Team:Freiburg/Notebook/lab activation

From 2013.igem.org

(Difference between revisions)
Line 66: Line 66:
Effector - Activation
Effector - Activation
</p>
</p>
-
<div align="center">
+
 
-
<img src="https://static.igem.org/mediawiki/2013/3/3e/Troll_Face.png" style="width:650px; margin-top:-2px;"></div>
+
<h2>09. September</h2>
 +
 
 +
<h3> Retrafo of Plasmids for the Midiprep</h3>
 +
<ul >
 +
Following plasmids are needed for activation and repression repeats:
 +
 
 +
<li >pRSet</li >
 +
<li >pKM600</li >
 +
<li >pKM604</li >
 +
<li >pKM605</li >
 +
<li >pKM606</li >
 +
<li >pKM607</li >
 +
<li >pKM603</li >
 +
<li >pIG2017</li >
 +
<li >pIG2013</li >
 +
<li >pSAM200</li >
 +
 
 +
</ul >
 +
 
 +
Retrafo was inoculated into Ampicillin medium (concentration of 1:1000 from Ampicillin and medium).
 +
 
 +
<h2>10. September</h2>
 +
 
 +
  <h3>Midiprep</h3>
 +
<p>Plasmids were prepped with the Midiprep kit of Promega according to the manufacturer's protocol.</p>
 +
 
 +
  <h3>Seeding of cells</h3>
 +
<p>4 24-well plates were seeded with 65,000 cells per well</p>
 +
 
 +
<h2>11. September</h2>
 +
  <h3>Transfection</h3>
 +
<ol>
 +
<li>40 µl Opti-MEM + 2.25 µl PEI-solution were mixed in a 1.5 ml Eppi.</li>
 +
<li>0.75 µg of the DNA of interest were prepaired in another Eppi .</li>
 +
<li>Addition of the DNA to former Eppi, vortexing for 10 s and incubation for 15 min at RT</li>
 +
<li>Solution was spread drop-wise to the cells in the dish</li>
 +
</ol>
 +
 
 +
  <h3>Medium change</h3>
 +
Medium was changed after 5 h.
 +
 
 +
<h2>13. September</h2>
 +
  <h3>Preparation for analyses</h3>
 +
<ul>
 +
<li>Supernatant was collected for SEAP measurement.</li>
 +
<li>Cells were frozen at - 80 °C for later on Western blot and luminescence measurement.</li>
 +
</ul>
 +
 
 +
<h2>14. September</h2> 
 +
  <h3>SEAP measurement</h3>
 +
<ul>
 +
<li>Collected supernatant and fresh cell culture medium was heated at 65 °C for 30 min, then centrifuged at 1250 g for 1 min.</li>
 +
<li>Supernatant was diluted in cell culture medium 1:4 (25 µl supernatant + 75 µl medium).</li>
 +
<li>80 µl of diluted supernatant was given to 100 µl of SEAP buffer.</li>
 +
<li>After addition of 20 µl pNPP (substrate of SEAP) the absorbance of the mix was measured every minute for 2 h at 405 nm.
 +
</ul>
 +
 
 +
 
 +
<h2>16. September</h2>
 +
  <h3>Cell lysis</h3>
 +
<ul>
 +
<li>250 µl of lysis buffer (containing Tris-HCl, EGTA, MgSO<sub>4</sub>, DTT and protease inhibitor) were applied to the thawn cells of each well.</li>
 +
<li>Incubation on ice for 10 min.</li>
 +
<li>Centrifugation at 15,000 g for 4 min.</li>
 +
</ul>
 +
 
