Team:Hong Kong HKUST/wetlab/notebook

From 2014.igem.org

(Difference between revisions)
Line 132: Line 132:
Wet lab<br>
Wet lab<br>
·      Transformation of pSB1C3-BBa_E0240, pSB1C3-BBa_B0032 and pSB1C3-BBa_K20600<br>
·      Transformation of pSB1C3-BBa_E0240, pSB1C3-BBa_B0032 and pSB1C3-BBa_K20600<br>
-
·      Transformation of BBa_B0034 and BBa_E0040 into DH10B<br>
+
·      <br>
·      <br>
·      <br>
·   <br>
·   <br>
Line 139: Line 139:
·      Found reference promoter J23101 in BBa_I20260 from part registry<br>
·      Found reference promoter J23101 in BBa_I20260 from part registry<br>
·      Looked for Pcombox gene sequence from the genomic DNA<br>
·      Looked for Pcombox gene sequence from the genomic DNA<br>
-
·      Bacterial inoculation of BBa_B0034 and BBa_E0040<br>
+
·      <br>
·   <br>
·   <br>
<br><b>June 11</b> <br>
<br><b>June 11</b> <br>
Line 145: Line 145:
·      Looked for Pcombox gene sequence from the genomic DNA<br>
·      Looked for Pcombox gene sequence from the genomic DNA<br>
·      Studied the Characteristic, function and mechnism of how promoters work<br>
·      Studied the Characteristic, function and mechnism of how promoters work<br>
-
·      Miniprep of BBa_B0034 and BBa_E0040<br>
+
·      <br>
·   <br>
·   <br>
<br><b>June 12</b> <br>
<br><b>June 12</b> <br>
Wet lab<br>
Wet lab<br>
·      Looked for Pcombox gene sequence from the genomic DNA<br>
·      Looked for Pcombox gene sequence from the genomic DNA<br>
-
·      Research on gene sequence of PcomX, how to quantify p~comE, range of concentration of  p~comE to use for characterization<br>
+
·      <br>
·      <br>
·      <br>
·   <br>
·   <br>
Line 156: Line 156:
Wet lab<br>
Wet lab<br>
·      Looked for Pcombox gene sequence from the genomic DNA<br>
·      Looked for Pcombox gene sequence from the genomic DNA<br>
-
·      Research on gene sequence of PcomX, how to quantify p~comE, range of concentration of  p~comE to use for characterization<br>
+
·      <br>
·      <br>
·      <br>
·   <br>
·   <br>
Line 169: Line 169:
·      Blast the gDNA of NCTC7465 strain with various strain of S. pneumoniae to look for Pcombox gene sequence<br>
·      Blast the gDNA of NCTC7465 strain with various strain of S. pneumoniae to look for Pcombox gene sequence<br>
·      Found a possible Pcombox<br>
·      Found a possible Pcombox<br>
-
·      Transformation of BBa_J04450 and BBa_I20260 into DH10B<br>
+
·      <br>
-
·      Bacterial inoculation of BBa_E0240<br>
+
·   <br>
·   <br>
<br><b>June 17</b> <br>
<br><b>June 17</b> <br>
Line 177: Line 176:
·      Found a possible Pcombox<br>
·      Found a possible Pcombox<br>
·      Searched for other possible Pcombox sequences<br>
·      Searched for other possible Pcombox sequences<br>
-
·      Miniprep of BBa_E0240<br>
 
-
·      Bacterial inoculation of BBa_J04450(CHL) and BBa_I20260<br>
 
·   <br>
·   <br>
<br><b>June 18</b> <br>
<br><b>June 18</b> <br>
Line 184: Line 181:
·      Designed primers for the Pcombox sequences<br>
·      Designed primers for the Pcombox sequences<br>
·      Received a Pcombox sequence from Wellcome Trust Sanger Institute<br>
·      Received a Pcombox sequence from Wellcome Trust Sanger Institute<br>
-
·      Miniprep of BBa_J04450(CHL) and BBa_I20260<br>
+
·      <br>
-
·      Bacterial inoculation of BBa_J04450(CHL) and BBa_I20260<br>
+
-
·      Digestion of BBa_J04450(CHL) and BBa_I20260<br>
+
-
·      Gel electrophoresis of digested products<br>
+
-
 
