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

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<h2 id="week10">Week 10</h2>
 
<h2 id="week10">Week 10</h2>
 
<h2 id="week11">Week 11</h2>
 
<h2 id="week11">Week 11</h2>
 +
 +
 +
<table >
 +
  <tr>
 +
    <td class="bottomline rightline first"><h3 style="padding-top:0;margin-top:0;margin-bottom:0;padding-bottom:0;">Construct <br>worked with</h3></td>
 +
    <td class="bottomline"><h3>Things done</h3></td>
 +
    <td class="bottomline"></td>
 +
    <td class="bottomline"></td>
 +
    <td class="bottomline"></td>
 +
    <td class="bottomline"></td>
 +
    <td class="bottomline"></td>
 +
    <td class="bottomline"><h3>July 27th -<br/> July 31st</h3></td>
 +
  </tr>
 +
  <tr>
 +
        <td class="first rightline"><div class="heightdiv"><h3>Constructing Propane Plasmid 1</h3></div></td>
 +
        <td class="red arrow" >
 +
            <p>Continue CAR1 <br/>colony <br/>screening</p>
 +
        </td>
 +
        <td class="blue arrow" >
 +
            <p>Screen more <br/> colonies</p>
 +
        </td>
 +
        <td class="blue arrow" >
 +
            <p>PCR purification</p>
 +
        </td>
 +
  </tr>
 +
  <tr>
 +
        <td class="first rightline"><div class="heightdiv"><h3></h3></div></td>
 +
        <td class="red arrow" >
 +
            <p>PCR for <br/>new CAR2</p>
 +
        </td>
 +
        <td class="blue arrow" >
 +
            <p>Gradient <br/>PCR with KAPA<br/> polymerase</p>
 +
        <td class="blue arrow" >
 +
            <p>PCR <br/> purification</p>
 +
        </td>
 +
  </tr>
 +
  <tr>
 +
        <td class="first rightline"><div class="heightdiv"><h3>Preparations</h3></div></td>
 +
        <td class="white arrow" >
 +
            <p>Re-restrict <br/>AH043</p>
 +
        </td>
 +
        <td class="white arrow" >
 +
            <p>Gel purification</p>
 +
        </td>   
 +
        <td class="red arrow" >
 +
            <p>Low yield</p>
 +
        </td> 
 +
        <td class="white arrow" >
 +
            <p>Re-restrict</p>
 +
        </td>     
 +
  </tr>
 +
    <tr>
 +
        <td class="first rightline"><div class="heightdiv"><h3></h3></div></td>
 +
           
 +
        </td>
 +
        <td class="white arrow" >
 +
            <p>o/n culture of AH031</p>
 +
        </td>
 +
<td class="blue arrow" >
 +
            <p>MiniPrep</p>
 +
        </td>
 +
</tr>
 +
    <tr>
 +
        <td class="first rightline"><div class="heightdiv"><h3></h3></div></td>
 +
           
 +
        </td>
 +
        <td class="blue arrow" >
 +
            <p>Transform <br/>AH033 into<br/> TOP10</p>
 +
        </td>
 +
<td class="white arrow" >
 +
            <p>o/n culture</p>
 +
        </td>
 +
<td class="white arrow" >
 +
            <p>MiniPrep</p>
 +
        </td>
 +
<td class="red arrow" >
 +
            <p>Low yield</p>
 +
        </td>
 +
<td class="white arrow" >
 +
            <p>o/n culture</p>
 +
        </td>
 +
<td class="white arrow" >
 +
            <p>MiniPrep</p>
 +
        </td>
 +
<td class="white arrow" >
 +
            <p>Low yield, <br/>but stored <br/>in -20°C</p>
 +
        </td>
 +
</tr>
 +
    <tr>
 +
        <td class="first rightline"><div class="heightdiv"><h3>Constructing Propane Plasmid 2</h3></div></td>
 +
           
 +
        </td>
 +
        <td class="blue arrow" >
 +
            <p style"font-size:12px">TOPO Blunt End <br/>Cloning for AtoB1<br/> and transformation<br/> into TOP10</p>
 +
        </td>
 +
<td class="white arrow" >
 +
            <p>Screening <br/>with colony <br/>PCR</p>
 +
        </td>
 +
<td class="blue arrow" >
 +
            <p>PCR <br/> purification</p>
 +
        </td>
 +
</tr>
 +
    <tr>
 +
        <td class="first rightline"><div class="heightdiv"><h3>Constructing Cellulose Plasmid</h3></div></td>
 +
           
