Team:Hong Kong HKUST/wetlab/notebook

From 2014.igem.org

(Difference between revisions)

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 <!---- 		SSSSSSSS   EEEEEEEE   P               T         EEEEEEEE   M         M   BBBBBBBB    EEEEEEEEE   R   	R	 2 0 1 3-------->
-<div id="satu" align="center"> <h2>September 2013</h2>
+<div id="satu" align="center"> <h2>September 2014</h2>
 	<div>
        <a href="#" class="head">Week 1</a>
        <div class="content" align="left" style="display: none;">
-<br><b>Sept xx</b> <br>
+<br><b>Sept 1</b> <br>
 Wet lab<br>
+·      Digestion check of pSB1C3-K880005.comW-FLAG.B0015 on XbaI and PstI-HF<br>
+·      Digestion check of pSB1C3-K880005.comX-myc.B0015.Combox.GFP on XmnI<br>
+·      Inoculation of pSB1C3-K880005.comX-myc.B0015.Combox.GFP<br>
+·      <br>
+·      <br>
+·      <br>
 ·      <br>
 ·      <br>
@@ Line 850: / Line 856: @@
 · 	   <br>
-<br><b>Sept xx</b> <br>
+<br><b>Sept 2</b> <br>
 Wet lab<br>
+·      Ligation of pSB1C3-K880005.comX-myc.B0015.Combox.GFP cut on EcoRI-HF and PstI-HF into pSB3K3 cut on EcoRI-HF and PstI-HF<br>
+·      Re-digestion of pSB1C3-K880005.comX-myc.B0015.Combox.GFP on EcoRI-HF and PstI-HF, gel extraction and gel purification<br>
+·      <br>
+·      <br>
+·      <br>
+·      <br>
 ·      <br>
 ·      <br>
@@ Line 857: / Line 869: @@
 · 	   <br>
-<br><b>Sept xx</b> <br>
+<br><b>Sept 3</b> <br>
 Wet lab<br>
+·      Streak plate for pSB1C3-K880005.comX-myc.B0015.Combox.GFP<br>
+·      Inoculation of pSB1C3-K880005.comW-FLAG.B0015<br>
+·      <br>
+·      <br>
+·      <br>
+·      <br>
 ·      <br>
 ·      <br>
@@ Line 864: / Line 882: @@
 · 	   <br>
-<br><b>Sept xx</b> <br>
+<br><b>Sept 4</b> <br>
 Wet lab<br>
+·      Digestion check of pSB1C3-K880005.comW-FLAG on XbaI and PstI-HF, gel extraction and gel purification<br>
+·      Restriction of Combox + GFP on EcoRI-HF and PstI-HF, gel extraction and gel purification<br>
+·      Ligation of Combox + GFP into pSB3K3 backbone cut on EcoRI-HF and PstI-HF<br>
+·      Transformation of pSB3K3-Combox.GFP ligation product<br>
+·      <br>
+·      <br>
 ·      <br>
 ·      <br>
@@ Line 871: / Line 895: @@
 · 	   <br>
-<br><b>Sept xx</b> <br>
+<br><b>Sept 5</b> <br>
 Wet lab<br>
+·      Inoculation of pSB3K3-Combox.GFP<br>
+·      <br>
+·      <br>
+·      <br>
+·      <br>
+·      <br>
 ·      <br>
 ·      <br>
@@ Line 884: / Line 914: @@
        <a href="#" class="head">Week 2</a>
        <div class="content" align="left" style="display: none;">
-<br><b>Sept xx</b> <br>
+<br><b>Sept 8</b> <br>
 Wet lab<br>
+·      Digestion check of pSB3K3-Combox.GFP on XmnI<br>
+·      <br>
+·      <br>
