Difference between revisions of "Team:Aalto-Helsinki/LabBook"

m (week5)
m (table lines added to first column)
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   </tr>
 
   </tr>
 
   <tr>
 
   <tr>
−
         <td class="first rightline"><div class="heightdiv"><h3>Preparations <br/> <span style="font-size:20px">Plates</span></h3></div></td>
+
         <td class="first rightline"><div class="heightdiv bottomline"><h3>Preparations <br/> <span style="font-size:20px">Plates</span></h3></div></td>
 
         <td class="white arrow" >
 
         <td class="white arrow" >
 
             <p>Making Cm <br/>plates</p>
 
             <p>Making Cm <br/>plates</p>
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   </tr>
 
   </tr>
 
   <tr>
 
   <tr>
−
         <td class="first rightline"><div class="heightdiv"><h3></h3></div></td>
+
         <td class="first rightline"><div class="heightdiv bottomline"><h3></h3></div></td>
 
         <td class="white arrow" >
 
         <td class="white arrow" >
 
             <p>o/n culture <br/> of E. coli <br/> BL21(DE3)</p>
 
             <p>o/n culture <br/> of E. coli <br/> BL21(DE3)</p>
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   </tr>
 
   </tr>
 
   <tr>
 
   <tr>
−
<td class="first rightline"><div class="heightdiv"><h3></h3></div></td>
+
<td class="first rightline"><div class="heightdiv bottomline"><h3></h3></div></td>
 
         <td>
 
         <td>
 
         </td>
 
         </td>
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   </tr>
 
   </tr>
 
<tr>
 
<tr>
−
         <td class="first rightline"><div class="heightdiv"><h3></h3></div></td>
+
         <td class="first rightline"><div class="heightdiv bottomline"><h3></h3></div></td>
 
          
 
          
 
         <td>
 
         <td>
Line 464: Line 464:
 
   </tr>
 
   </tr>
 
   <tr>
 
   <tr>
−
         <td class="first rightline"><div class="heightdiv"><h3>Preparations <br/><span style="font-size:20px">Propagating</span></h3></div></td>
+
         <td class="first rightline"><div class="heightdiv bottomline"><h3>Preparations <br/><span style="font-size:20px">Propagating</span></h3></div></td>
 
         <td class="white arrow" >
 
         <td class="white arrow" >
 
             <p style="font-size:13px;">Transform <br/>&nbsp;&nbsp;&nbsp; AH020 & AH021 <br/> into TOP10</p>
 
             <p style="font-size:13px;">Transform <br/>&nbsp;&nbsp;&nbsp; AH020 & AH021 <br/> into TOP10</p>
Line 522: Line 522:
 
   </tr>
 
   </tr>
 
   <tr>
 
   <tr>
−
         <td class="first rightline"><div class="heightdiv"><h3>Preparations <br/><span style="font-size:20px">Propagating</span></h3></div></td>
+
         <td class="first rightline"><div class="heightdiv bottomline"><h3>Preparations <br/><span style="font-size:20px">Propagating</span></h3></div></td>
  
 
         <td class="white arrow" >
 
         <td class="white arrow" >
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         </td>
 
         </td>
 
         <td class="redup arrow" >
 
         <td class="redup arrow" >
−
             <p>AH016 wrong <br/>size gel</p>
+
             <p>AH016 <br/>wrong size<br/> on gel</p>
 
         </td>
 
         </td>
 
   </tr>
 
   </tr>
Line 622: Line 622:
 
         <td class="first rightline"><div class="heightdiv"><h3>Testing RBS's <br/> <span style="font-size:20px">Assembly</span></h3></div></td>
 
         <td class="first rightline"><div class="heightdiv"><h3>Testing RBS's <br/> <span style="font-size:20px">Assembly</span></h3></div></td>
 
         <td class="white arrow" >
 
         <td class="white arrow" >
−
             <p style="font-size:12px">Screening AH009 & <br/>AH013-AH015 by <br/>gel electrophoresis</p>
+
             <p style="font-size:12px">Screening AH009 <br/>& AH013-AH015 <br/>by gel <br/> electrophoresis</p>
 
