Difference between revisions of "Team:CityU HK/Notebook"
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− | <td>Date</td> | + | <td width="20%">Date</td> |
<td>Group 1</td> | <td>Group 1</td> | ||
<td>Group 2</td> | <td>Group 2</td> | ||
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</tr> | </tr> | ||
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− | <td>Date</td> | + | <td width="20%">Date</td> |
<td>Group 1</td> | <td>Group 1</td> | ||
<td>Group 2</td> | <td>Group 2</td> | ||
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</tr> | </tr> | ||
<tr> | <tr> | ||
− | <td>Date</td> | + | <td width="20%">Date</td> |
<td>Group 1</td> | <td>Group 1</td> | ||
<td>Group 3</td> | <td>Group 3</td> | ||
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</tr> | </tr> | ||
<tr> | <tr> | ||
− | <td>Date</td> | + | <td width="20%">Date</td> |
<td>Group 1</td> | <td>Group 1</td> | ||
<td>Group 3</td> | <td>Group 3</td> | ||
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Gene name or plasmid name [x/y]: the gene fragment or plasmid flanked with the restriction sites x and y at the ends <br> | Gene name or plasmid name [x/y]: the gene fragment or plasmid flanked with the restriction sites x and y at the ends <br> | ||
− | -A ribosome binding site (RBS) is linked upstream of each gene | + | -A ribosome binding site (RBS) is linked upstream of each gene <br> |
− | -Coloring refers to sub-tasks in that particular group | + | -Coloring refers to sub-tasks in that particular group <br> |
-The cells used for transformation were competent JM109 <i>E. coli</i> cells</p> | -The cells used for transformation were competent JM109 <i>E. coli</i> cells</p> | ||
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</tr> | </tr> | ||
<tr> | <tr> | ||
− | <td>Date</td> | + | <td width="20%">Date</td> |
− | <td>Group 1</td> | + | <td width="20%">Group 1</td> |
− | <td>Group 2</td> | + | <td width="20%">Group 2</td> |
− | <td>Group 3</td> | + | <td width="20%">Group 3</td> |
− | <td>Group 4</td> | + | <td width="20%">Group 4</td> |
</tr> | </tr> | ||
<tr> | <tr> | ||
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<td>Friday 12</td> | <td>Friday 12</td> | ||
<td></td> | <td></td> | ||
− | <td><li>Ligation of the [E/P] digested Rzλ(co) insert (from June 11) with the [E/P] digested vector pSB1C3</li> <li>Transformation of the ligaiton product into competent <i>E. coli</i> cells</td> | + | <td><li>Ligation of the [E/P] digested Rzλ(co) insert (from June 11) with the [E/P] digested vector pSB1C3</li> <li>Transformation of the ligaiton product into competent <i>E. coli</i> cells</li></td> |
<td></td> | <td></td> | ||
<td></td> | <td></td> | ||
Line 744: | Line 744: | ||
</table> | </table> | ||
+ | <table id="t01" border="1"> | ||
+ | <tr> | ||
+ | <th colspan="5">Week 5 : June 15 – 19</th> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td colspan="5"></td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td width="20%">Date</td> | ||
+ | <td width="20%">Group 1</td> | ||
+ | <td width="20%">Group 2</td> | ||
+ | <td width="20%">Group 3</td> | ||
+ | <td width="20%">Group 4</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td>Monday 15</td> | ||
+ | <td colspan="4" bgcolor="#FFB2D1"></td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td>Tuesday 16</td> | ||
+ | <td></td> | ||
+ | <td><li>Colony PCR on June 12 transformed cells (Result: no bands amplified)</li></td> | ||
+ | <td><li>Ligation of the [E/P] digested Rλ(co) insert (from June 12) into the [E/P] digested vector pSB1C3</li> <li>Transformation of the ligation product into competent <i>E. coli</i> cells</li></td> | ||
+ | <td></td> | ||
+ | </tr> | ||
+ | |||
+ | <tr> | ||
+ | <td>Wednesday 17</td> | ||
+ | <td></td> | ||
+ | <td></td> | ||
+ | <td><li>Colony PCR on June 16 transformed cells (Result: no bands amplified)</li></td> | ||
+ | <td></td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td>Thursday 18</td> | ||
+ | <td></td> | ||
+ | <td><li>Redo the ligation of the [E/P] digested Rzλ(co) insert into the [E/P] digested vector pSB1C3 </li> <li>Transformation of the ligation product into competent <i>E. coli</i> cells</li></td> | ||
+ | <td><li>Redo the extraction of the plasmid pGOv4-Rλ(co)</li> <li>Restriction digestion with [E/P]</li></td> | ||
+ | <td></td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td>Friday 19</td> | ||
+ | <td></td> | ||
+ | <td><li>Colony PCR on June 18 transformed cells (Result: seen bands of the expected size)</li></td> | ||
+ | <td><li>Gel purification of June 18 digest</li></td> | ||
+ | <td></td> | ||
+ | </tr> | ||
+ | </table> | ||
+ | |||
+ | <table id="t01" border="1"> | ||
+ | <tr> | ||
