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>
<strong>legend:</strong>
<br /><hr />
<br /><hr />
-
<br />rbs.033- TOP
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<br />rbs.033- TOP10 without construct
<br />
<br />
-
<br />rbs.004- 1) B0030
+
<br />rbs.004- 1) <a href="http://partsregistry.org/Part:BBa_B0030">B0030</a>
-
<br />rbs.005- 2) B0030
+
<br />rbs.005- 2) <a href="http://partsregistry.org/Part:BBa_B0030">B0030</a>
-
<br />rbs.006- 3) B0030
+
<br />rbs.006- 3) <a href="http://partsregistry.org/Part:BBa_B0030">B0030</a>
<br />
<br />
-
<br />rbs.007- 1) B0031
+
<br />rbs.007- 1) <a href="http://partsregistry.org/Part:BBa_B0031">B0031</a>
-
<br />rbs.008- 2) B0031
+
<br />rbs.008- 2) <a href="http://partsregistry.org/Part:BBa_B0031">B0031</a>
-
<br />rbs.009- 3) B0031
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<br />rbs.009- 3) <a href="http://partsregistry.org/Part:BBa_B0031">B0031</a>
<br />
<br />
-
<br />rbs.010- 1) B0032
+
<br />rbs.010- 1) <a href="http://partsregistry.org/Part:BBa_B0032">B0032</a>
-
<br />rbs.011- 2) B0032
+
<br />rbs.011- 2) <a href="http://partsregistry.org/Part:BBa_B0032">B0032</a>
-
<br />rbs.012- 3) B0032
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<br />rbs.012- 3) <a href="http://partsregistry.org/Part:BBa_B0032">B0032</a>
<br />
<br />
-
<br />rbs.013- 1) B0033
+
<br />rbs.013- 1) <a href="http://partsregistry.org/Part:BBa_B0033">B0033</a>
-
<br />rbs.014- 2) B0033
+
<br />rbs.014- 2) <a href="http://partsregistry.org/Part:BBa_B0033">B0033</a>
-
<br />rbs.015- 3) B0033
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<br />rbs.015- 3) <a href="http://partsregistry.org/Part:BBa_B0033">B0033</a>
<br />
<br />
-
<br />rbs.003- 1) B0034
+
<br />rbs.003- 1) <a href="http://partsregistry.org/Part:BBa_B0034">B0034</a>
-
<br />rbs.016- 2) B0034
+
<br />rbs.016- 2) <a href="http://partsregistry.org/Part:BBa_B0034">B0034</a>
-
<br />rbs.017- 3) B0034
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<br />rbs.017- 3) <a href="http://partsregistry.org/Part:BBa_B0034">B0034</a>
<br />
<br />
-
<br />rbs.018- 1) J61100
+
<br />rbs.018- 1) <a href="http://partsregistry.org/Part:BBa_J61100">J61100</a>
-
<br />rbs.019- 2) J61100
+
<br />rbs.019- 2) <a href="http://partsregistry.org/Part:BBa_J61100">J61100</a>
-
<br />rbs.020- 3) J61100
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<br />rbs.020- 3) <a href="http://partsregistry.org/Part:BBa_J61100">J61100</a>
<br />
<br />
-
<br />rbs.021- 1) J61101
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<br />rbs.021- 1) <a href="http://partsregistry.org/Part:BBa_J61101">J61101</a>
-
<br />rbs.022- 2) J61101
+
<br />rbs.022- 2) <a href="http://partsregistry.org/Part:BBa_J61101">J61101</a>
-
<br />rbs.023- 3) J61101
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<br />rbs.023- 3) <a href="http://partsregistry.org/Part:BBa_J61101">J61101</a>
<br />
<br />
-
<br />rbs.024- 1) J61107
+
<br />rbs.024- 1) <a href="http://partsregistry.org/Part:BBa_J61107">J61107</a>
-
<br />rbs.025- 2) J61107
+
<br />rbs.025- 2) <a href="http://partsregistry.org/Part:BBa_J61107">J61107</a>
-
<br />rbs.026- 3) J61107
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<br />rbs.026- 3) <a href="http://partsregistry.org/Part:BBa_J61107">J61107</a>
<br />
<br />
-
<br />rbs.027- 1) J61117
+
<br />rbs.027- 1) <a href="http://partsregistry.org/Part:BBa_J61117">J61117</a>
-
<br />rbs.028- 2) J61117
+
<br />rbs.028- 2) <a href="http://partsregistry.org/Part:BBa_J61117">J61117</a>
-
<br />rbs.029- 3) J61117
+
<br />rbs.029- 3) <a href="http://partsregistry.org/Part:BBa_J61117">J61117</a>
<br />
<br />
-
<br />rbs.030- 1) J61127
+
<br />rbs.030- 1) <a href="http://partsregistry.org/Part:BBa_J61127">J61127</a>
-
<br />rbs.031- 2) J61127
+
<br />rbs.031- 2) <a href="http://partsregistry.org/Part:BBa_J61127">J61127</a>
-
<br />rbs.032- 3) J61127
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<br />rbs.032- 3) <a href="http://partsregistry.org/Part:BBa_J61127">J61127</a>
-
<br />
+
 
