Team:Warsaw/Calendar-Stage1/2 September 2010
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+ | <br> 02.09.2010 Wednesday | ||
+ | <br> | ||
+ | <br><div class="note"> Previous day: Set up liquid cultures of E.coli TOP10 with measured constructs [Ania O.]</div> | ||
+ | <br> We used a protocol described <a href="https://2010.igem.org/Team:Warsaw/Stage1/RBSMeas">here</a> | ||
+ | <br> | ||
+ | <br><div class="note"> Testing the strenght of RBS [Ania O.,Cherry]</div> | ||
- | < | + | <br>Preparation of samples by dilluting the bacteria cultures and examining them in flow cytometer (all according the <a href="https://2010.igem.org/Team:Warsaw/Stage1/RBSMeas">protocol</a> |
- | + | <br> | |
- | < | + | <br><div class="note"> Data analysis with Cell Quest and Microsoft Excel[Cherry]</div> |
- | < | + | <br> |
- | + | <strong>legend:</strong> | |
- | < | + | <br /><hr /> |
- | < | + | <br />rbs.033- TOP10 without construct |
- | + | <br /> | |
- | + | <br />rbs.004- 1) <a href="http://partsregistry.org/Part:BBa_B0030">B0030</a> | |
- | < | + | <br />rbs.005- 2) <a href="http://partsregistry.org/Part:BBa_B0030">B0030</a> |
- | + | <br />rbs.006- 3) <a href="http://partsregistry.org/Part:BBa_B0030">B0030</a> | |
- | + | <br /> | |
- | + | <br />rbs.007- 1) <a href="http://partsregistry.org/Part:BBa_B0031">B0031</a> | |
- | < | + | <br />rbs.008- 2) <a href="http://partsregistry.org/Part:BBa_B0031">B0031</a> |
- | + | <br />rbs.009- 3) <a href="http://partsregistry.org/Part:BBa_B0031">B0031</a> | |
- | + | <br /> | |
- | + | <br />rbs.010- 1) <a href="http://partsregistry.org/Part:BBa_B0032">B0032</a> | |
- | < | + | <br />rbs.011- 2) <a href="http://partsregistry.org/Part:BBa_B0032">B0032</a> |
- | + | <br />rbs.012- 3) <a href="http://partsregistry.org/Part:BBa_B0032">B0032</a> | |
- | + | <br /> | |
- | + | <br />rbs.013- 1) <a href="http://partsregistry.org/Part:BBa_B0033">B0033</a> | |
- | < | + | <br />rbs.014- 2) <a href="http://partsregistry.org/Part:BBa_B0033">B0033</a> |
- | + | <br />rbs.015- 3) <a href="http://partsregistry.org/Part:BBa_B0033">B0033</a> | |
- | + | <br /> | |
- | + | <br />rbs.003- 1) <a href="http://partsregistry.org/Part:BBa_B0034">B0034</a> | |
- | < | + | <br />rbs.016- 2) <a href="http://partsregistry.org/Part:BBa_B0034">B0034</a> |
- | + | <br />rbs.017- 3) <a href="http://partsregistry.org/Part:BBa_B0034">B0034</a> | |
- | + | <br /> | |
- | + | <br />rbs.018- 1) <a href="http://partsregistry.org/Part:BBa_J61100">J61100</a> | |
- | < | + | <br />rbs.019- 2) <a href="http://partsregistry.org/Part:BBa_J61100">J61100</a> |
- | + | <br />rbs.020- 3) <a href="http://partsregistry.org/Part:BBa_J61100">J61100</a> | |
- | + | <br /> | |
- | + | <br />rbs.021- 1) <a href="http://partsregistry.org/Part:BBa_J61101">J61101</a> | |
- | < | + | <br />rbs.022- 2) <a href="http://partsregistry.org/Part:BBa_J61101">J61101</a> |