 +
        </td>
 +
        <td class="red arrow" >
 +
            <p>PCR for <br/>Cen1 & Cen2</p>
 +
        </td>
 +
<td class="blue arrow" >
 +
            <p>Gradient PCR <br/>with KAPA <br/>polymerase</p>
 +
        </td>
 +
<td class="blue arrow" >
 +
            <p>PCR <br/> purification for <br/> Cen2</p>
 +
        </td>
 +
</tr>
 +
    <tr>
 +
        <td class="first rightline"><div class="heightdiv"><h3></h3></div></td>
 +
        <td>   
 +
        </td>
 +
        <td>
 +
        </td>
 +
<td class="blue arrow" >
 +
            <p>Gel purification <br/> for Cen1</p>
 +
        </td>
 +
</tr>
 +
    <tr>
 +
        <td class="first rightline"><div class="heightdiv"><h3>Constructing Propane Plasmid 1</h3></div></td>
 +
           
 +
        </td>
 +
        <td class="red arrow" >
 +
            <p style="font-size:12px">Re-do colony <br/>PCR for CAR3 <br/>successful TOPO colony</p>
 +
        </td>
 +
<td class="red arrow" >
 +
            <p>Re-do colony PCR</p>
 +
        </td>
 +
</tr>
 +
    <tr>
 +
        <td class="first rightline"><div class="heightdiv"><h3></h3></div></td>
 +
        <td>   
 +
        </td>
 +
        <td class="whitedown arrow" >
 +
            <p>o/n culture of the colony</p>
 +
        </td>
 +
<td class="white arrow" >
 +
            <p>MiniPrep</p>
 +
        </td>
 +
<td class="red arrow" >
 +
            <p>PCR</p>
 +
        </td>
 +
</tr>
 +
    <tr>
 +
        <td class="first rightline"><div class="heightdiv"><h3>Constructing Cellulose Plasmid</h3></div></td>
 +
        <td>   
 +
        </td>
 +
        <td class="white arrow" >
 +
            <p>2nd PCR <br/> for BglX <br/> (from AH021)</p>
 +
        </td>
 +
<td class="white arrow" >
 +
            <p>Stored in -4°C <br/>over the <br/>weekend</p>
 +
        </td>
 +
</tr>
 +
    <tr>
 +
        <td class="first rightline"><div class="heightdiv"><h3>Constructing Violacein construct</h3></div></td>
 +
        <td>   
 +
        </td>
 +
        <td class="white arrow" >
 +
            <p>2nd PCR <br/> for VioA <br/> (from AH020)</p>
 +
        </td>
 +
<td class="white arrow" >
 +
            <p>Stored in -4°C <br/>over the <br/>weekend</p>
 +
        </td>
 +
</tr>
 +
    <tr>
 +
        <td class="first rightline"><div class="heightdiv"><h3>Constructing Violacein construct</h3></div></td>
 +
 +
        <td class="blue arrow" >
 +
            <p>KAPA gradient <br/>PCR for AtoB3,4<br/> & CAR3</p>
 +
        </td>
 +
<td class="white arrow" >
 +
            <p>Gel purification <br/> for AtoB4 & Car3</p>
 +
        </td>
 +
</tr>
 +
    <tr>
 +
        <td class="first rightline"><div class="heightdiv"><h3></h3></div></td>
 +
        <td>   
 +
        </td>
 +
        <td class="whitedown arrow" >
 +
            <p>PCR <br/> purification <br/> for AtoB3</p>
 +
        </td>
 +
</tr>
 +
</table>
 +
 +
 
<h2 id="week12">Week 12</h2>
 
<h2 id="week12">Week 12</h2>
 
<h2 id="week13">Week 13</h2>
 
<h2 id="week13">Week 13</h2>

Revision as of 08:27, 12 August 2015

Lab Book

An example of what the table could look like:

Construct
worked with

Things done

Lab 1.1.2015
Monday

CAR

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text, there
is lot of it

another CAR?

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text, there
is lot of it

Ado?

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Ado cont.