+
-
 
+
<br><b>June 19</b> <br>
<br><b>June 19</b> <br>
· Digestion of pSB1C3-BBa_E0240 at EcoRI and SpeI<br>
· Digestion of pSB1C3-BBa_E0240 at EcoRI and SpeI<br>
-
· Miniprep of BBa_J04450(CHL) and BBa_I20260<br>
+
· <br>
-
· Digestion of BBa_J04450(CHL) <br>
+
· <br>
-
· Gel electrophoresis of digested product<br>
+
· <br>
-
· Bacterial inoculation of BBa_J04450(CHL) <br>
+
-
 
+
-
 
+
<br><b>June 20</b> <br>
<br><b>June 20</b> <br>
· Amended primers of Pcombox sequences<br>
· Amended primers of Pcombox sequences<br>
-
· Miniprep of BBa_J04450(CHL) <br>
+
· <br>
-
· Digestion of BBa_J04450(CHL)<br>
+
· <br>
-
· Gel electrophoresis of digested product<br>
+
· <br>
Line 215: Line 204:
·      Primer design for PCR of comX-myc and comW-FLAG from genomic DNA of S. Pneumoniae NCTC 7465 strain<br>
·      Primer design for PCR of comX-myc and comW-FLAG from genomic DNA of S. Pneumoniae NCTC 7465 strain<br>
·      Designed plasmid construct for Pcombox<br>
·      Designed plasmid construct for Pcombox<br>
-
·      Bacterial inoculation of BBa_J04450(CHL)<br>
+
·      <br>
·      <br>
·      <br>
·      <br>
·      <br>
Line 226: Line 215:
·      Designed forward and reverse oligos of 67bp Pcombox<br>
·      Designed forward and reverse oligos of 67bp Pcombox<br>
·      Transformation of pSB1C3-BBa_I13504<br>
·      Transformation of pSB1C3-BBa_I13504<br>
-
·      Miniprep of BBa_J04450(CHL)<br>
+
·      <br>
-
·      Transformation of BBa_J04450(KAN)<br>
+
·      <br>
-
·      Bacterial inoculation of BBa_E0240<br>
+
·      <br>
·   <br>
·   <br>
<br><b>June 25</b> <br>
<br><b>June 25</b> <br>
Line 235: Line 224:
·      Inoculation of BBa_K880005<br>
·      Inoculation of BBa_K880005<br>
·      Inoculation of pSB1C3-BBa_E0240<br>
·      Inoculation of pSB1C3-BBa_E0240<br>
-
·      Miniprep of BBa_E0240<br>
+
·      <br>
-
·      Digestion of BBa_E0240<br>
+
·      <br>
-
·      Transformation of BBa_J04450(KAN)<br>
+
·      <br>
-
·      Bacterial inoculation of BBa_J04450(CHL)<br>
+
·      <br>
·      <br>
·      <br>
·      <br>
·      <br>
Line 246: Line 235:
·      Digestion of BBa_K880005 plasmid extraction product with SpeI and PstI, gel extraction and gel purification<br>
·      Digestion of BBa_K880005 plasmid extraction product with SpeI and PstI, gel extraction and gel purification<br>
·      Digestion of pSB1C3-BBa_E0240 at XbaI and PstI<br>
·      Digestion of pSB1C3-BBa_E0240 at XbaI and PstI<br>
-
·      Gel electrophoresis of digested BBa_E0240<br>
+
·      <br>
-
·     Gel extraction and purification of digested BBa_E0240 to obtain the insert  <br>
+
·   <br>
-
·      Miniprep of BBa_J04450(CHL) <br>
+
-
·      Digestion of BBa_J04450(CHL) <br>
+
-
·      Gel electrophoresis of digested BBa_J04450(CHL)<br>
+
-
·      Gel extraction and purification of digested BBa_J04450(CHL) to obtain pSB1C3<br>
+
-
·      Bacterial inoculation of BBa_K880005<br>
+
-
 