-
<br />
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<br /><br />cytometer plots:
-
<hr />
+
<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 />
<br />
<br />
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<br />
<br />
<br />
<br />
-
<hr />
+
<br /><br /><strong>Cell Quest data processed with Microsoft Excel:</strong><br /><hr /><br />
-
<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">
<table border="1" style="border-collapse: collapse">
   <tr>
   <tr>
-
     <td width="20%" rowspan="2">rbs raw data</td>
+
     <td width="20%" rowspan="2">part</td>
     <td width="40%" colspan="2">geo mean</td>
     <td width="40%" colspan="2">geo mean</td>
     <td width="40%" colspan="2">peak channel</td>
     <td width="40%" colspan="2">peak channel</td>
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<table border="1" style="border-collapse: collapse">
<table border="1" style="border-collapse: collapse">
   <tr>
   <tr>
-
     <td width="20%" rowspan="2">rbs means</td>
+
     <td width="20%" rowspan="2">part means</td>
     <td width="40%" colspan="2">geo mean %B0034</td>
     <td width="40%" colspan="2">geo mean %B0034</td>
     <td width="40%" colspan="2">peak channel %B0034</td>
     <td width="40%" colspan="2">peak channel %B0034</td>
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<tr><td>J61101</td><td>27%</td><td>23%</td><td>100%</td><td>23%</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>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>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>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>B0030</td><td>135%</td><td>113%</td><td>57233%</td><td>108%</td></tr>

Latest revision as of 20:03, 27 October 2010

Example Tabs


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
top1,131,101,001,00
1) B0030659,651134,441,001433,00
2) B0030954,011596,951715,001715,00
3) B0030633,971278,361,001485,00
mean749,211336,58572,331544,33
1) B0031181,89292,731,00327,00
2) B0031364,01623,601,00723,00
3) B0031174,81293,391,00283,00
mean240,24403,241,00444,33
1) B0032106,08164,611,00245,00
2) B003228,7365,321,0067,00
3) B0032145,17220,271,00237,00
mean93,33150,071,00183,00
1) B00334,935,691,007,00
2) B00333,092,831,001,00
3) B00333,443,821,004,00
mean3,824,111,004,00
1) B0034357,811112,271,001197,00
2) B0034705,271189,971,001433,00
3) B0034605,001259,441,001654,00
mean556,031187,231,001428,00
1) J6110013,2923,491,0035,00
2) J6110011,3219,181,0022,00
3) J6110020,4029,911,0045,00
mean15,0024,191,0034,00
1) J61101114,13212,721,00283,00
2) J61101117,92221,761,00264,00
3) J61101223,47370,241,00437,00
mean151,84268,241,00328,00
1) J6110759,50121,761,00143,00
2) J6110782,37161,981,00237,00
3) J6110762,99132,141,00205,00
mean68,29138,631,00195,00
1) J6111713,5423,181,0036,00
2) J6111724,5740,391,0052,00
3) J6111714,2724,281,0035,00
mean17,4629,281,0041,00
1) J6112745,87124,241,00212,00
2) J6112746,82120,561,00143,00
3) J6112737,5698,111,0093,00
mean43,42114,301,00149,33



part means geo mean %B0034 peak channel %B0034
all m1 all m1
top0%0%100%0%
J611003%2%100%2%
J6110127%23%100%23%
J6110712%12%100%14%
J611173%2%100%3%
J611278%10%100%10%
B0030135%113%57233%108%
B003143%34%100%31%
B003217%13%100%13%
B00331%0%100%0%
B0034100%100%100%100%







Retrieved from "http://2010.igem.org/Team:Warsaw/Calendar-Stage1/2_September_2010"