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Here is my
text, there
is lot of it

Week 1

Construct
worked with

Things done

May 18th -
May 22nd

Plates

Making Cm
plates

Stored in
+4°C

Competent Cells

Preparing
solutions for
competent cells

Stored in
+4°C

Competent Cells

o/n culture
of E. coli
TOP10

Chemical
competent
cells protocol

Tranformation
efficiency kit

Competent Cells

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

Chemical
competent
cells protocol

Tranformation
efficiency kit

Colonies are
the wrong color

Propagations

Transformed
  AH001-AH008
into TOP10

 AH001-AH004
& AH006

Stored in
+4°C

No colonies for
   AH005, AH007
or AH008

Week 2

Construct
worked with

Things done

May 25th -
May 29th

Propagations

Transformed
AH007-AH009,
AH005 & AH019
into TOP10

AH007-AH009
& AH019

o/n cultures

MiniPrep

No colonies
for AH005

Re-transform
into TOP10

Plates in rt
over weekend

Competent Cells

o/n culture
of BL21(DE3)
transformants

MiniPrep

PCR with
VF2 & VR

  Smeared gels

Assembly
Testing RBS's

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

AH001+
   AH003+AH008
-> AH013

Repeat
ligation

Restrict &
extract
from gel

 Transformation
into TOP10

Plates in rt
over weekend

Propagations

o/n culture of
  AH001-AH004
& AH006

MiniPrep

Week 3

Construct
worked with

Things done

June 1st -
June 5th

Assembly
Testing RBS's

No colonies
for AH011
or AH014

re-assemble

Restrict &
extract
from gel

Ligate &
tranform
into TOP10

No colonies

Assembly
Testing RBS's

AH005 &
AH013 OK

o/n cultures

MiniPrep

Propagations

Transform
    AH020 & AH021
into TOP10

Plates in rt
 over weekend

Week 4

Construct
worked with

Things done

June 8th -
June 12th

Assembly
Propagations

o/n cultures
for AH020
& AH021

MiniPrep

Assembly
Testing RBS's

Re-assembling
   AH011, AH013
& AH014

Transform into TOP10

o/n cultures

MinPrep

Assembly
Testing RBS's

Assembling
AH015

  Ligate AH002+
  AH005+AH008

Restrict &
extract
from gel

Transform into TOP10

o/n cultures

MiniPrep

Propagations

Transform
    AH020 & AH021
into TOP10

Plates in rt
over weekend

Week 5

Week 6

Construct
worked with

Things done

June 22nd -
June 26th

Assembly
Testing RBS's

Re-assembling AH016 &
AH018

Transformation
into BL21(DE3)

No colonies

Testing RBS's

o/n cultures of
  AH016 & AH018
in TOP10

MiniPrep

Transform
into BL21(DE3)

Plates in rt
over the
weekend

Measurement
Testing RBS's

AH018 in
BL21(DE3)

o/n culture

IPTG induction &
    blue chromoprotein
measurement

No blue chromoprotein

Refresh on IPTG plate

No blue chromoprotein

Producing linearized backbones

o/n cultures of
AH007-AH009

MiniPrep

Restrict &
extract
from gel

Week 7

Construct
worked with

Things done

June 29th -
July 3rd

Preparations
Testing RBS's

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

Measurement
Testing RBS's

Refresh AH016 &
AH018 on
IPTG plate

No blue
chromoprotein

Violacein construct

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

Construct
worked with

Things done

July 6th -
July 10th

Constructing Cellulose system

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

Preparations

Preparing
  PK BL21(DE3)
competent cells

Cells stored
in -80°C

Testing RBS's

Transform
AH016 & AH018
into PK BL21(DE3)

Refresh
transformants
on IPTG plates

No blue
chromoprotein

Violacein Construct

Gradient PCR for
AH020 with
P024&P025

PCR
purification

Week 9

Week 10

Week 11

Construct
worked with

Things done

July 27th -
July 31st

Constructing Propane Plasmid 1

Continue CAR1
colony
screening

Screen more
colonies

PCR purification

PCR for
new CAR2

Gradient
PCR with KAPA
polymerase

PCR
purification

Preparations

Re-restrict
AH043

Gel purification

Low yield

Re-restrict

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

Constructing Propane Plasmid 2

TOPO Blunt End
Cloning for AtoB1
and transformation
into TOP10

Screening
with colony
PCR

PCR
purification

Constructing Cellulose Plasmid

PCR for
Cen1 & Cen2

Gradient PCR
with KAPA
polymerase

PCR
purification for
Cen2

Gel purification
for Cen1

Constructing Propane Plasmid 1

Re-do colony
PCR for CAR3
successful TOPO colony

Re-do colony PCR

o/n culture of the colony

MiniPrep

PCR

Constructing Cellulose Plasmid

2nd PCR
for BglX
(from AH021)

Stored in -4°C
over the
weekend

Constructing Violacein construct

2nd PCR
for VioA
(from AH020)

Stored in -4°C
over the
weekend

Constructing Violacein construct

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