+
<br><b>June 27</b> <br>
<br><b>June 27</b> <br>
Wet lab<br>
Wet lab<br>
Line 259: Line 242:
·      Digestion of pSB3K3-BBa_J04450 at XbaI and PstI<br>
·      Digestion of pSB3K3-BBa_J04450 at XbaI and PstI<br>
·      Gel purification of pSB1C3-BBa_E0240<br>
·      Gel purification of pSB1C3-BBa_E0240<br>
-
·     Miniprep of BBa_K880005  <br>
+
·   <br>
Line 325: Line 308:
·      Gel purification of digested BBa_E0240 and BBa_J04450<br>
·      Gel purification of digested BBa_E0240 and BBa_J04450<br>
·   Inoculation of pSB3K3-BBa_J04450<br>
·   Inoculation of pSB3K3-BBa_J04450<br>
-
·     PcomX Transformation<br>
+
·   <br>
-
·      PcomCDE Oligo annealing, ligation, transformation<br>
+
-
·      J04450 Plasmid Extraction<br>
+
-
·      E0240:Plasmid extraction (6 Falcon tubes); Nanodrop; Digestion by XbaI and SpeI, CutSmart as Buffer (only do 3 tubes); Gel electrophoresis; Gel extraction (INSERT!!! FRONT band); Gel purification<br>
+
-
·      B0015: Plasmid extraction (3 Falcon tubes); Nanodrop<br>
+
-
·      comED58E: PCR  <br>
+
·   <br>
·   <br>
·   <br>
·   <br>
Line 338: Line 316:
·      PCR of comX-myc using Vent DNA Polymerase, PCR clean up<br>
·      PCR of comX-myc using Vent DNA Polymerase, PCR clean up<br>
·      Digestion of pSB1C30-BBa_E0240 and pSB3K3-BBa_J04450 at XbaI and PstI<br>
·      Digestion of pSB1C30-BBa_E0240 and pSB3K3-BBa_J04450 at XbaI and PstI<br>
-
·      comED58E :Phusion PCR<br>
+
·      <br>
-
·      E0240: Gel purification<br>
+
·      <br>
·      <br>
·      <br>
·      <br>
·      <br>
Line 362: Line 340:
·      Submitted primers for Gibson assembly of pSB3K3-100bpPcombox<br>
·      Submitted primers for Gibson assembly of pSB3K3-100bpPcombox<br>
·      Inoculation of pSB3K3-BBa_J04450<br>
·      Inoculation of pSB3K3-BBa_J04450<br>
-
·     E0240 - Bacterial inoculation  <br>
+
·   <br>
-
·     pSB1C3-PcomX: Bacterial inoculation  <br>
+
·   <br>
-
·     pSB1C3- PcomCDE: Bacterial inoculation, Streaking  <br>
+
·   <br>
-
·      comED58E :PCR cleanup; Digestion with EcoRI and PstI; Ligation with pSB1C3; Transformation<br>
+
<br> <b> July 8</b> <br>
<br> <b> July 8</b> <br>
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·      Gel purification of digested BBa_J04450<br>
·      Gel purification of digested BBa_J04450<br>
·      Received pCEPcin from Universite de Toulouse, France<br>
·      Received pCEPcin from Universite de Toulouse, France<br>
-
·      J04450 (KAN): Digestion by EcoRI and PstI; Gel electrophoresis; Gel extraction<br>
+
·      <br>
-
·      E0240: Plasmid extraction<br>
+
-
·      pSB1C3-PcomX: Plasmid extraction<br>
+
-
·      pSB1C3- PcomCDE: Plasmid extraction<br>
+
-
·      comED58E: Bacterial inoculation; Ligation (redo); Transformation (redo)<br>
+
·      <br>
·      <br>
·   <br>
·   <br>
Line 391: Line 364:
·      PCR of 100bp Pcombox using Phusion polymerase<br>
·      PCR of 100bp Pcombox using Phusion polymerase<br>
·      Inoculation of pCEPcin<br>
·      Inoculation of pCEPcin<br>
-
·      E0240-PcomX & PcomCDE: Digestion w/ EcoRI and PstI; Gel electrophoresis<br>
+
·      <br>
-
·      J04450 (KAN): Gel purification; NanoDrop (low conc)<br>
+
-
·      comED58E:Plasmid extraction; NanoDrop; Gel electrophoresis (not comE); Bacterial inoculation (redo)<br>
+
·      <br>
·      <br>
·   <br>
·   <br>
Line 1,393: Line 1,364:
<br><b>June 2</b> <br>
<br><b>June 2</b> <br>
Wet lab<br>
Wet lab<br>
-
·      Restrcition digestion of ligated pSB3K3-160Pcombox-BBa_E0240<br>
 