         </td>
 
         </td>
 
         <td class="blue arrow" >
 
         <td class="blue arrow" >
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         </td>
 
         </td>
 
         <td class="white arrow" >
 
         <td class="white arrow" >
−
             <p>Assembling <br/>AH016 & AH018</p>
+
             <p>Assembling <br/>AH016 & <br/>AH018</p>
 
         </td>
 
         </td>
 
         <td class="white arrow" >
 
         <td class="white arrow" >
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         </td>
 
         </td>
 
         <td class="reddown arrow" >
 
         <td class="reddown arrow" >
−
             <p>AH014 incorrect <br/>size</p>
+
             <p>AH014 <br/>incorrect size</p>
 
         </td>
 
         </td>
 
         <td class="white arrow" >
 
         <td class="white arrow" >
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         </td>
 
         </td>
 
         <td class="red arrow" >
 
         <td class="red arrow" >
−
             <p>Colonies are not blue</p>
+
             <p>Colonies are <br/>not blue</p>
 
         </td>
 
         </td>
 
   </tr>
 
   </tr>
 
   <tr>
 
   <tr>
−
         <td class="first rightline"><div class="heightdiv"><h3></h3></div></td>
+
         <td class="first rightline"><div class="heightdiv bottomline"><h3></h3></div></td>
 
         <td class="white arrow" >
 
         <td class="white arrow" >
−
             <p>Re-assembling <br/>AH016 & AH018</p>
+
             <p>Re-assembling <br/>AH016 &<br/> AH018</p>
 
         </td>
 
         </td>
 
         <td class="blue arrow" >
 
         <td class="blue arrow" >
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         </td>
 
         </td>
 
         <td class="red arrow" >
 
         <td class="red arrow" >
−
             <p>Colonies are not blue</p>
+
             <p>Colonies are <br/> not blue</p>
 
         </td>
 
         </td>
 
   </tr>
 
   </tr>
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         </td>
 
         </td>
 
         <td class="red arrow" >
 
         <td class="red arrow" >
−
             <p>Low concentration</p>
+
             <p>Low <br/>concentration</p>
 
         </td>
 
         </td>
 
   </tr>
 
   </tr>
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   </tr>
 
   </tr>
 
   <tr>
 
   <tr>
−
         <td class="first rightline"><div class="heightdiv"><h3>Testing RBS's <br/><span style="font-size:20px"> Assembly</span></h3></div></td>
+
         <td class="first rightline"><div class="heightdiv bottomline"><h3>Testing RBS's <br/><span style="font-size:20px"> Assembly</span></h3></div></td>
 
         <td class="white arrow" >
 
         <td class="white arrow" >
 
             <p>Re-assembling AH016 & <br/>AH018</p>
 
             <p>Re-assembling AH016 & <br/>AH018</p>
Line 719: Line 719:
 
   </tr>
 
   </tr>
 
   <tr>
 
   <tr>
−
         <td class="first rightline"><div class="heightdiv"><h3>Testing RBS's <br/>Propagation</h3></div></td>
+
         <td class="first rightline"><div class="heightdiv bottomline"><h3>Testing RBS's <br/>Propagation</h3></div></td>
 
         <td class="white arrow" >
 
         <td class="white arrow" >
 
             <p style="font-size:12px">o/n cultures of <br/>&nbsp;AH016 & AH018 <br/> in TOP10</p>
 
             <p style="font-size:12px">o/n cultures of <br/>&nbsp;AH016 & AH018 <br/> in TOP10</p>
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   </tr>
 
   </tr>
 
     <tr>
 
     <tr>
−
         <td class="first rightline"><div class="heightdiv"><h3></h3></div></td>
+
         <td class="first rightline"><div class="heightdiv bottomline"><h3></h3></div></td>
 
         <td>
 
         <td>
 
         </td>
 
         </td>
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   </tr>
 
   </tr>
 
   <tr>
 
   <tr>
−
         <td class="first rightline"><div class="heightdiv"><h3>Preparations <br/> <span style="font-size:20px">Linearized Backbones</span></h3></div></td>
+
         <td class="first rightline"><div class="heightdiv bottomline"><h3>Preparations <br/> <span style="font-size:20px">Linearized Backbones</span></h3></div></td>
 
