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

m (fixing week1)
m (week 9)
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<h2 id="week9">Week 9</h2>
 
<h2 id="week9">Week 9</h2>
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 +
<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 13th -<br/> July 17th</h3></td>
 +
  </tr>
 +
  <tr>
 +
        <td class="first rightline"><div class="heightdiv"><h3>Preparations</h3></div></td>
 +
 +
        <td class="white arrow" >
 +
            <p>o/n culture of AH029</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>
 +
        <td class="blueup arrow" >
 +
            <p>CAR2 OK</p>
 +
        </td>
 +
        <td class="blue arrow" >
 +
            <p>PCR <br/>purification</p>
 +
        </td>
 +
  </tr>
 +
 +
  <tr>
 +
        <td class="first rightline"><div class="heightdiv"><h3>Propane Plasmids 1 & 2</h3></div></td>
 +
       
 +
<td class="white arrow" >
 +
            <p>PCR for <br/> CAR1-3 & <br/> AtoB1-2</p>
 +
        </td>
 +
        <td class="red arrow" >
 +
            <p>CAR1,3 & AtoB1-2 <br/> unspecific bands</p>
 +
        </td>
 +
        <td class="red arrow" >
 +
            <p>Gradient PCR <br/>for CAR3 & 4</p>
 +
        </td>
 +
  </tr>
 +
 
 +
 +
  <tr>
 +
        <td class="first rightline"><div class="heightdiv"><h3></h3></div></td>
 +
        <td></td>
 +
        <td></td>
 +
<td class="white arrow" >
 +
            <p>PCR with DMSO <br/>for CAR1, 3 <br/> & AtoB1, 2</p>
 +
        </td>
 +
        <td class="red arrow" >
 +
            <p style="color:red">dunnowhat</p>
 +
        </td>
 +
  </tr>
 +
 +
  <tr>
 +
        <td class="first rightline"><div class="heightdiv"><h3>GFP brick</h3></div></td>
 +
 +
<td class="white arrow" >
 +
            <p>o/n culture<br/> of AH044</p>
 +
        </td>
 +
        <td class="blue arrow" >
 +
            <p>MiniPrep</p>
 +
        </td>
 +
  </tr>
 +
  <tr>
 +
        <td class="first rightline"><div class="heightdiv"><h3>Propane Plasmid 2</h3></div></td>
 +
 +
<td class="white arrow" >
 +
            <p>PCR for <br/>AtoB3-4</p>
 +
        </td>
 +
        <td class="red arrow" >
 +
            <p>Unspecific<br/> bands</p>
 +
        </td>
 +
        <td class="white arrow" >
 +
            <p>AtoB 4 <br/>extracted <br/>from gel</p>
 +
        </td>
 +
        <td class="red arrow" >
 +
            <p>Low <br/>concentration</p>
 +
        </td>
 +
  </tr>
 +
  <tr>
 +
        <td class="first rightline"><div class="heightdiv"><h3></h3></div></td>
 +
        <td></td>
 +
<td class="whitedown arrow" >
 +
            <p>Gradient <br/>PCR for <br/>AtoB3</p>
 +
        </td>
 +
        <td class="blue arrow" >
 +
            <p>Extract & <br/> purify <br/>from gel</p>
 +
        </td>
 +
  </tr>
 +
</table>
 +
 
<h2 id="week10">Week 10</h2>
 
<h2 id="week10">Week 10</h2>
 
<h2 id="week11">Week 11</h2>
 
<h2 id="week11">Week 11</h2>

Revision as of 10:21, 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

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

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

AH001+
   AH003+AH008
-> AH013

Repeat
ligation

Restrict &
extract
from gel

 Transformation
into TOP10

Plates in rt
over weekend

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

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

Construct
worked with

Things done

July 13th -
July 17th

Preparations

o/n culture of AH029

MiniPrep

CAR2 OK

PCR
purification

Propane Plasmids 1 & 2

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

o/n culture
of AH044

MiniPrep

Propane Plasmid 2

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

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

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