·      <br>
·      <br>
·      <br>
·      <br>
Line 1,603: Line 1,573:
<br> <b> July 7 </b> <br>
<br> <b> July 7 </b> <br>
Wet lab<br>
Wet lab<br>
-
· Oligos phosphorilation <br>
+
·     <br>
-
· Ligation of TAs and CRs <br>
+
·     <br>
-
· Colony PCR <br>
+
·     <br>
-
· Digest Receptor Backbone pSB1C3<br>
+
·   <br>
-
. Agar-LB plates<br>
+
-
. Inoculation for transformded BioBricks<br>
+
-
. Primer Design for TA construct Gibson Assembly<br>
+
-
. Gel check for the colony PCR<br>
+
-
. P<sub>bad</sub> PCR amplification<br>
+
<br> <b> July 8 </b> <br>
<br> <b> July 8 </b> <br>
Wet lab<br>
Wet lab<br>
-
· Transformation of ligated TAs and CRs<br>
+
·     <br>
-
· Miniprep previous TAs CRs constructs <br>
+
·     <br>
-
· Restrict check previous TAs CRs constructs <br>
+
·     <br>
-
· Colony PCR for CRs and TAs<br>
+
·   <br>
-
. Re-ligation of TAs and CRs<br>
+
-
. P<sub>bad</sub> PCR clean up and Digestion <br>
+
-
. Ligation of P<sub>bad</sub> with pSB1C3<br>
+
-
. Sequencing preparation of P<sub>bad</sub><br>
+
-
 
+
<br> <b> July 9</b> <br>
<br> <b> July 9</b> <br>
Wet lab<br>
Wet lab<br>
-
· Transformation of Re-ligated TAs and CRs<br>
+
·     <br>
-
· Colony PCR<br>
+
·     <br>
-
· Gibson assembly master mix preparation<br>
+
·     <br>
-
 
+
·   <br>
<br> <b> July 10</b> <br>
<br> <b> July 10</b> <br>
Wet lab<br>
Wet lab<br>
-
· Sequencing preparation of P<sub>bad</sub><br>
+
·     <br>
-
· Miniprep previous TAs CRs constructs <br>
+
·     <br>
-
· Restrict check previous TAs CRs constructs <br>
+
·     <br>
-
· Colony PCR<br>
+
·   <br>
-
. Inoculation for glycerol stocks <br>
+
-
. Digest Receptor Backbone , digestion of BBa_ E0240 with EcoR1-HF and Xbal and gel purification <br>
+
-
 
+
<br> <b> July 11</b> <br>
<br> <b> July 11</b> <br>
Wet lab<br>
Wet lab<br>
-
· Pbad digestion and gel purification, Digestion of PBAD-pSB1C3 with EcoR1-HF and Spe1 and gel purification <br>
+
·     <br>
-
· Ligation of pBAD and E0240<br>
+
·     <br>
-
· Overlaping  PCR design<br>
+
·     <br>
-
· Gibson assembly master mix preparation<br>
+
·   <br>
-
. Glycerol stock<br>
+
-
. Competent cells preparations for  DH5a and DH10B<br>
+
-
. Run gel for yesterday's restriction check<br>
+
-
. Miniprep  E0240, mRFP, B0015<br>
+
-
. Colony PCR<br>
+
-
. One full set re-ligation (short time) <br>
+
-
. Miniprep I13401 and K592009<br>
+
       </div>
       </div>
   </div>
   </div>
Line 1,661: Line 1,611:
<br> <b> July 14 </b> <br>
<br> <b> July 14 </b> <br>
Wet lab<br>
Wet lab<br>
-
. Gibson assembly master mix preparation<br>
+
·      <br>
-
. Trevor's PCR<br>
+
·      <br>
-
. Ligation of pBAD an E0240<br>
+
·      <br>
-
. Competent cells preparations for  DH5a and DH10B<br>
+
·   <br>
-
. Prepare receptor backbone for oligo anealing, pSB1C3-J04450 (EcoRI, SpeI)<br>
+
 