         <td class="white arrow" >
 
         <td class="white arrow" >
 
             <p style="font-size:12px">Transform <br/>AH007-AH009 <br/> into TOP10</p>
 
             <p style="font-size:12px">Transform <br/>AH007-AH009 <br/> into TOP10</p>
Line 806: Line 806:
 
   </tr>
 
   </tr>
 
   <tr>
 
   <tr>
−
         <td class="first rightline"><div class="heightdiv"><h3>Testing RBS's</h3></div></td>
+
         <td class="first rightline"><div class="heightdiv bottomline"><h3>Testing RBS's</h3></div></td>
 
         <td class="red arrow" >
 
         <td class="red arrow" >
 
             <p style="color:red;font-size:12px">o/n cultures of <br/> &nbsp;&nbsp;AH016&AH018 <br/> in TOP10</p>
 
             <p style="color:red;font-size:12px">o/n cultures of <br/> &nbsp;&nbsp;AH016&AH018 <br/> in TOP10</p>
Line 818: Line 818:
 
   </tr>
 
   </tr>
 
   <tr>
 
   <tr>
−
         <td class="first rightline"><div class="heightdiv"><h3>Testing RBS's <br/><span style="font-size:20px"> Measurement</span></h3></div></td>
+
         <td class="first rightline"><div class="heightdiv bottomline"><h3>Testing RBS's <br/><span style="font-size:20px"> Measurement</span></h3></div></td>
 
         <td class="white arrow" >
 
         <td class="white arrow" >
 
             <p style="font-size:12px">Refresh AH016 &<br/>AH018 on <br/> IPTG plate</p>
 
             <p style="font-size:12px">Refresh AH016 &<br/>AH018 on <br/> IPTG plate</p>
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   </tr>
 
   </tr>
 
   <tr>
 
   <tr>
−
         <td class="first rightline"><div class="heightdiv"><h3>Preparations <span style="font-size:20px">Competent Cells</span></h3></div></td>
+
         <td class="first rightline"><div class="heightdiv bottomline"><h3>Preparations <span style="font-size:20px">Competent Cells</span></h3></div></td>
 
         <td class="white arrow" >
 
         <td class="white arrow" >
 
             <p>Preparing <br/>&nbsp;&nbsp;PK BL21(DE3)<br/> competent cells</p>
 
             <p>Preparing <br/>&nbsp;&nbsp;PK BL21(DE3)<br/> competent cells</p>
Line 909: Line 909:
 
   </tr>
 
   </tr>
 
   <tr>
 
   <tr>
−
         <td class="first rightline"><div class="heightdiv"><h3></h3></div></td>
+
         <td class="first rightline"><div class="heightdiv bottomline"><h3></h3></div></td>
 
         <td class="white arrow" >
 
         <td class="white arrow" >
 
             <p>AH029 into <br/> TOP10</p>
 
             <p>AH029 into <br/> TOP10</p>
Line 918: Line 918:
 
   </tr>
 
   </tr>
 
     <tr>
 
     <tr>
−
         <td class="first rightline"><div class="heightdiv"><h3>Testing RBS's</h3></div></td>
+
         <td class="first rightline"><div class="heightdiv bottomline"><h3>Testing RBS's</h3></div></td>
 
              
 
              
 
         </td>
 
         </td>
Line 970: Line 970:
  
 
   <tr>
 
   <tr>
−
<td class="first rightline"><div class="heightdiv"><h3></h3></div></td>
+
<td class="first rightline"><div class="heightdiv bottomline"><h3></h3></div></td>
  
 
         <td>
 
         <td>
Line 998: Line 998:
  
 
   <tr>
 
   <tr>
−
         <td class="first rightline"><div class="heightdiv"><h3></h3></div></td>
+
         <td class="first rightline"><div class="heightdiv bottomline"><h3></h3></div></td>
 
         <td></td>
 
         <td></td>
 
<td class="whitedown arrow" >
 
<td class="whitedown arrow" >
Line 1,009: Line 1,009:
  