- | + | <br />rbs.023- 3) <a href="http://partsregistry.org/Part:BBa_J61101">J61101</a> | |
- | + | <br /> | |
- | + | <br />rbs.024- 1) <a href="http://partsregistry.org/Part:BBa_J61107">J61107</a> | |
- | < | + | <br />rbs.025- 2) <a href="http://partsregistry.org/Part:BBa_J61107">J61107</a> |
- | + | <br />rbs.026- 3) <a href="http://partsregistry.org/Part:BBa_J61107">J61107</a> | |
- | + | <br /> | |
- | + | <br />rbs.027- 1) <a href="http://partsregistry.org/Part:BBa_J61117">J61117</a> | |
- | + | <br />rbs.028- 2) <a href="http://partsregistry.org/Part:BBa_J61117">J61117</a> | |
- | </ | + | <br />rbs.029- 3) <a href="http://partsregistry.org/Part:BBa_J61117">J61117</a> |
+ | <br /> | ||
+ | <br />rbs.030- 1) <a href="http://partsregistry.org/Part:BBa_J61127">J61127</a> | ||
+ | <br />rbs.031- 2) <a href="http://partsregistry.org/Part:BBa_J61127">J61127</a> | ||
+ | <br />rbs.032- 3) <a href="http://partsregistry.org/Part:BBa_J61127">J61127</a> | ||
+ | <br /><br />cytometer plots: | ||
+ | <br>FSC- Forward Scatter, cell size | ||
+ | <br>SSC- Side Scatter, cell complexity | ||
+ | <br>FL-1- FL-1 sensor, cell fluorescence | ||
+ | <br /><br /><br /><strong>Cytometer data processed with Cell Quest:</strong><br /><hr /><br /> | ||
+ | <br /> | ||
+ | <br /> | ||
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+ | <img src="https://static.igem.org/mediawiki/2010/0/0a/RBS.2.09_01.png" /> | ||
+ | <img src="https://static.igem.org/mediawiki/2010/a/aa/RBS.2.09_02.png" /> | ||
+ | <img src="https://static.igem.org/mediawiki/2010/8/82/RBS.2.09_03.png" /> | ||
+ | <img src="https://static.igem.org/mediawiki/2010/8/8e/RBS.2.09_04.png" /> | ||
+ | <img src="https://static.igem.org/mediawiki/2010/f/fd/RBS.2.09_05.png" /> | ||
+ | <img src="https://static.igem.org/mediawiki/2010/9/9f/RBS.2.09_06.png" /> | ||
+ | <img src="https://static.igem.org/mediawiki/2010/e/ef/RBS.2.09_07.png" /> | ||
+ | <img src="https://static.igem.org/mediawiki/2010/4/47/RBS.2.09_08.png" /> | ||
+ | <img src="https://static.igem.org/mediawiki/2010/f/fd/RBS.2.09_09.png" /> | ||
+ | <img src="https://static.igem.org/mediawiki/2010/0/0f/RBS.2.09_10.png" /> | ||
+ | <img src="https://static.igem.org/mediawiki/2010/c/c9/RBS.2.09_11.png" /> | ||
+ | |||
+ | <br /> | ||
+ | <br /> | ||
+ | <br /><br /><strong>Cell Quest data processed with Microsoft Excel:</strong><br /><hr /><br /> | ||
+ | <br>geo mean- geometric mean of fluorescence of events in FL1 | ||
+ | <br>peak channel- nr of channel which recorded the biggest nr of events<br><br /> | ||
+ | |||
+ | <table border="1" style="border-collapse: collapse"> | ||
+ | <tr> | ||
+ | <td width="20%" rowspan="2">part</td> | ||
+ | <td width="40%" colspan="2">geo mean</td> | ||
+ | <td width="40%" colspan="2">peak channel</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td width="20%">all</td> | ||