-
. One full set of re-ligation (short time) <br>
+
-
. One full set of re-ligation (O/N) <br>
+
-
. Preparations for Pbad re-Characterization <br>
+
<br> <b> July 15 </b> <br>
<br> <b> July 15 </b> <br>
Wet lab<br>
Wet lab<br>
-
· Inoculation for pBAD-GFP-TT<br>
+
·     <br>
-
· (2nd time) Colony PCR usning VF2 and VR<br>
+
·     <br>
-
· Design primer for pBAD promoter sequencing <br>
+
·     <br>
-
· Gibson assembly master mix preparation<br>
+
·   <br>
-
. Preparations for Pbad re-characterization <br>
+
-
. Competent cells preparations for  DH5a and DH10B<br>
+
-
. One full set re-ligation (O/N) <br>
+
-
. Prepare receptor backbone for oligo anealing <br>
+
<br> <b> July 16</b> <br>
<br> <b> July 16</b> <br>
Wet lab<br>
Wet lab<br>
-
· Gibson assembly master mix preparation<br>
+
·     <br>
-
· Preparations for Pbad re-characterization <br>
+
·     <br>
-
· Competent cells preparations for  DH5a and DH10B<br>
+
·     <br>
-
· Prepare receptor backbone for oligo anealing <br>
+
·   <br>
-
· Innoculate succesful oligo annealing colonies<br>
+
-
· Oligo annealing products C. PCR<br>
+
-
 
+
<br> <b> July 17</b> <br>
<br> <b> July 17</b> <br>
Wet lab<br>
Wet lab<br>
-
· Gibson assembly master mix preparation<br>
+
·     <br>
-
· Pbad re-characterization <br>
+
·     <br>
-
· Miniprep CRs TAs<br>
+
·     <br>
-
· Restric check CRs,TAs<br>
+
·   <br>
-
. Oligo annealing products C. PCR<br>
+
-
. Prepare receptor backbone for oligo anealing <br>
+
-
. Restrict CRs plasmids for GFP.dTT<br>
+
-
. Restrict TAs plasmids for dTT<br>
+
-
. Restrict GFP.dTT for CRs<br>
+
-
. Restrict dTT for TAs<br>
+
-
. Ligate CR.GFP.dTT<br>
+
-
. Ligate TA.dTT<br>
+
-
. Transform Ligated CR.GFP.dTT<br>
+
-
. Transform Ligated TA.dTT<br>
+
-
. Transform-Ligate Annealed oligos<br>
+
-
 
+
<br> <b> July 18</b> <br>
<br> <b> July 18</b> <br>
Wet lab<br>
Wet lab<br>
-
· Gibson assembly for amilCP<br>
+
·     <br>
-
· Pbad re-characterization <br>
+
·     <br>
-
· Colony PCR <br>
+
·     <br>
-
· Prepare receptor backbone for oligo anealing <br>
+
·   <br>
-
· Restrict GFP.dTT for CRs<br>
+
-
· Restrict dTT for TAs<br>
+
-
· M9 mininaml medium preparation<br>
+
-
· Colony PCR <br>
+
-
· plate streaking for pBAD-E0240<br>
+
-
· inoculation of TAs and CRs<br>
+
-
 