 +
  <h3>Renilla luminescence measurement</h3>
 +
<ul>
 +
<li>80 µl of supernatant were pipetted in a white 96 well plate.</li>
 +
<li>Measurement of luminescence (every 2 min for 30 min) immediately after addition of 20 µl Renilla substrate in PBS.</li>
 +
</ul>
 +
<br>
 +
<div>
 +
<table class="imgtxt" width="800px">
 +
<tr>
 +
<td> <img class="imgtxt" width="800px" src="https://static.igem.org/mediawiki/2013/8/80/Figure_activation_A%26R_I_Freiburg_2013.PNG"> </td>
 +
</tr>
 +
<tr>
 +
<td> <b>SEAP activity normalized to Renilla expression</b><br>
 +
The value of TetR-VP16 is 64,6 which is too high to be shown.
 +
</td>
 +
</tr>
 +
</table>
 +
The different SEAP plasmids showed very differing background levels of SEAP expression. When Cas9-VP16 without a crRNA was cotransfected there was a reduction of SEAP expression in two cases, whereas in all other samples the SEAP level stayed unaltered. An activation in SEAP expression in comparison to the cells that were not transfected with Cas9-VP16 was only detectable for the EMX1 target sequence (5 fold).<br>
 +
SEAP activation with TetR-VP16 was much stronger, most probably because there are 13 binding sites for TetR-VP16, but only one for Cas9-VP16.
 +
</div>
 +
 
 +
<h2>17. September</h2>
 +
  <h3>Protein precipitation</h3>
 +
<p>As the cell lysis needed to be done with a high amount of lysis buffer, proteins are too much diluted for western blotting. Thus, they were precipitated:</p>
 +
<ul>
 +
<li>The remaining lysates of the triplikates (~ 80 µl) were put together in a new epi.</li>
 +
<li>Addition of TCA to a final concentration of 10 % and 1 µg BSA.</li>
 +
<li>Incubation for 30 min on ice.</li>
 +
<li>Centrifugation for 30 min at full speed and 4 °C.</li>
 +
<li>Removal of supernatant and addition of 500 µl acetone.</li>
 +
<li>Incubation on ice over night.</li>
 +
<li>Centrifugation for 15 min at full speed and 4 °C.</li>
 +
<li>Removal of acetone and nair drying for 20 min.</li>
 +
<li>Addition of 20 µl 2x SDS-loading dye and 0.5 µl Tris-HCl (pH = 8.8).</li>
 +
<li>Heating at 95 °C for 5 min.</li>
 +
</ul>
 +
 
 +
<h2>18. September</h2>
 +
  <h3>SDS-gel run</h3>
 +
<p>SDS-gel was loaded with 18 µl of each sample. A voltage of 80 V was applied till the loading dye bands reached the border between collection and separation gel, then the voltage was increased to 120 V.</p>
 +
 
 +
  <h3>Western Blotting</h3>
 +
<ul>
 +
<li>Activation of PVDF-membrane for 10 min in methanol.</li>
 +
<li>Short incubation of Whatman papers and the PVDF-membrane in transfer buffer.</li>
 +
<li>Loading of western blot apperature: (-) - Whatman paper - SDS-gel - PVDF-membrane - Whatman paper - (+).</li>
 +
<li>200 mA were applied for 1.5 h.</li>
 +
</ul>
 +
 
 +
  <h3>Antibody treatment I</h3>
 +
<ul>
 +
<li>Incubation of PVDF membrane in blocking buffer (4 % milkpowder in TBS-T) for 1 h.</li>
 +
<li>Incubation with anti HA antibody (in 2 % milkpowder in TBS-T) over night at 4 °C.</li>
 +
<li>3 x washing with TBS-T for 5 min, each.</li>
 +
<li>Incubation with anti mouse antibody for 1 h.</li>
 +
<li>4 x washing with TBS-T for 10 min, each.</li>
 +
<li>Measurement of luminescence after addition of ECL I + ECL II solution.</li>
 +
<li>Air drying of the membrane for further antibody treatments.</li>
 +
</ul>
 +
 
 +
<h2>19. September</h2>
 +
 
 +
  <h3>Seeding of cells</h3>
 +
<p>3 24-well plates were seeded with 65,000 cells per well.</p>
 +
 