+ | <td width="20%">m1</td> | ||
+ | <td width="20%">all</td> | ||
+ | <td width="20%">m1</td> | ||
+ | </tr> | ||
+ | |||
+ | <tr><td>top</td><td>1,13</td><td>1,10</td><td>1,00</td><td>1,00</td></tr> | ||
+ | <tr><td>1) B0030</td><td>659,65</td><td>1134,44</td><td>1,00</td><td>1433,00</td></tr> | ||
+ | <tr><td>2) B0030</td><td>954,01</td><td>1596,95</td><td>1715,00</td><td>1715,00</td></tr> | ||
+ | <tr><td>3) B0030</td><td>633,97</td><td>1278,36</td><td>1,00</td><td>1485,00</td></tr> | ||
+ | <tr><td>mean</td><td>749,21</td><td>1336,58</td><td>572,33</td><td>1544,33</td></tr> | ||
+ | <tr><td>1) B0031</td><td>181,89</td><td>292,73</td><td>1,00</td><td>327,00</td></tr> | ||
+ | <tr><td>2) B0031</td><td>364,01</td><td>623,60</td><td>1,00</td><td>723,00</td></tr> | ||
+ | <tr><td>3) B0031</td><td>174,81</td><td>293,39</td><td>1,00</td><td>283,00</td></tr> | ||
+ | <tr><td>mean</td><td>240,24</td><td>403,24</td><td>1,00</td><td>444,33</td></tr> | ||
+ | <tr><td>1) B0032</td><td>106,08</td><td>164,61</td><td>1,00</td><td>245,00</td></tr> | ||
+ | <tr><td>2) B0032</td><td>28,73</td><td>65,32</td><td>1,00</td><td>67,00</td></tr> | ||
+ | <tr><td>3) B0032</td><td>145,17</td><td>220,27</td><td>1,00</td><td>237,00</td></tr> | ||
+ | <tr><td>mean</td><td>93,33</td><td>150,07</td><td>1,00</td><td>183,00</td></tr> | ||
+ | <tr><td>1) B0033</td><td>4,93</td><td>5,69</td><td>1,00</td><td>7,00</td></tr> | ||
+ | <tr><td>2) B0033</td><td>3,09</td><td>2,83</td><td>1,00</td><td>1,00</td></tr> | ||
+ | <tr><td>3) B0033</td><td>3,44</td><td>3,82</td><td>1,00</td><td>4,00</td></tr> | ||
+ | <tr><td>mean</td><td>3,82</td><td>4,11</td><td>1,00</td><td>4,00</td></tr> | ||
+ | <tr><td>1) B0034</td><td>357,81</td><td>1112,27</td><td>1,00</td><td>1197,00</td></tr> | ||
+ | <tr><td>2) B0034</td><td>705,27</td><td>1189,97</td><td>1,00</td><td>1433,00</td></tr> | ||
+ | <tr><td>3) B0034</td><td>605,00</td><td>1259,44</td><td>1,00</td><td>1654,00</td></tr> | ||
+ | <tr><td>mean</td><td>556,03</td><td>1187,23</td><td>1,00</td><td>1428,00</td></tr> | ||
+ | <tr><td>1) J61100</td><td>13,29</td><td>23,49</td><td>1,00</td><td>35,00</td></tr> | ||
+ | <tr><td>2) J61100</td><td>11,32</td><td>19,18</td><td>1,00</td><td>22,00</td></tr> | ||
+ | <tr><td>3) J61100</td><td>20,40</td><td>29,91</td><td>1,00</td><td>45,00</td></tr> | ||
+ | <tr><td>mean</td><td>15,00</td><td>24,19</td><td>1,00</td><td>34,00</td></tr> | ||
+ | <tr><td>1) J61101</td><td>114,13</td><td>212,72</td><td>1,00</td><td>283,00</td></tr> | ||
+ | <tr><td>2) J61101</td><td>117,92</td><td>221,76</td><td>1,00</td><td>264,00</td></tr> | ||
+ | <tr><td>3) J61101</td><td>223,47</td><td>370,24</td><td>1,00</td><td>437,00</td></tr> | ||
+ | <tr><td>mean</td><td>151,84</td><td>268,24</td><td>1,00</td><td>328,00</td></tr> | ||
+ | <tr><td>1) J61107</td><td>59,50</td><td>121,76</td><td>1,00</td><td>143,00</td></tr> | ||