 
   <tr>
 
   <tr>
−
         <td class="first rightline"><div class="heightdiv"><h3>GFP Brick <span style="font-size:20px">Construction</span></h3></div></td>
+
         <td class="first rightline"><div class="heightdiv bottomline"><h3>GFP Brick <span style="font-size:20px">Construction</span></h3></div></td>
  
 
<td class="white arrow" >
 
<td class="white arrow" >
Line 1,076: Line 1,076:
 
   </tr>
 
   </tr>
 
   <tr>
 
   <tr>
−
         <td class="first rightline"><div class="heightdiv"><h3></h3></div></td>
+
         <td class="first rightline"><div class="heightdiv bottomline"><h3></h3></div></td>
 
         <td class="red arrow" >
 
         <td class="red arrow" >
 
             <p>PCR for <br/>new CAR2</p>
 
             <p>PCR for <br/>new CAR2</p>
Line 1,087: Line 1,087:
 
   </tr>
 
   </tr>
 
   <tr>
 
   <tr>
−
         <td class="first rightline"><div class="heightdiv"><h3>Preparations <span style="font-size:20px">Linearized Backbones</span></h3></div></td>
+
         <td class="first rightline"><div class="heightdiv bottomline"><h3>Preparations <span style="font-size:20px">Linearized Backbones</span></h3></div></td>
 
         <td class="white arrow" >
 
         <td class="white arrow" >
 
             <p>Re-restrict <br/>AH043</p>
 
             <p>Re-restrict <br/>AH043</p>
Line 1,112: Line 1,112:
 
</tr>
 
</tr>
 
     <tr>
 
     <tr>
−
         <td class="first rightline"><div class="heightdiv"><h3></h3></div></td>
+
         <td class="first rightline"><div class="heightdiv bottomline"><h3></h3></div></td>
 
              
 
              
 
         </td>
 
         </td>
Line 1,138: Line 1,138:
 
</tr>
 
</tr>
 
     <tr>
 
     <tr>
−
         <td class="first rightline"><div class="heightdiv"><h3>Propane Plasmid 2 <span style="font-size:20px">Construction</span></h3></div></td>
+
         <td class="first rightline"><div class="heightdiv bottomline"><h3>Propane Plasmid 2 <span style="font-size:20px">Construction</span></h3></div></td>
 
              
 
              
 
         </td>
 
         </td>
Line 1,175: Line 1,175:
 
</tr>
 
</tr>
 
     <tr>
 
     <tr>
−
         <td class="first rightline"><div class="heightdiv"><h3></h3></div></td>
+
         <td class="first rightline"><div class="heightdiv bottomline"><h3></h3></div></td>
 
          
 
          
 
         <td class="white arrow" >
 
         <td class="white arrow" >
Line 1,196: Line 1,196:
 
</tr>
 
</tr>
 
     <tr>
 
     <tr>
−
         <td class="first rightline"><div class="heightdiv"><h3></h3></div></td>
+
         <td class="first rightline"><div class="heightdiv bottomline"><h3></h3></div></td>
 
         <td>     
 
         <td>     
 
         </td>
 
         </td>
Line 1,211: Line 1,211:
  
 
     <tr>
 
     <tr>
−
         <td class="first rightline"><div class="heightdiv"><h3>Violacein Plasmid <span style="font-size:2px">Construction</span></h3></div></td>
+
         <td class="first rightline"><div class="heightdiv"><h3>Violacein Plasmid <span style="font-size:20px">Construction</span></h3></div></td>
 
    
 
    
 
         <td class="white arrow" >
 
         <td class="white arrow" >

Revision as of 12:44, 14 August 2015

Lab Book

An example of what the table could look like:

Construct
worked with

Things done

Lab 1.1.2015
Monday

CAR

Here is my text

Here is my text

Here is my text

Here is my text

Here is my text

Here is my text

Here is my
text, there
is lot of it

another CAR?

Here is my text

Here is my text

Here is my text

Here is my text

Here is my text

Here is my text

Here is my
text, there
is lot of it

Ado?

Here is my text

Here is my text

Here is my text

Here is my text

Here is my text

Ado cont.