 +
  <h3>Antibody treatment II</h3>
 +
<ul>
 +
<li>Reactivation in methanol.</li>
 +
<li>1 x washing with TBS-T for 5 min.</li>
 +
<li>Incubation of PVDF membrane in blocking buffer (4 % milkpowder in TBS-T) for 30 min.</li>
 +
<li>Incubation with anti beta-actin antibody (in 2 % milkpowder in TBS-T) over night at 4 °C.</li>
 +
<li>3 x washing with TBS-T for 5 min, each.</li>
 +
<li>Incubation with anti mouse antibody for 1 h.</li>
 +
<li>4 x washing with TBS-T for 10 min, each.</li>
 +
<li>Measurement of luminescence after addition of ECL I + ECL II solution (500 µl each).</li>
 +
</ul>
 +
<br>
 +
<div>
 +
<table class="imgtxt" width="500px">
 +
<tr>
 +
<td> <img class="imgtxt" width="500px" src="https://static.igem.org/mediawiki/2013/3/3e/Figure_westerm_blot_A%26R_I_Freiburg_2013.PNG"> </td>
 +
</tr>
 +
<tr>
 +
<td> <b>Western blot </b><br>
 +
In every well that was transfected with Cas9-VP16 there was more or less the same expression of fhis fusion protein.
 +
</td>
 +
</tr>
 +
</table>
 +
 
 +
</div>
 +
 
 +
<h2>20. September</h2>
 +
 
 +
  <h3>Transfection</h3>
 +
<ol>
 +
<li>40 µl Opti-MEM + 2.25 µl PEI-solution were mixed in a 1.5 ml Eppi.</li>
 +
<li>0.75 µg of the DNA of interest were prepaired in another Eppi .</li>
 +
<li>Addition of the DNA to former Eppi, vortexing for 10 s and incubation for 15 min at RT</li>
 +
<li>Solution was spread drop-wise to the cells in the dish</li>
 +
</ol>
 +
<p>Ratio of DNA amount (mass): <br>
 +
reporter plasmid (SEAP) : effector plasmid (Cas9) : RNA plasmid<br>
 +
1 : 4 : 4 </p>
 +
 
 +
  <h3>Medium change</h3>
 +
Medium was changed after 4.5 h. 
 +
 
 +
<h2>22. September</h2>
 +
 
 +
  <h3>Medium removal</h3>
 +
<ul>
 +
<li>Supernatant was collected for SEAP measurement.</li>
 +
<li>Cells were frozen at - 80 °C for later on Western blotting.</li>
 +
</ul>
 +
 
 +
  <h3>Preparation for SEAP measurement</h3>
 +
<p>Collected supernatant and fresh cell culture medium was heated at 65 °C for 30 min, then centrifuged at 1250 g for 1 min.</p>
 +
 
 +
<h2>23. September</h2>
 +
 +
  <h3>SEAP measurement</h3>
 +
<ul>
 +
<li>Supernatant of wells containing CMV:SEAP was diluted in cell culture medium 1:10 (10 µl supernatant + 90 µl medium).</li>
 +
<li>80 µl of (diluted) supernatant was given to 100 µl of SEAP buffer.</li>
 +
<li>After addition of 20 µl pNPP (substrate of SEAP) the absorbance of the mix was measured every minute for 2 h at 405 nm.
 +
</ul>
 +
<br>
 +
<div>
 +
<table class="imgtxt" width="800px">
 +
<tr>
 +
<td> <img class="imgtxt" width="800px" src="https://static.igem.org/mediawiki/2013/8/8c/Figure_activation_A%26R_II_Freiburg_2013.PNG"> </td>
 +
</tr>
 +
<tr>
 +
<td> <b>SEAP activity [U/L]</b><br>
 +
pIG2004: Cas9-VP16 (not in iGEM standard); pIG2005: Cas9 (not in iGEM standard); PhyB: negative control; all other Cas9 constucts are in iGEM standard (with the indicated promoter)
 +
</td>
 +
</tr>
 +
</table>
 +
In comparison to the negative control the non standardized constructs repress the SEAP expression only slightly, whereas there is a strong repression by the standardized constructs, when driven by a CMV promoter. The repression of Cas9-KRAB seems to be a little stronger than the effect of Cas9 alone. But just like in the last experiment, the repression of Cas9-KRAB with a wrong crRNA is as strong as the repression with the right one.
 +
</div>
 +
 
 +
  <h3>Seeding of cells</h3>
 +
<p>4 24-well plates were seeded with 65,000 cells per well</p>
 +
 
 +
<h2>24. September</h2>
 +
 
 +
  <h3>Repeat of seeding of cells</h3>
 +
<p>4 24-well plates were seeded with 65,000 cells per well again, as the cell density of the first seeding was too low.</p>
 +
 