+·      <br>
+·      <br>
+·      <br>
 ·      <br>
 ·      <br>
@@ Line 892: / Line 928: @@
-<br><b>Sept xx</b> <br>
+<br><b>Sept 9</b> <br>
 Wet lab<br>
+·      <br>
+·      <br>
+·      <br>
+·      <br>
+·      <br>
+·      <br>
 ·      <br>
 ·      <br>
@@ Line 899: / Line 941: @@
 · 	   <br>
-<br><b>Sept xx</b> <br>
+<br><b>Sept 10</b> <br>
 Wet lab<br>
+·      Streak plate for pSB3K3-Combox.GFP<br>
+·      <br>
+·      <br>
+·      <br>
+·      <br>
+·      <br>
 ·      <br>
 ·      <br>
@@ Line 906: / Line 954: @@
 · 	   <br>
-<br><b>Sept xx</b> <br>
+<br><b>Sept 11</b> <br>
 Wet lab<br>
+·      <br>
+·      <br>
+·      <br>
+·      <br>
+·      <br>
+·      <br>
 ·      <br>
 ·      <br>
@@ Line 913: / Line 967: @@
 · 	   <br>
-<br><b>Sept xx</b> <br>
+<br><b>Sept 12</b> <br>
 Wet lab<br>
+·      <br>
+·      <br>
+·      <br>
+·      <br>
+·      <br>
+·      <br>
 ·      <br>
 ·      <br>
@@ Line 924: / Line 984: @@
        <a href="#" class="head">Week 3</a>
        <div class="content" align="left" style="display: none;">
-<br><b>Sept xx</b> <br>
+<br><b>Sept 15</b> <br>
 Wet lab<br>
+·      Inoculation of pSB1C3-K880005.comW-FLAG<br>
+·      <br>
+·      <br>
+·      <br>
+·      <br>
+·      <br>
 ·      <br>
 ·      <br>
@@ Line 932: / Line 998: @@
-<br><b>Sept xx</b> <br>
+<br><b>Sept 16</b> <br>
 Wet lab<br>
+·      Digestion of pSB1C3-K880005.comW-FLAG on EcoRI-HF and SpeI<br>
+·      <br>
+·      <br>
+·      <br>
+·      <br>
+·      <br>
 ·      <br>
 ·      <br>
@@ Line 939: / Line 1,011: @@
 · 	   <br>
-<br><b>Sept xx</b> <br>
+<br><b>Sept 17</b> <br>
 Wet lab<br>
+·      Digestion of pSB1C3-K880005.comW-FLAG on XbaI and PstI<br>
+·      Ligation of pSB1C3-K880005.comW-FLAG cut on EcoRI-HF and SpeI into pSB1C3-B0015 cut on EcoRI-HF and XbaI<br>
+·      Digestion check of  pSB1C3-K880005.comX-myc.B0015 on XbaI and PstI<br>
+·      Digestion check of pSB1C3-K880005.comX-myc.B0015.Combox on XmnI<br>
+·      Digestion check of Combox + GFP on XmnI and PstI<br>
+·      <br>
 ·      <br>
 ·      <br>
@@ Line 946: / Line 1,024: @@
 · 	   <br>
-<br><b>Sept xx</b> <br>
+<br><b>Sept 18</b> <br>
 Wet lab<br>
+·      Ligation of comX-myc into pSB1C3 cut on XbaI and PstI<br>
+·      Inoculation of pSB1C3-K880005.comW-FLAG.B0015<br>
+·      <br>
+·      <br>
+·      <br>
+·      <br>
 ·      <br>
 ·      <br>
@@ Line 953: / Line 1,037: @@
 · 	   <br>
-<br><b>Sept xx</b> <br>
+<br><b>Sept 19</b> <br>
 Wet lab<br>
+·      Digestion check of pSB1C3-K880005.comW-FLAG.B0015 on XbaI and PstI<br>
+·      <br>
+·      <br>
+·      <br>
+·      <br>
+·      <br>
 ·      <br>
 ·      <br>
@@ Line 966: / Line 1,056: @@
