br>
           Dry the electrodes with a kimwipe prior to loading.
           Dry the electrodes with a kimwipe prior to loading.
-
 
+
<br>
           Use the EC2 setting.
           Use the EC2 setting.
-
 
+
<br>
6) Listen for arcing.
6) Listen for arcing.
-
 
+
<br>
           A cracking sound means all the cells are dead.
           A cracking sound means all the cells are dead.
-
 
+
<br>
           Note the time constant: 5 is good, 5.8 is great.
           Note the time constant: 5 is good, 5.8 is great.
-
 
+
<br>
7) Immediately recover the cells.
7) Immediately recover the cells.
-
 
+
<br>
           Add the 1 ml of preloaded LB and pipet up and down to mix.
           Add the 1 ml of preloaded LB and pipet up and down to mix.
-
 
+
<br>
           Collect 1 ml of cells, some volume is lost in the cuvette.
           Collect 1 ml of cells, some volume is lost in the cuvette.
-
 
+
<br>
8) Incubate 1/2 h at 37 °C with shaking.
8) Incubate 1/2 h at 37 °C with shaking.
-
 
+
<br>
9) Plate 10/200 ul of recovered cells on selective plates.
9) Plate 10/200 ul of recovered cells on selective plates.
-
 
+
<br>
           Use antibiotic appropriate to the part being integrated.
           Use antibiotic appropriate to the part being integrated.
-
 
+
<br>
           Let the other 900 ul rest overnight at room temperature.
           Let the other 900 ul rest overnight at room temperature.
-
 
+
<br>
10) Concentrate and plate the remaining cells
10) Concentrate and plate the remaining cells
-
 
+
<br>
           Spin down quickly and resuspend in 100 ul LB before plating.
           Spin down quickly and resuspend in 100 ul LB before plating.
-
 
+
<br>
Transformed cells should be incubated at 37 °C.
Transformed cells should be incubated at 37 °C.
-
 
+
<br>
Colonies should appear 24-48 h after plating.
Colonies should appear 24-48 h after plating.
-
 
+
<br>
Cotransform into parental/keio delta pyRF: pS006* (Cas9 in Amp BB) + pS004'(gRNA in Chl BB).
Cotransform into parental/keio delta pyRF: pS006* (Cas9 in Amp BB) + pS004'(gRNA in Chl BB).
-
 
+
<br>
-
Plating of 10/100ul on  
+
<br>
-
1. Amp plates -> selection for only Cas9
+
Plating of 10/100ul on <br>
-
2. Chl plates -> selection for only gRNA
+
1. Amp plates -> selection for only Cas9<br>
-
3. Amp/Chl plates -> selection for theoretically functional system
+
2. Chl plates -> selection for only gRNA<br>
 +
3. Amp/Chl plates -> selection for theoretically functional system<br>

Revision as of 10:54, 25 October 2013

Detect

Wedsnesday 3rd October

Killing assay to test specifity of CRISPR Cas

Electrocompetent cells (delta PyrF, parental, NEB)
1) Start Culture
2) When the cells reach an OD600 of 0.2.
3) Harvest the cells.
When the cells reach an OD600 of between 0.6 and 0.8 (OD: 0,683)
Centrifuge at 4 °C for 10 min at 4000 rpm.
4) Wash and combine the cells.
Remove the supernatant.
Resuspend the cells in 25 ml of ice cold water
5) Wash the cells 2 more times.
Centrifuge at 4 °C for 10 min at 4000 rpm.
Resuspend in 50 ml of ice cold water.
Repeat.
6) Wash and concentrate the cells for electroporation.
Centrifuge at 4 °C for 10 min at 4000 rpm.
Resuspend in 1-2 ml of ice cold water.
We will use 200 ul of washed cells per transformation.

Transformation
1) Prepare BD tubes with a pipette filled with LB at the interior of each tube (pipette supplied with the electroporation cuvette)
2) Test the purity of the electrocompetent cells.
Add 200 ul of washed cells to a cuvette.
3) Mix the cells and DNA in a cuvette.
200 ul of washed cells with 200 ng of PCR product.
Keep the cuvette on ice until just before the electroporation.
4) Preload a pipette with 1 ml of LB.
5) Pulse the cuvette with voltage.
Dry the electrodes with a kimwipe prior to loading.
Use the EC2 setting.
6) Listen for arcing.
A cracking sound means all the cells are dead.
Note the time constant: 5 is good, 5.8 is great.
7) Immediately recover the cells.
Add the 1 ml of preloaded LB and pipet up and down to mix.
Collect 1 ml of cells, some volume is lost in the cuvette.
8) Incubate 1/2 h at 37 °C with shaking.
9) Plate 10/200 ul of recovered cells on selective plates.
Use antibiotic appropriate to the part being integrated.
Let the other 900 ul rest overnight at room temperature.
10) Concentrate and plate the remaining cells
Spin down quickly and resuspend in 100 ul LB before plating.
Transformed cells should be incubated at 37 °C.
Colonies should appear 24-48 h after plating.
Cotransform into parental/keio delta pyRF: pS006* (Cas9 in Amp BB) + pS004'(gRNA in Chl BB).

Plating of 10/100ul on
1. Amp plates -> selection for only Cas9
2. Chl plates -> selection for only gRNA
3. Amp/Chl plates -> selection for theoretically functional system

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