 +
<h2>25. September</h2>
 +
 
 +
  <h3>Transfection</h3>
 +
<ol>
 +
<li>40 µl Opti-MEM + 0.75 µg of the DNA of interest were mixed in a 1.5 ml Eppi.</li>
 +
<li>Addition of 2.25 µl PEI-solution, vortexing for 10 s and incubation for at least 15 min at RT</li>
 +
<li>Solution was spread drop-wise to the cells in the dish</li>
 +
</ol>
 +
<p>Ratio of DNA amount (mass): <br>
 +
reporter plasmid (SEAP) : effector plasmid (Cas9) : RNA plasmid<br>
 +
1 : 4 : 4 <br>
 +
Additionally a plasmid coding for Renilla luciferase was cotransfected (5 % of DNA amount)</p>
 +
 
 +
<h2>26. September</h2>
 +
 
 +
  <h3>Medium change</h3>
 +
Medium was changed after 8 h.
 +
 
 +
  <h3>Cell lysis of transfection of 20. September</h3>
 +
<ul>
 +
<li>80 µl of RIPA lysis buffer were applied to the thawn cells of each well.</li>
 +
<li>Incubation on ice for 10 min.</li>
 +
<li>Sonification 3 x 30 s at maximum.</li>
 +
<li>Centrifugation at 10,000 g for 10 min.</li>
 +
<li>40 µl of supernatant were mixed with 10 µl 5 x SDS sample buffer.</li>
 +
<li>Heating for 5 min at 95 °C.</li>
 +
</ul>
 +
 
 +
  <h3>SDS-gel run</h3>
 +
<p>SDS-gel was loaded with 40 µl of each sample. A voltage of 80 V was applied till the loading dye bands reached the border between collection and separation gel, then the voltage was increased to 120 V.</p>
 +
 
 +
  <h3>Western Blotting</h3>
 +
<ul>
 +
<li>Activation of PVDF-membrane for 10 min in methanol.</li>
 +
<li>Short incubation of Whatman papers and the PVDF-membrane in transfer buffer.</li>
 +
<li>Loading of western blot apperature: (-) - Whatman paper - SDS-gel - PVDF-membrane - Whatman paper - (+).</li>
 +
<li>200 mA were applied for 1.5 h.</li>
 +
</ul>
 +
 
 +
  <h3>Antibody treatment I</h3>
 +
<ul>
 +
<li>Incubation of PVDF membrane in blocking buffer (4 % milkpowder in TBS-T) for 1 h.</li>
 +
<li>Incubation with anti HA antibody (in 2 % milkpowder in TBS-T) over night at 4 °C.</li>
 +
<li>3 x washing with TBS-T for 5 min, each.</li>
 +
<li>Incubation with anti mouse antibody for 1 h.</li>
 +
<li>4 x washing with TBS-T for 10 min, each.</li>
 +
<li>Measurement of luminescence after addition of ECL I + ECL II solution.</li>
 +
<li>Air drying of the membrane for further antibody treatments.</li>
 +
</ul>
 +
 

Revision as of 11:41, 27 September 2013


Effector - Activation

09. September

Retrafo of Plasmids for the Midiprep

    Following plasmids are needed for activation and repression repeats:
  • pRSet
  • pKM600
  • pKM604
  • pKM605
  • pKM606
  • pKM607
  • pKM603
  • pIG2017
  • pIG2013
  • pSAM200
Retrafo was inoculated into Ampicillin medium (concentration of 1:1000 from Ampicillin and medium).

10. September

Midiprep

Plasmids were prepped with the Midiprep kit of Promega according to the manufacturer's protocol.

Seeding of cells

4 24-well plates were seeded with 65,000 cells per well

11. September

Transfection

  1. 40 µl Opti-MEM + 2.25 µl PEI-solution were mixed in a 1.5 ml Eppi.
  2. 0.75 µg of the DNA of interest were prepaired in another Eppi .
  3. Addition of the DNA to former Eppi, vortexing for 10 s and incubation for 15 min at RT
  4. Solution was spread drop-wise to the cells in the dish

Medium change

Medium was changed after 5 h.

13. September

Preparation for analyses

  • Supernatant was collected for SEAP measurement.
  • Cells were frozen at - 80 °C for later on Western blot and luminescence measurement.