+ | <tr><td>2) J61107</td><td>82,37</td><td>161,98</td><td>1,00</td><td>237,00</td></tr> | ||
+ | <tr><td>3) J61107</td><td>62,99</td><td>132,14</td><td>1,00</td><td>205,00</td></tr> | ||
+ | <tr><td>mean</td><td>68,29</td><td>138,63</td><td>1,00</td><td>195,00</td></tr> | ||
+ | <tr><td>1) J61117</td><td>13,54</td><td>23,18</td><td>1,00</td><td>36,00</td></tr> | ||
+ | <tr><td>2) J61117</td><td>24,57</td><td>40,39</td><td>1,00</td><td>52,00</td></tr> | ||
+ | <tr><td>3) J61117</td><td>14,27</td><td>24,28</td><td>1,00</td><td>35,00</td></tr> | ||
+ | <tr><td>mean</td><td>17,46</td><td>29,28</td><td>1,00</td><td>41,00</td></tr> | ||
+ | <tr><td>1) J61127</td><td>45,87</td><td>124,24</td><td>1,00</td><td>212,00</td></tr> | ||
+ | <tr><td>2) J61127</td><td>46,82</td><td>120,56</td><td>1,00</td><td>143,00</td></tr> | ||
+ | <tr><td>3) J61127</td><td>37,56</td><td>98,11</td><td>1,00</td><td>93,00</td></tr> | ||
+ | <tr><td>mean</td><td>43,42</td><td>114,30</td><td>1,00</td><td>149,33</td></tr> | ||
+ | </table> | ||
+ | <br /> | ||
+ | <br /> | ||
+ | <br /> | ||
+ | |||
+ | <table border="1" style="border-collapse: collapse"> | ||
+ | <tr> | ||
+ | <td width="20%" rowspan="2">part means</td> | ||
+ | <td width="40%" colspan="2">geo mean %B0034</td> | ||
+ | <td width="40%" colspan="2">peak channel %B0034</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td width="20%">all</td> | ||
+ | <td width="20%">m1</td> | ||
+ | <td width="20%">all</td> | ||
+ | <td width="20%">m1</td> | ||
+ | </tr> | ||
+ | |||
+ | <tr><td>top</td><td>0%</td><td>0%</td><td>100%</td><td>0%</td></tr> | ||
+ | <tr><td>J61100</td><td>3%</td><td>2%</td><td>100%</td><td>2%</td></tr> | ||
+ | <tr><td>J61101</td><td>27%</td><td>23%</td><td>100%</td><td>23%</td></tr> | ||
+ | <tr><td>J61107</td><td>12%</td><td>12%</td><td>100%</td><td>14%</td></tr> | ||
+ | <tr><td>J61117</td><td>3%</td><td>2%</td><td>100%</td><td>3%</td></tr> | ||
+ | <tr><td>J61127</td><td>8%</td><td>10%</td><td>100%</td><td>10%</td></tr> | ||
+ | <tr><td>B0030</td><td>135%</td><td>113%</td><td>57233%</td><td>108%</td></tr> | ||
+ | <tr><td>B0031</td><td>43%</td><td>34%</td><td>100%</td><td>31%</td></tr> | ||
+ | <tr><td>B0032</td><td>17%</td><td>13%</td><td>100%</td><td>13%</td></tr> | ||
+ | <tr><td>B0033</td><td>1%</td><td>0%</td><td>100%</td><td>0%</td></tr> | ||
+ | <tr><td>B0034</td><td>100%</td><td>100%</td><td>100%</td><td>100%</td></tr> | ||
+ | </table> | ||
+ | <br /> | ||
+ | <br /> | ||
+ | <br /> | ||
+ | <img src="https://static.igem.org/mediawiki/2010/3/31/RBS.2.09_xls_1.gif" /> | ||
+ | <br /> | ||
+ | <br /> | ||
+ | <br /> | ||
+ | <br /> | ||
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Latest revision as of 20:03, 27 October 2010
02.09.2010 Wednesday
Previous day: Set up liquid cultures of E.coli TOP10 with measured constructs [Ania O.]