        <a href="#" class="head">Week 4</a>
        <div class="content" align="left" style="display: none;">
-<br><b>Sept xx</b> <br>
+<br><b>Sept 22</b> <br>
 Wet lab<br>
+·      Digestion check of pSB1C3-K880005.comX-myc.B0015 on XbaI and PstI<br>
+·      Inoculation of pSB1C3-K880005.comW-FLAG.B0015<br>
+·      <br>
+·      <br>
+·      <br>
 ·      <br>
 ·      <br>
@@ Line 973: / Line 1,068: @@
 · 	   <br>
-<br><b>Sept xx</b> <br>
+<br><b>Sept 23</b> <br>
 Wet lab<br>
+·      Digestion of pSB1C3-K880005.comW-FLAG.B0015 of EcoRI-HF and SpeI-HF<br>
+·      Digestion of pSB1C3-K880005.comX-myc.B0015 and pSB1C3-K880005.comX on EcoRI-HF and SpeI-HF, gel extraction and gel purification<br>
+·      Ligation of pSB1C3-K880005.comX into pSB1C3-B0015 cut on EcoRI-HF and XbaI<br>
+·      <br>
+·      <br>
+·      <br>
 ·      <br>
 ·      <br>
@@ Line 980: / Line 1,081: @@
 · 	   <br>
-<br><b>Sept xx</b> <br>
+<br><b>Sept 24</b> <br>
 Wet lab<br>
+·      Digestion check of pSB1C3-K880005.comX.B0015 on XbaI and PstI, gel extraction and gel purification<br>
+·      <br>
+·      <br>
+·      <br>
+·      <br>
+·      <br>
 ·      <br>
 ·      <br>
@@ Line 987: / Line 1,094: @@
 · 	   <br>
-<br><b>Sept xx</b> <br>
+<br><b>Sept 25</b> <br>
 Wet lab<br>
+·      <br>
+·      <br>
+·      <br>
+·      <br>
+·      <br>
+·      <br>
 ·      <br>
 ·      <br>
@@ Line 994: / Line 1,107: @@
 · 	   <br>
-<br><b>Sept xx</b> <br>
+<br><b>Sept 26</b> <br>
 Wet lab<br>
+·      <br>
+·      <br>
+·      <br>
+·      <br>
+·      <br>
+·      <br>
 ·      <br>
 ·      <br>
@@ Line 1,007: / Line 1,126: @@
        <a href="#" class="head">Week 5</a>
        <div class="content" align="left" style="display: none;">
-<br><b>Sept xx</b> <br>
+<br><b>Sept 29</b> <br>
 Wet lab<br>
+·      <br>
+·      <br>
+·      <br>
+·      <br>
+·      <br>
+·      <br>
 ·      <br>
 ·      <br>
@@ Line 1,015: / Line 1,140: @@
-<br><b>Sept xx</b> <br>
+<br><b>Sept 30</b> <br>
 Wet lab<br>
+·      Digestion of  RBS+comX-myc+B0015 on XbaI and PstI<br>
+·      <br>
+·      <br>
+·      <br>
+·      <br>
+·      <br>
 ·      <br>
 ·      <br>
@@ Line 1,024: / Line 1,155: @@
 <br><b>Sept xx</b> <br>
 Wet lab<br>
+·      <br>
+·      <br>
+·      <br>
+·      <br>
+·      <br>
+·      <br>
 ·      <br>
 ·      <br>
@@ Line 1,031: / Line 1,168: @@
 <br><b>Sept xx</b> <br>
 Wet lab<br>
+·      <br>
+·      <br>
+·      <br>
+·      <br>
+·      <br>
+·      <br>
 ·      <br>
 ·      <br>
@@ Line 1,038: / Line 1,181: @@
 <br><b>Sept xx</b> <br>
 Wet lab<br>
+·      <br>
+·      <br>
+·      <br>
+·      <br>
+·      <br>
+·      <br>
 ·      <br>
 ·      <br>