14. September

SEAP measurement

  • Collected supernatant and fresh cell culture medium was heated at 65 °C for 30 min, then centrifuged at 1250 g for 1 min.
  • Supernatant was diluted in cell culture medium 1:4 (25 µl supernatant + 75 µl medium).
  • 80 µl of diluted supernatant was given to 100 µl of SEAP buffer.
  • After addition of 20 µl pNPP (substrate of SEAP) the absorbance of the mix was measured every minute for 2 h at 405 nm.

16. September

Cell lysis

  • 250 µl of lysis buffer (containing Tris-HCl, EGTA, MgSO4, DTT and protease inhibitor) were applied to the thawn cells of each well.
  • Incubation on ice for 10 min.
  • Centrifugation at 15,000 g for 4 min.

Renilla luminescence measurement

  • 80 µl of supernatant were pipetted in a white 96 well plate.
  • Measurement of luminescence (every 2 min for 30 min) immediately after addition of 20 µl Renilla substrate in PBS.

SEAP activity normalized to Renilla expression
The value of TetR-VP16 is 64,6 which is too high to be shown.
The different SEAP plasmids showed very differing background levels of SEAP expression. When Cas9-VP16 without a crRNA was cotransfected there was a reduction of SEAP expression in two cases, whereas in all other samples the SEAP level stayed unaltered. An activation in SEAP expression in comparison to the cells that were not transfected with Cas9-VP16 was only detectable for the EMX1 target sequence (5 fold).
SEAP activation with TetR-VP16 was much stronger, most probably because there are 13 binding sites for TetR-VP16, but only one for Cas9-VP16.

17. September

Protein precipitation

As the cell lysis needed to be done with a high amount of lysis buffer, proteins are too much diluted for western blotting. Thus, they were precipitated:

  • The remaining lysates of the triplikates (~ 80 µl) were put together in a new epi.
  • Addition of TCA to a final concentration of 10 % and 1 µg BSA.
  • Incubation for 30 min on ice.
  • Centrifugation for 30 min at full speed and 4 °C.
  • Removal of supernatant and addition of 500 µl acetone.
  • Incubation on ice over night.
  • Centrifugation for 15 min at full speed and 4 °C.
  • Removal of acetone and nair drying for 20 min.
  • Addition of 20 µl 2x SDS-loading dye and 0.5 µl Tris-HCl (pH = 8.8).
  • Heating at 95 °C for 5 min.

18. September

SDS-gel run

SDS-gel was loaded with 18 µl of each sample. A voltage of 80 V was applied till the loading dye bands reached the border between collection and separation gel, then the voltage was increased to 120 V.

Western Blotting

  • Activation of PVDF-membrane for 10 min in methanol.
  • Short incubation of Whatman papers and the PVDF-membrane in transfer buffer.
  • Loading of western blot apperature: (-) - Whatman paper - SDS-gel - PVDF-membrane - Whatman paper - (+).
  • 200 mA were applied for 1.5 h.

Antibody treatment I

  • Incubation of PVDF membrane in blocking buffer (4 % milkpowder in TBS-T) for 1 h.
  • Incubation with anti HA antibody (in 2 % milkpowder in TBS-T) over night at 4 °C.
  • 3 x washing with TBS-T for 5 min, each.
  • Incubation with anti mouse antibody for 1 h.
  • 4 x washing with TBS-T for 10 min, each.
  • Measurement of luminescence after addition of ECL I + ECL II solution.
  • Air drying of the membrane for further antibody treatments.

19. September

Seeding of cells

3 24-well plates were seeded with 65,000 cells per well.

Antibody treatment II

  • Reactivation in methanol.
  • 1 x washing with TBS-T for 5 min.
  • Incubation of PVDF membrane in blocking buffer (4 % milkpowder in TBS-T) for 30 min.
  • Incubation with anti beta-actin antibody (in 2 % milkpowder in TBS-T) over night at 4 °C.
  • 3 x washing with TBS-T for 5 min, each.
  • Incubation with anti mouse antibody for 1 h.
  • 4 x washing with TBS-T for 10 min, each.
  • Measurement of luminescence after addition of ECL I + ECL II solution (500 µl each).

Western blot
In every well that was transfected with Cas9-VP16 there was more or less the same expression of fhis fusion protein.