We used a protocol described here
Testing the strenght of RBS [Ania O.,Cherry]
Preparation of samples by dilluting the bacteria cultures and examining them in flow cytometer (all according the protocol
Data analysis with Cell Quest and Microsoft Excel[Cherry]
legend:
rbs.033- TOP10 without construct
rbs.004- 1) B0030
rbs.005- 2) B0030
rbs.006- 3) B0030
rbs.007- 1) B0031
rbs.008- 2) B0031
rbs.009- 3) B0031
rbs.010- 1) B0032
rbs.011- 2) B0032
rbs.012- 3) B0032
rbs.013- 1) B0033
rbs.014- 2) B0033
rbs.015- 3) B0033
rbs.003- 1) B0034
rbs.016- 2) B0034
rbs.017- 3) B0034
rbs.018- 1) J61100
rbs.019- 2) J61100
rbs.020- 3) J61100
rbs.021- 1) J61101
rbs.022- 2) J61101
rbs.023- 3) J61101
rbs.024- 1) J61107
rbs.025- 2) J61107
rbs.026- 3) J61107
rbs.027- 1) J61117
rbs.028- 2) J61117
rbs.029- 3) J61117
rbs.030- 1) J61127
rbs.031- 2) J61127
rbs.032- 3) J61127
cytometer plots:
FSC- Forward Scatter, cell size
SSC- Side Scatter, cell complexity
FL-1- FL-1 sensor, cell fluorescence
Cytometer data processed with Cell Quest:
Cell Quest data processed with Microsoft Excel:
geo mean- geometric mean of fluorescence of events in FL1
peak channel- nr of channel which recorded the biggest nr of events
part | geo mean | peak channel | ||
all | m1 | all | m1 | |
top | 1,13 | 1,10 | 1,00 | 1,00 |
1) B0030 | 659,65 | 1134,44 | 1,00 | 1433,00 |
2) B0030 | 954,01 | 1596,95 | 1715,00 | 1715,00 |
3) B0030 | 633,97 | 1278,36 | 1,00 | 1485,00 |
mean | 749,21 | 1336,58 | 572,33 | 1544,33 |
1) B0031 | 181,89 | 292,73 | 1,00 | 327,00 |
2) B0031 | 364,01 | 623,60 | 1,00 | 723,00 |
3) B0031 | 174,81 | 293,39 | 1,00 | 283,00 |
mean | 240,24 | 403,24 | 1,00 | 444,33 |
1) B0032 | 106,08 | 164,61 | 1,00 | 245,00 |
2) B0032 | 28,73 | 65,32 | 1,00 | 67,00 |
3) B0032 | 145,17 | 220,27 | 1,00 | 237,00 |
mean | 93,33 | 150,07 | 1,00 | 183,00 |
1) B0033 | 4,93 | 5,69 | 1,00 | 7,00 |
2) B0033 | 3,09 | 2,83 | 1,00 | 1,00 |
3) B0033 | 3,44 | 3,82 | 1,00 | 4,00 |
mean | 3,82 | 4,11 | 1,00 | 4,00 |
1) B0034 | 357,81 | 1112,27 | 1,00 | 1197,00 |
2) B0034 | 705,27 | 1189,97 | 1,00 | 1433,00 |
3) B0034 | 605,00 | 1259,44 | 1,00 | 1654,00 |
mean | 556,03 | 1187,23 | 1,00 | 1428,00 |
1) J61100 | 13,29 | 23,49 | 1,00 | 35,00 |
2) J61100 | 11,32 | 19,18 | 1,00 | 22,00 |
3) J61100 | 20,40 | 29,91 | 1,00 | 45,00 |
mean | 15,00 | 24,19 | 1,00 | 34,00 |
1) J61101 | 114,13 | 212,72 | 1,00 | 283,00 |
2) J61101 | 117,92 | 221,76 | 1,00 | 264,00 |
3) J61101 | 223,47 | 370,24 | 1,00 | 437,00 |
mean | 151,84 | 268,24 | 1,00 | 328,00 |
1) J61107 | 59,50 | 121,76 | 1,00 | 143,00 |
2) J61107 | 82,37 | 161,98 | 1,00 | 237,00 |
3) J61107 | 62,99 | 132,14 | 1,00 | 205,00 |
mean | 68,29 | 138,63 | 1,00 | 195,00 |
1) J61117 | 13,54 | 23,18 | 1,00 | 36,00 |
2) J61117 | 24,57 | 40,39 | 1,00 | 52,00 |
3) J61117 | 14,27 | 24,28 | 1,00 | 35,00 |
mean | 17,46 | 29,28 | 1,00 | 41,00 |
1) J61127 | 45,87 | 124,24 | 1,00 | 212,00 |
2) J61127 | 46,82 | 120,56 | 1,00 | 143,00 |
3) J61127 | 37,56 | 98,11 | 1,00 | 93,00 |
mean | 43,42 | 114,30 | 1,00 | 149,33 |
part means | geo mean %B0034 | peak channel %B0034 | ||
all | m1 | all | m1 | |
top | 0% | 0% | 100% | 0% |
J61100 | 3% | 2% | 100% | 2% |
J61101 | 27% | 23% | 100% | 23% |
J61107 | 12% | 12% | 100% | 14% |
J61117 | 3% | 2% | 100% | 3% |
J61127 | 8% | 10% | 100% | 10% |
B0030 | 135% | 113% | 57233% | 108% |
B0031 | 43% | 34% | 100% | 31% |
B0032 | 17% | 13% | 100% | 13% |
B0033 | 1% | 0% | 100% | 0% |
B0034 | 100% | 100% | 100% | 100% |