Revision as of 15:38, 6 October 2014

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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

June xx
Wet lab
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June xx
Wet lab
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June xx
Wet lab
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June xx
Wet lab
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Week 2

June xx
Wet lab
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June xx
Wet lab
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June xx
Wet lab
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June xx
Wet lab
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Week 3

June xx
Wet lab
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June xx
Wet lab
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June xx
Wet lab
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June xx
Wet lab
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Week 4

June 23
Wet lab
· Transformation of BBa_B0015 from iGEM Kit Plate 2011 and BBa_K880005
· Primer design for PCR of comX-myc and comW-FLAG from genomic DNA of S. Pneumoniae NCTC 7465 strain
·
·
·
·
·
·

June 24
Wet lab
· Inoculation of BBa_B0015
·
·
·
·
·
·
·

June 25
Wet lab
· Digestion of BBa_B0015 plasmid extraction product with XbaI and PstI, gel extraction and gel purification
· Inoculation of BBa_K880005
·
·
·
·
·
·
·
·

June 26
Wet lab
· Digestion of BBa_K880005 plasmid extraction product with SpeI and PstI, gel extraction and gel purification
·
·
·

June 27
Wet lab
· Ligation of BBa_B0015 insert cut with XbaI and PstI into pSB1C3-K880005 backbone cut with SpeI and PstI as negative control
·
·
·

Week 5

June 30
Wet lab
· Digestion of BBa_B0015 plasmid extraction product with XbaI and PstI, gel extraction and gel purification
· Gel check of purified BBa_B0015 insert
· Transformation of ligated pSB1C3-K880005.B0015
·
·
·
·
·
·
·

July 2014

Week 1

July 2
Wet lab
· Arrival of primers order for comX-myc and comW-FLAG
· Dilution of primers and design of experiment for both comX-myc and comW-FLAG
· Inoculation of ligated pSB1C3-K880005.B0015
·
·
·

July 3
Wet lab
· PCR of comX-myc using Taq DNA Polymerase with ThermoPol Buffer to check whether primers are functional
· Gel check for comX-myc PCR product (PCR product present)
· PCR of comX-myc using Phusion High-Fidelity PCR Master Mix with HF Buffer
· Gel check for comX-myc PCR product (no PCR product present)
· Restriction digestion check on some candidate colonies of ligated pSB1C3-K880005.B0015 with XbaI and PstI
·
·
·
·

July 4
Wet lab
· PCR of comX-myc using Vent DNA Polymerase, PCR clean up
·
·
·
·
·
·
·
·

July 5
Wet lab
·
·
·
·
·
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·
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·

July 6
Wet lab
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·
·
·
·
·
·
·
·

Week 2

July 7
Wet lab
· Digestion of comX-myc with XbaI and PstI
· Gel check of digested comX-myc, digestion clean up
· PCR of comW-FLAG using Vent DNA Polymerase
· Gel check for comW-FLAG PCR product, PCR clean up
· Dephosporylation of digested pSB1C3-K880005 backbone cut with SpeI and PstI
·
·
·
·

July 8
Wet lab
· Ligation of comX-myc cut with XbaI and PstI into pSB1C3-K880005 backbone cut with SpeI and PstI
· 2nd attempt of ligation of BBa_B0015 insert cut with XbaI and PstI into dephosporylated pSB1C3-K880005 backbone cut with SpeI and PstI as negative control
· Transformation of ligation products
·
·
·
·
·
·

July 9
Wet lab
· Inoculation of ligated pSB1C3-K880005.B0015 (2nd attempt) and ligated pSB1C3-K880005.comX-myc
·
·
·
·
·
·
·
·

July 10
Wet lab
· Another PCR of comW-FLAG using Vent DNA Polymerase
· Gel check for comW-FLAG PCR product, PCR clean up
· Restriction digestion check on some candidate colonies of ligated pSB1C3-K880005.B0015 (2nd attempt) and ligated pSB1C3-K880005.comX-myc
· Gel check and insert wanted present in several candidate colonies of ligated pSB1C3-K880005.B0015 (2nd attempt), but no insert wanted present in any candidate colonies of ligated pSB1C3-K880005.comX-myc
·
·
·
·

July 11
Wet lab
· Digestion of comW-FLAG with XbaI and PstI, digestion clean up
·
·
·
·
·
·
·

Week 3

July 14
Wet lab
· Ligation of comW-FLAG cut on XbaI and PstI into dephosporylated pSB1C3-K880005 backbone cut on SpeI and PstI
· Transformation of ligation products
· Inoculation of ligated dephosporylated pSB1C3-K880005.comX-myc
·
·
·
·
·
·

July 15
Wet lab
· Digestion check of ligated pSB1C3-K880005.comX-myc
· Digestion of pSB1C3-K880005.comX-myc on SpeI and PstI, but no insert wanted present
· PCR of comX using Vent DNA Polymerase, PCR clean-up
· Colony PCR of pSB1C3-K880005.comX-myc using Taq DNA Polymerase
· Gel check of pSB1C3-K880005.comX-myc PCR product (no PCR product present)
· Inoculation of dephosporylated pSB1C3-K880005.comX-myc, dephosporylated pSB1C3-K880005.comW-FLAG
·
·
·