+
-
<br> <b> July 19</b> <br>
+
-
Wet lab<br>
+
-
. Pbad re-characterization <br>
+
       </div>
       </div>
   </div>
   </div>
Line 1,731: Line 1,649:
<br> <b> July 21 </b> <br>
<br> <b> July 21 </b> <br>
Wet lab<br>
Wet lab<br>
-
· Gibson assembly for amilCP<br>
+
·     <br>
-
. Miniprep CRs TAs<br>
+
·      <br>
-
. Restrict check pSB1C3-TAs/CRs constructs <br>
+
·      <br>
-
. Restrict GFP.dTT for CRs<br>
+
·   <br>
-
. Restrict Pbad for TAs<br>
+
-
. Restrict B0015 EcoR1 and XbaI<br>
+
-
. J04450 backbone extraction <br>
+
-
. Colony PCR <br>
+
-
. inoculation of TAs and CRs<br>
+
-
. prepare Pbad L(+) A. concentration gradients for characterization <br>
+
-
. Restrict CRs<br>
+
-
. Restrict TAs-Version1<br>
+
-
. Restrict TAs-Version2<br>
+
-
. Ligate CR.GFP.dTT<br>
+
-
. Ligate TA.dTT<br>
+
-
. Transform Pbad.TA<br>
+
-
. Transform CR.GFP.dTT<br>
+
-
. Transform Gibson assembly <br>
+
-
 
+
<br> <b> July 22 </b> <br>
<br> <b> July 22 </b> <br>
Wet lab<br>
Wet lab<br>
-
· Colony PCR <br>
+
·     <br>
-
. Miniprep CRs TAs <br>
+
·      <br>
-
. Restrict check pSB1C3-TAs/CRs constructs <br>
+
·      <br>
-
. Restrict B0015-Version2<br>
+
·   <br>
<br> <b> July 23</b> <br>
<br> <b> July 23</b> <br>
Wet lab<br>
Wet lab<br>
-
· Inoculation candidate colony or construct <br>
+
·     <br>
-
. Miniprep and restrict check innoculations<br>
+
·      <br>
-
. Gibson assembly check<br>
+
·      <br>
-
. Gibson PCR<br>
+
·   <br>
-
. Teach inoue competent cells to main project<br>
+
-
. Miniprep of B0015, pBAD-E0240<br>
+
-
. glycerol stock (pBAD-E0240)<br>
+
-
. Re-Re-ligation of oligo annealing O/N <br>
+
<br> <b> July 24</b> <br>
<br> <b> July 24</b> <br>
Wet lab<br>
Wet lab<br>
-
· miniprep candidate colony or construct <br>
+
·     <br>
-
. Restrict check pSB1C3-TAs/CRs constructs<br>  
+
·      <br>
-
. Re-Re-ligation trasnformation<br>
+
·      <br>
-
. Re-Re-ligation trasnformation V.X<br>
+
·   <br>
-
. Gibson assembly check<br>
+
<br> <b> July 25</b> <br>
<br> <b> July 25</b> <br>
Wet lab<br>
Wet lab<br>
-
· Certification day (safety evaluation)<br>
+
·     <br>
·      <br>
·      <br>
·      <br>
·      <br>
Line 2,195: Line 2,093:
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Revision as of 17:58, 10 October 2014




Notebook

Throughout the course of our project, we have continuously recorded our daily work, such as wetlab activities and research findings. The notebook for Pneuumonsensor and Riboregulator are displayed separately.






Pneumosensor

June 2014

Week 1
Week 2
Week 3
Week 4
Week 5

July 2014

Week 1
Week 2
Week 3
Week 4
Week 5

August 2014

Week 1
Week 2
Week 3
Week 4
Week 5

September 2014

Week 1
Week 2
Week 3
Week 4
Week 5





Riboregulator

June 2014

Week 1
Week 2
Week 3
Week 4
Week 5

July 2014

Week 1
Week 2
Week 3
Week 4
Week 5

August 2014

Week 1
Week 2
Week 3
Week 4
Week 5

September 2014

Week 1
Week 2
Week 3
Week 4
Week 5

Home

Pneumosensor

Riboregulator

Human Practice

Team

WetLab

Achievement