20. September

Transfection

  1. 40 µl Opti-MEM + 2.25 µl PEI-solution were mixed in a 1.5 ml Eppi.
  2. 0.75 µg of the DNA of interest were prepaired in another Eppi .
  3. Addition of the DNA to former Eppi, vortexing for 10 s and incubation for 15 min at RT
  4. Solution was spread drop-wise to the cells in the dish

Ratio of DNA amount (mass):
reporter plasmid (SEAP) : effector plasmid (Cas9) : RNA plasmid
1 : 4 : 4

Medium change

Medium was changed after 4.5 h.

22. September

Medium removal

  • Supernatant was collected for SEAP measurement.
  • Cells were frozen at - 80 °C for later on Western blotting.

Preparation for SEAP measurement

Collected supernatant and fresh cell culture medium was heated at 65 °C for 30 min, then centrifuged at 1250 g for 1 min.

23. September

SEAP measurement

  • Supernatant of wells containing CMV:SEAP was diluted in cell culture medium 1:10 (10 µl supernatant + 90 µl medium).
  • 80 µl of (diluted) supernatant was given to 100 µl of SEAP buffer.
  • After addition of 20 µl pNPP (substrate of SEAP) the absorbance of the mix was measured every minute for 2 h at 405 nm.

SEAP activity [U/L]
pIG2004: Cas9-VP16 (not in iGEM standard); pIG2005: Cas9 (not in iGEM standard); PhyB: negative control; all other Cas9 constucts are in iGEM standard (with the indicated promoter)
In comparison to the negative control the non standardized constructs repress the SEAP expression only slightly, whereas there is a strong repression by the standardized constructs, when driven by a CMV promoter. The repression of Cas9-KRAB seems to be a little stronger than the effect of Cas9 alone. But just like in the last experiment, the repression of Cas9-KRAB with a wrong crRNA is as strong as the repression with the right one.

Seeding of cells

4 24-well plates were seeded with 65,000 cells per well

24. September

Repeat of seeding of cells

4 24-well plates were seeded with 65,000 cells per well again, as the cell density of the first seeding was too low.

25. September

Transfection

  1. 40 µl Opti-MEM + 0.75 µg of the DNA of interest were mixed in a 1.5 ml Eppi.
  2. Addition of 2.25 µl PEI-solution, vortexing for 10 s and incubation for at least 15 min at RT
  3. Solution was spread drop-wise to the cells in the dish

Ratio of DNA amount (mass):
reporter plasmid (SEAP) : effector plasmid (Cas9) : RNA plasmid
1 : 4 : 4
Additionally a plasmid coding for Renilla luciferase was cotransfected (5 % of DNA amount)

26. September

Medium change

Medium was changed after 8 h.

Cell lysis of transfection of 20. September

  • 80 µl of RIPA lysis buffer were applied to the thawn cells of each well.
  • Incubation on ice for 10 min.
  • Sonification 3 x 30 s at maximum.
  • Centrifugation at 10,000 g for 10 min.
  • 40 µl of supernatant were mixed with 10 µl 5 x SDS sample buffer.
  • Heating for 5 min at 95 °C.

SDS-gel run

SDS-gel was loaded with 40 µl of each sample. A voltage of 80 V was applied till the loading dye bands reached the border between collection and separation gel, then the voltage was increased to 120 V.

Western Blotting

  • Activation of PVDF-membrane for 10 min in methanol.
  • Short incubation of Whatman papers and the PVDF-membrane in transfer buffer.
  • Loading of western blot apperature: (-) - Whatman paper - SDS-gel - PVDF-membrane - Whatman paper - (+).
  • 200 mA were applied for 1.5 h.

Antibody treatment I

  • Incubation of PVDF membrane in blocking buffer (4 % milkpowder in TBS-T) for 1 h.
  • Incubation with anti HA antibody (in 2 % milkpowder in TBS-T) over night at 4 °C.
  • 3 x washing with TBS-T for 5 min, each.
  • Incubation with anti mouse antibody for 1 h.
  • 4 x washing with TBS-T for 10 min, each.
  • Measurement of luminescence after addition of ECL I + ECL II solution.
  • Air drying of the membrane for further antibody treatments.

Retrieved from "http://2013.igem.org/Team:Freiburg/Notebook/lab_activation"