Here is my text

Here is my text

Here is my text

Here is my text

Here is my
text, there
is lot of it

Week 1

Worked With

WorkFlow

May 18th -
May 22nd

Preparations
Plates

Making Cm
plates

Stored in
+4°C

Preparations
Competent Cells

Preparing
solutions for
competent cells

Stored in
+4°C

o/n culture
of E. coli
TOP10

Chemical
competent
cells protocol

Tranformation
efficiency kit

o/n culture
of E. coli
BL21(DE3)

Chemical
competent
cells protocol

Tranformation
efficiency kit

Colonies are
the wrong color

Preparations
Propagations

Transformed
  AH001-AH008
into TOP10

 AH001-AH004
& AH006

Stored in
+4°C

No colonies for
   AH005, AH007
or AH008

Week 2

Worked With

WorkFlow

May 25th -
May 29th

Preparations
Propagating

Transformed
AH007-AH009,
AH005 & AH019
into TOP10

AH007-AH009
& AH019

o/n cultures

MiniPrep

o/n culture of
 AH001-AH004
& AH006

MiniPrep

No colonies
for AH005

Re-transform
into TOP10

Plates in rt
over weekend

Checking
Competent Cells

o/n culture
of BL21(DE3)
transformants

MiniPrep

PCR with
VF2 & VR

  Smeared gels

AH001+
   AH003+AH008
-> AH013

Repeat
ligation

Restrict &
extract
from gel

 Transformation
into TOP10

Plates in rt
over weekend

Testing RBS's
Assembly

Restrict
AH001-AH004
& AH006-AH008

Ligation

AH002+
  AH004+AH008
-> AH014

Repeat
ligation

Restrict &
extract
from gel

 Transformation
into TOP10

Plates in rt
over weekend

AH001+
   AH006+AH008
-> AH011

Repeat
ligation

Restrict &
extract
from gel

 Transformation
into TOP10

Plates in rt
over weekend

Week 3

Worked With

WorkFlow

June 1st -
June 5th

Preparations
Propagating

Transform
    AH020 & AH021
into TOP10

Plates in rt
 over weekend

Testing RBS's
Assembly

No colonies
for AH011
or AH014

re-assemble

Restrict &
extract
from gel

Ligate &
tranform
into TOP10

No colonies

AH005 &
AH013 OK

o/n cultures

MiniPrep

Week 4

Worked With

WorkFlow

June 8th -
June 12th

Preparations
Propagating

o/n cultures
for AH020
& AH021

MiniPrep

Testing RBS's
Assembly

Re-assembling
  AH011, AH013
& AH014

Transform into TOP10

o/n cultures

MinPrep

Assembling
AH015

  Ligate AH002+
  AH005+AH008

Restrict &
extract
from gel

Transform into TOP10

o/n cultures

MiniPrep

Week 5

Worked With

WorkFlow

June 15th -
June 19th

AH016
wrong size
on gel

Colonies in
BL21(DE3)

o/n cultures
& MiniPrep

AH018 OK
on gel

Testing RBS's
Assembly

Screening AH009
& AH013-AH015
by gel
electrophoresis

AH009, AH013
& AH015 OK

Assembling
AH016 &
AH018

Transform into TOP10 & BL21(DE3)

T7 promoter
doesn't work
in TOP10...

AH014
incorrect size

Assembling AH017
with multiple
AH014 plasmids

Restrict &
extract
from gel

Transform into BL21(DE3)

Colonies are
not blue

Re-assembling
AH016 &
AH018

Restrict
extract
from gel

Transform into
BL21(DE3)

Colonies are
not blue

Preparations
Linearized Backbones

o/n cultures of
AH007-AH009

MiniPrep

Restrict &
extract
from gel

Low
concentration

Week 6

Worked With

WorkFlow

June 22nd -
June 26th

Testing RBS's
Assembly

Re-assembling AH016 &
AH018

Transform
into
BL21(DE3)

No colonies

Testing RBS's
Propagation

o/n cultures of
 AH016 & AH018
in TOP10

MiniPrep

Transform
into
BL21(DE3)