July 16
Wet lab
· Digestion check of ligated pSB1C3-K880005.comW-FLAG
· Colony PCR of pSB1C3-K880005.comW-FLAG
· Gel check of pSB1C3-K880005.comW-FLAG PCR product (no PCR product present)
· PCR of comW using Vent DNA Polymerase (no PCR product present)
· Digestion of comX on XbaI and PstI
·
·
·
·

July 17
Wet lab
· PCR of comX-myc and comX using Vent DNA Polymerase
· Gel check of comX-myc and comX PCR product, PCR clean-up
· PCR of comW using Vent DNA Polymerase
· Gel extraction and gel purification of comW PCR product
· Dephosporylation of BBa_K880005
·
·
·
·

July 18
Wet lab
· PCR of comX using Vent DNA Polymerase
· Gel check of comX PCR product, PCR clean-up
· Digestion of comX PCR product on XbaI and PstI, digestion clean-up
· Digestion of comX-myc and comW PCR products, digestion clean-up
· Gel extraction and gel purification of digested comX and comX-myc
·
·
·

Week 4

July 21
Wet lab
· Gel purification of comX and comX-myc
· Ligation of comX-myc into dephosporylated pSB1C3-K880005 backbone with 1:4, 1:7, 1:10 ratio
· Ligation of comW-FLAG into dephosporylated pSB1C3-K880005 backbone with 1:4, 1:7, 1:10 ratio
· Ligation of comX into dephosporylated pSB1C3-K880005 backbone with 1:3 and 1:5 ratio
· Ligation of comW into dephosporylated pSB1C3-K880005 backbone with 1:4, 1:7, 1:10 ratio
· Colony PCR of pSB1C3-K880005.comW-FLAG using Taq DNA Polymerase
·
·
·

July 22
Wet lab
· Colony PCR of comX, comW, comX-myc, comW-FLAG and use BBa_J04450 as the positive control using Taq DNA Polymerase (no PCR product present)
· Inoculation of comX, comW, comX-myc, comW-FLAG
·
·
·
·
·
·
·

July 23
Wet lab
· Digestion check of comX, comW, comX-myc, comW-FLAG colony PCR products on XbaI and SpeI
· Inoculation of comW-FLAG
·
·
·
·
·
·
·

July 24
Wet lab
· Digestion check of pSB1C3-K880005.comW-FLAG on XbaI and SpeI-HF
· Ligation of comW-FLAG into dephosporylated pSB1C3-K880005 backbone
· Ligation of comX-myc into dephosporylated pSB1C3-K880005 backbone
· PCR of comX-myc and comX using Vent DNA Polymerase, gel extraction and gel purification
· Digestion of comX-myc and comX on XbaI and PstI-HF
·
·
·
·

July 25
Wet lab
· Colony PCR of comX-myc using Taq DNA Polymerase
· Gel check of comX-myc PCR product (no PCR product present)
·
·
·
·
·
·
·

Week 5

July 28
Wet lab
· Colony PCR of comX-myc using Taq DNA Polymerase
· Colony PCR of comw-FLAG using Taq DNA Polymerase
· Inoculation of comX-myc and comW-FLAG
·
·
·
·

July 29
Wet lab
· Digestion check of comX-myc and comW-FLAG on XbaI and PstI-HF
· Transformation of comX-myc and comW-FLAG
·
·
·
·
·

July 30
Wet lab
· Digestion check of comX-myc and comW-FLAG
· Inoculation of comX-myc and comW-FLAG
· Streaking plates of comX-myc and comW-FLAG
·
·
·
·

July 31
Wet lab
· Digestion check of comX-myc and comW-FLAG on XbaI and PstI-HF
· Redigest comW-FLAG on XmnI and NcoI
· PCR sequencing for comW and comX
· Ethanol precipitation for comW and comX
·
·
·

August 2014

Week 1

Aug xx
Wet lab
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Aug xx
Wet lab
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Aug xx
Wet lab
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Aug xx
Wet lab
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Week 2

Aug xx
Wet lab
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Aug xx
Wet lab
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Aug xx
Wet lab
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Aug xx
Wet lab
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Week 3