+ | <th colspan="5">Week 6 : June 22 – 26</th> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td colspan="5"></td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td width="20%">Date</td> | ||
+ | <td width="20%">Group 1</td> | ||
+ | <td width="20%">Group 2</td> | ||
+ | <td width="20%">Group 3</td> | ||
+ | <td width="20%">Group 4</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td>Monday 22</td> | ||
+ | <td></td> | ||
+ | <td></td> | ||
+ | <td></td> | ||
+ | <td></td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td>Tuesday 23</td> | ||
+ | <td></td> | ||
+ | <td></td> | ||
+ | <td><li>Redo the extraction of the plasmid pGOv4-Rλ(co)</li> <li>Restriction digestion with [E/P]</li> <li>Gel purification</li></td> | ||
+ | <td></td> | ||
+ | </tr> | ||
+ | |||
+ | <tr> | ||
+ | <td>Wednesday 24</td> | ||
+ | <td></td> | ||
+ | <td></td> | ||
+ | <td></td> | ||
+ | <td></td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td>Thursday 25</td> | ||
+ | <td></td> | ||
+ | <td></td> | ||
+ | <td><li>Ligation of the [E/P] digested Rλ(co) insert into the [E/P] digested pSB1C3 vector</li> <li>Transformation of the ligation product into competent <i>E. coli</i> cells</li></td> | ||
+ | <td></td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td>Friday 26</td> | ||
+ | <td></td> | ||
+ | <td></td> | ||
+ | <td><li>Colony PCR on June 25 transformed cells (Result: showed no bands)</li></td> | ||
+ | <td></td> | ||
+ | </tr> | ||
+ | </table> | ||
+ | |||
+ | <table id="t01" border="1"> | ||
+ | <tr> | ||
+ | <th colspan="5">Week 7 : June 29 – July 3</th> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td colspan="5"></td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td width="20%">Date</td> | ||
+ | <td width="20%">Group 1</td> | ||
+ | <td width="20%">Group 2</td> | ||
+ | <td width="20%">Group 3</td> | ||
+ | <td width="20%">Group 4</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td>Monday 29</td> | ||
+ | <td></td> | ||
+ | <td><li>Extraction of the plasmid pSB1C3-Rzλ(co) (from June 18 transformed cells)</li></td> | ||
+ | <td><li>Colony PCR on June 25 transformed cells (Result: again showed no bands)</li></td> | ||
+ | <td></td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td>Tuesday 30</td> | ||
+ | <td></td> | ||
+ | <td></td> | ||
+ | <td><li>Sequencing result confirmed the presence of Rλ(co) insert in pSB1C3</li></td> | ||
+ | <td></td> | ||
+ | </tr> | ||
+ | |||
+ | <tr> | ||
+ | <td>Wednesday 1</td> | ||
+ | <td colspan="4" bgcolor="#FFB2D1"></td> | ||
+ | </tr> | ||
+ | |||
+ | <tr> | ||
+ | <td>Thursday 2</td> | ||
+ | <td><li>PCR amplification of the BBa_K124017 SλWT(ori) gene</li></td> | ||
+ | <td><li><font color="#D633FF">PCR amplification of the BBa_K124017 Rλ(ori) gene</font></li> <li><font color="#D633FF">Rλ(ori) PCR product purification</font></li> <li><font color="#0099FF">Transformation of pGOv4-SλWT(co) into competent <i>E. coli</i> cells</font></li></td> | ||
+ | <td><li><font color="#D633FF">PCR amplification of the BBa_K124017 Rzλ(ori) gene</font></li> <li><font color="#D633FF">Rzλ(ori) PCR product purification</font></li> <li><font color="#D633FF">Restriction digestion with [E/P]</font></li></td> | ||
+ | <td><li>PCR amplification of the BBa_K124017 Rλ(ori) gene</li> <li>Rλ(ori) PCR product purification</li></td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td>Friday 3</td> | ||
+ | <td><li>Restriction digestion of pSB1C3 vector with [E/X]</li></td> | ||
+ | <td><li>Restriction digestion of Rλ(co) with [E/P]</li> <li>Gel purification</li></td> | ||
+ | <td>[1]<li><font color="#D633FF">Gel purification of July 2 [E/P] digested Rzλ(ori)</font></li> <li>Ligation of the [E/P] digested <font color="#D633FF">Rzλ(ori) insert </font>into [E/P] digested pSB1C3 vector</li> [2] <li><font color="#0099FF">Extraction of the plasmid pSB1C3-Rλ(co) (from June 25 transformed cells)</font></li> <li><font color="#0099FF">Restriction digestion with [S/P]</li> <li>Gel purification</font></li> [3] <li><font color="#D633FF">Restriction digestion of June 2 Rzλ(ori) with [X/P] & Heat kill</font></li> <li><font color="#00CC00">Ligation of [X/P] digested Rzλ(ori) insert into [S/P] digested pSB1C3-Rλ(co) vector</li></td> | ||
+ | <td><li>Extraction of the plasmid pSB1C3-Rλ(co) (from Gp3 June 25 transformed cells)</li></td> | ||
+ | </tr> | ||
+ | </table> | ||
Revision as of 16:39, 19 August 2015
Keys to the table:
[?/?]: Names of restriction enzyme used for digestion:; E, EcoRI; X, XbaI; S, SpeI; P, PstI
- A ribosome binding site (RBS) is linked upstream to each gene
- The host cells used for transformation were competent JM109 E. coli cells
PCR amplification of the lacZ and lacY genes.