Plates in rt
over the
weekend

Testing RBS's
Measurement

AH018 in
BL21(DE3)

o/n culture

IPTG induction &
    blue chromoprotein
measurement

No blue chromoprotein

Refresh on
IPTG plate

No blue chromoprotein

Preparations
Linearized Backbones

o/n cultures of
AH007-AH009

MiniPrep

Restrict &
extract
from gel

Week 7

Worked With

WorkFlow

June 29th -
July 3rd

Preparations
Linearized Backbones

Transform
AH007-AH009
into TOP10

No colonies
(mistake in
protocol)

Use iGEM's
linearized
backbones

Testing RBS's

o/n cultures of
  AH016&AH018
in TOP10

IPTG
induction

No Blue
chromoprotein

Testing RBS's
Measurement

Refresh AH016 &
AH018 on
IPTG plate

No blue
chromoprotein

Violacein Plasmid
Construction

PCR AH20
with
P012&P013

PCR
purification

VioA waits
for 2nd PCR

PCR AH20
with
P024&P025

PCR
unsuccesful

PCR AH20
with
P034&P035

PCR
purification

VioE waits
for 2nd PCR

Week 8

Worked With

WorkFlow

July 6th -
July 10th

Preparations Competent Cells

Preparing
  PK BL21(DE3)
competent cells

Cells stored
in -80°C

Cellulose Plasmid
Construction

PCR AH021
with
P019&P020

Problem with
PCR machine

Re-do PCR

PCR
purifcation

BglX waits for
2nd PCR

AH029 into
TOP10

Transformants
stored in
+4°C

Testing RBS's

Transform AH016
& AH018 into
PK BL21(DE3)

Refresh
transformants
on IPTG plates

No blue
chromoprotein

Violacein Plasmid
Construction

Gradient PCR for
AH020 with
P024&P025

PCR
purification

Week 9

Worked With

WorkFlow

July 13th -
July 17th

Preparations
Propagations

o/n culture
of AH029

MiniPrep

CAR2 OK

PCR
purification

Propane Plasmids 1&2 Construction

PCR for
CAR1-3 &
AtoB1-2

CAR1,3 &
AtoB1-2
unspecific bands

Gradient PCR
for CAR3 & 4

PCR with DMSO
for CAR1, 3
& AtoB1, 2

dunnowhat

GFP Brick Construction

o/n culture
of AH044

MiniPrep

Propane Plasmid 2 Construction

PCR for
AtoB3-4

Unspecific
bands

AtoB 4
extracted
from gel

Low
concentration

Gradient
PCR for
AtoB3

Extract &
purify
from gel

Week 10

Week 11

Worked With

WorkFlow

July 27th -
July 31st

Propane Plasmid 1 Construction

Continue CAR1
colony
screening

Screen more
colonies

PCR purification

PCR for
new CAR2

Gradient PCR
with KAPA
polymerase

PCR
purification

Preparations Linearized Backbones

Re-restrict
AH043

Gel purification

Low yield

Re-restrict

Propagations

o/n culture
of AH031

MiniPrep

Transform
AH033 into
TOP10

o/n culture

MiniPrep

Low yield

o/n culture

MiniPrep

Low yield,
but stored
in -20°C

Propane Plasmid 2 Construction

TOPO Blunt End
Cloning for AtoB1
and transformation
into TOP10

Screening
with colony
PCR

PCR
purification

Cellulose Plasmid Construction

PCR for
Cen1 & Cen2

Gradient PCR
with KAPA
polymerase

PCR
purification for
Cen2

Gel purification
for Cen1

2nd PCR
for BglX
(from AH021)

Stored in -4°C
over the
weekend

Propane Plasmid 1 Construction

Re-do colony
PCR for CAR3
successful TOPO colony

Re-do
colony PCR

o/n culture of
the colony

MiniPrep

PCR

Violacein Plasmid Construction

2nd PCR
for VioA
(from AH020)

Stored in -4°C
over the
weekend

KAPA gradient
PCR for AtoB3,4
& CAR3

Gel purification
for AtoB4 & Car3

PCR
purification
for AtoB3

Week 12

Week 13

Week 14

Week 15

Week 16

Week 17

Week 18