Aug xx
Wet lab
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Aug xx
Wet lab
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Aug xx
Wet lab
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Aug xx
Wet lab
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Week 4

Aug xx
Wet lab
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Aug xx
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Aug xx
Wet lab
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Aug xx
Wet lab
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September 2014

Week 1

Sept 1
Wet lab
· Digestion check of pSB1C3-K880005.comW-FLAG.B0015 on XbaI and PstI-HF
· Digestion check of pSB1C3-K880005.comX-myc.B0015.Combox.GFP on XmnI
· Inoculation of pSB1C3-K880005.comX-myc.B0015.Combox.GFP
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Sept 2
Wet lab
· Ligation of pSB1C3-K880005.comX-myc.B0015.Combox.GFP cut on EcoRI-HF and PstI-HF into pSB3K3 cut on EcoRI-HF and PstI-HF
· Re-digestion of pSB1C3-K880005.comX-myc.B0015.Combox.GFP on EcoRI-HF and PstI-HF, gel extraction and gel purification
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Sept 3
Wet lab
· Streak plate for pSB1C3-K880005.comX-myc.B0015.Combox.GFP
· Inoculation of pSB1C3-K880005.comW-FLAG.B0015
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Sept 4
Wet lab
· Digestion check of pSB1C3-K880005.comW-FLAG on XbaI and PstI-HF, gel extraction and gel purification
· Restriction of Combox + GFP on EcoRI-HF and PstI-HF, gel extraction and gel purification
· Ligation of Combox + GFP into pSB3K3 backbone cut on EcoRI-HF and PstI-HF
· Transformation of pSB3K3-Combox.GFP ligation product
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Sept 5
Wet lab
· Inoculation of pSB3K3-Combox.GFP
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Week 2

Sept 8
Wet lab
· Digestion check of pSB3K3-Combox.GFP on XmnI
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Sept 9
Wet lab
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Sept 10
Wet lab
· Streak plate for pSB3K3-Combox.GFP
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Sept 11
Wet lab
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Sept 12
Wet lab
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Week 3

Sept 15
Wet lab
· Inoculation of pSB1C3-K880005.comW-FLAG
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Sept 16
Wet lab
· Digestion of pSB1C3-K880005.comW-FLAG on EcoRI-HF and SpeI
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Sept 17
Wet lab
· Digestion of pSB1C3-K880005.comW-FLAG on XbaI and PstI
· Ligation of pSB1C3-K880005.comW-FLAG cut on EcoRI-HF and SpeI into pSB1C3-B0015 cut on EcoRI-HF and XbaI
· Digestion check of pSB1C3-K880005.comX-myc.B0015 on XbaI and PstI
· Digestion check of pSB1C3-K880005.comX-myc.B0015.Combox on XmnI
· Digestion check of Combox + GFP on XmnI and PstI
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Sept 18
Wet lab
· Ligation of comX-myc into pSB1C3 cut on XbaI and PstI
· Inoculation of pSB1C3-K880005.comW-FLAG.B0015
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Sept 19
Wet lab
· Digestion check of pSB1C3-K880005.comW-FLAG.B0015 on XbaI and PstI
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Week 4

Sept 22
Wet lab
· Digestion check of pSB1C3-K880005.comX-myc.B0015 on XbaI and PstI
· Inoculation of pSB1C3-K880005.comW-FLAG.B0015
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Sept 23
Wet lab
· Digestion of pSB1C3-K880005.comW-FLAG.B0015 of EcoRI-HF and SpeI-HF
· Digestion of pSB1C3-K880005.comX-myc.B0015 and pSB1C3-K880005.comX on EcoRI-HF and SpeI-HF, gel extraction and gel purification
· Ligation of pSB1C3-K880005.comX into pSB1C3-B0015 cut on EcoRI-HF and XbaI
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Sept 24
Wet lab
· Digestion check of pSB1C3-K880005.comX.B0015 on XbaI and PstI, gel extraction and gel purification
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Sept 25
Wet lab
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Sept 26
Wet lab
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Week 5

Sept 29
Wet lab
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Sept 30
Wet lab
· Digestion of RBS+comX-myc+B0015 on XbaI and PstI
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Riboregulator

June 2013

Week 1

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July 2013

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August 2013

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Week 3

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Week 5

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September 2013

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Week 5

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