Week 1 : May 18 – 22 | ||||
---|---|---|---|---|
Date | Group 1 | Group 2 | Group 3 | Group 4 |
Monday 18 | ||||
Tuesday 19 | ||||
Wednesday 20 | ||||
Thursday 21 | ||||
Friday 22 |
Week 2 : May 25 – 29 | ||||
---|---|---|---|---|
Date | Group 1 | Group 2 | Group 3 | Group 4 |
Monday 25 | ||||
Tuesday 26 | ||||
Wednesday 27 | ||||
Thursday 28 | ||||
Friday 29 |
Groups 1 & 3 and Groups 2 & 4 used different cloning strategies to assemble the biobrick J23100_lacZ-lacY.
Week 3 : June 1 – 5 | ||||
---|---|---|---|---|
Date | Group 1 | Group 3 | Group 2 | Group 4 |
Monday 1 | ||||
Tuesday 2 | ||||
Wednesday 3 | ||||
Thursday 4 | ||||
Friday 5 |
Week 4 : June 8 – 12 | ||||
---|---|---|---|---|
Date | Group 1 | Group 3 | Group 2 | Group 4 |
Monday 8 | ||||
Tuesday 9 | ||||
Wednesday 10 |
Week 8 : July 6 – 10 | ||
---|---|---|
Date | Remarks | |
Monday 6 | ||
Tuesday 7 | Not successful | |
Wednesday 8 | Not successful | |
Thursday 9 | ||
Friday 10 | Not successful |
Week 9 : July 13 – 18 | ||
---|---|---|
Date | Remarks | |
Monday 13 | Successful | |
Tuesday 14 | Successful | |
Wednesday 15 | Successful | |
Thursday 16 | Successful | |
Friday 17 | ||
Saturday 18 | Successful |
Week 10 : July 20 – 25 | ||
---|---|---|
Date | Remarks | |
Monday 20 | Successful | |
Tuesday 21 | ||
Wednesday 22 | ||
Thursday 23 | ||
Friday 24 |
Keys to the table:
ori: original gene sequence, without codon optimization
co: codon optimized
λ Lysis(o_o_o): SλWT(ori)-Rλ(ori)-Rzλ(ori)
λLysis(c_c_c): SλWT(co)-Rλ(co)-Rzλ(co)
λLysis_Sm(o_c_c): Sλmut(ori)-Rλ(co)-Rzλ(co)
λLysis_Sm(c_c_c): Sλmut(co)-Rλ(co)-Rzλ(co)
[x/y]: restriction sites digested: E, EcoRI; X, XbaI; S, SpeI; P, PstI
Gene name or plasmid name [x/y]: the gene fragment or plasmid flanked with the restriction sites x and y at the ends
-A ribosome binding site (RBS) is linked upstream of each gene
-Coloring refers to sub-tasks in that particular group
-The cells used for transformation were competent JM109 E. coli cells
Week 4 : June 8 – 12 | ||||
---|---|---|---|---|
Date | Group 1 | Group 2 | Group 3 | Group 4 |
Monday 8 | ||||
Tuesday 9 | ||||
Wednesday 10 | ||||
Thursday 11 | ||||
Friday 12 |
Week 5 : June 15 – 19 | ||||
---|---|---|---|---|
Date | Group 1 | Group 2 | Group 3 | Group 4 |
Monday 15 | ||||
Tuesday 16 | ||||
Wednesday 17 | ||||
Thursday 18 | ||||
Friday 19 |
Week 6 : June 22 – 26 | ||||
---|---|---|---|---|
Date | Group 1 | Group 2 | Group 3 | Group 4 |
Monday 22 | ||||
Tuesday 23 | ||||
Wednesday 24 | ||||
Thursday 25 | ||||
Friday 26 |
Week 7 : June 29 – July 3 | ||||
---|---|---|---|---|
Date | Group 1 | Group 2 | Group 3 | Group 4 |
Monday 29 | ||||
Tuesday 30 | ||||
Wednesday 1 | ||||
Thursday 2 | ||||
Friday 3 | [1] |