Team:DTU-Denmark/Biobrick Workshop

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{{:Team:DTU-Denmark/Templates/StartPage|}}
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{{:Team:DTU-Denmark/Templates/StartPage|BioBrick Workshop}}
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<div class="overviewPage">
<div class="overviewPage">
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==BioBrick Workshop==
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<div class="overviewBox">
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[[File:DTU_iGEM_workshop_marts_2013_0722.png|800px|thumb|center|iGEM Denmark 2013.]]
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==The idea==
-
We planned and hosted a three-days BioBrick workshop to introduce ourselves and the other iGEM teams from Denmark (SDU, KU) to the lab skills necessary to complete our projects. The workshop consisted of a mix of lectures, lab work and social events.
+
We planned and hosted a three-day BioBrick workshop to introduce ourselves and the other iGEM teams from Denmark ([https://2013.igem.org/Team:SDU-Denmark SDU], [https://2013.igem.org/Team:UNIK_Copenhagen KU]) to the lab skills necessary to complete our projects. The workshop consisted of a mix of lectures, lab work and social events.
 +
Lectures were on the BioBrick standards, BioBricks registry, project and time management, biosafety considerations, and the methods used over the lab experiments of the workshop, such as: [https://www.youtube.com/watch?v=7EiVttJpXH4 USER cloning], PCR reactions and purification of plasmids, etc.
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[[File:DTU_iGEM_workshop_marts_2013_038.jpg|150px|thumb|left|During the lab work.]]
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== Purpose ==
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The purpose of this workshop was to serve as an assembly tutorial to cover lab techniques independent of organism and project.  We combined 5 parts using USER cloning in E. coli, and validated that the transformation was successful.
 +
And of course, also to have fun!!
 +
== Agenda ==
 +
Preparation (Done at DTU, by DTU team earlier in the week).
-
Lectures were on the BioBrick standards, BioBricks registry, project and time management, and the methods used over the lab experiments of the workshop, such as: USER cloning, PCR reactions and purification of plasmids, etc.
+
Prepare plates (4 per team).
 +
Prepare colonies to use for validating that the transformation has worked.
 +
'''Friday March 8th'''
 +
13:00 -- Welcome, Introductions (Chris Workman).
 +
13:30 -- Lecture: Introduction to working with Biobricks (Thomas Trolle).
 +
Discussion of the Biobrick standard.
 +
Overview of the lab process.
 +
14:30 -- Lecture: What is the biobrick registry, and how to find parts (Damian Plichta).
 +
Work through an example of finding parts to reach a particular goal.
-
The purpose of this workshop was to served as an assembly tutorial that covered skills independent of organism and project. And of course to have fun!!
+
15:00 -- Lecture: Introduction to the weekend project and USER cloning (Mathilde Lund).
-
[[File:DTU_iGEM_workshop_marts_2013_004.jpg|170px|thumb|left|Creative use of pipettes!]]
+
-
[[File:DTU_iGEM_workshop_marts_2013_009.jpg|400px|thumb|right|Classic case of photobombing!]]
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 +
What is USER cloning?
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</div>
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USER cloning with Biobricks.
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<div style="clear: both;"></div>
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== Project ==
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16:30 -- Lecture: PHUSER (Hans Jasper Genee).
-
We will combine 5 parts using USER cloning in E. coli, and will validate that the transformation was successful.
+
17:00 -- Tour of the lab.
-
== Agenda ==
+
Introduction to the equipment and techniques that will be over the weekend.
-
Preparation (Done at DTU, by DTU team earlier in the week)
+
18:00 -- Social dinner in CBS kitchen.
-
Prepare plates (4 per team)
+
-
Prepare colonies to use for validating that the transformation has worked
+
-
Friday March 8th
 
-
Location: 208/62
 
-
13:00 -- Welcome, Introductions (Chris Workman)
+
'''Saturday March 9th'''
-
13:30 -- Lecture: Introduction to working with Biobricks (Thomas Trolle)
+
9:00 -- Introduction to labwork (Mathilde Lund).
-
Discussion of the Biobrick standard
+
-
Overview of the lab process
+
-
14:30 -- Lecture: What is the biobrick registry, and how to find parts (Damian Plichta)
+
Safety considerations when working in the lab.
-
Work through an example of finding parts to reach a particular goal.
+
-
15:00 -- Lecture: Introduction to the weekend project and USER cloning (Mathilde Lund)
+
How to run PCR.
-
What is USER cloning?
+
-
USER cloning with Biobricks
+
-
16:30 -- Lecture: PHUSER (Hans Jasper Genee)
+
10:30 -- Begin work on the project.
-
17:00 -- Tour of the lab
+
# Prepare PCR reaction mix (2 PCR reaction pr team) SOP1.
-
Introduction to the equipment and techniques that will be over the weekend
+
# Prepare USER cloning reaction mix SOP 3 + handout note (1 positive and 1 negative reaction per team).
-
18:00 -- Social dinner in CBS kitchen
+
Step 1 and 2 can both be stored several hours at 4°C.
 +
12:00 -- Lunch
 +
13:30 -- Lecture: Advice on project management and time management (Julie Rank).
-
Saturday March 9th
+
14:00 -- Continue work on project in the lab (Transform cells and plate, incubate overnight).
-
Location:  
+
-
9:00 -- Introduction to labwork (Mathilde Lund)
+
# Prepare 1 analytical gel for each team  + 2 purification gels SOP2 2.
-
Safety considerations when working in the lab.
+
# While waiting for the gel, prepare samples for analytical gel + purification electrophorese SOP2.
-
How to run PCR
+
# Prepare transformation of USER cloning SOP3.
 +
# While waiting for the transformation: Load analytical gel + purification gel electrophorese SOP2.
 +
# Heatshock of transformation and plating of transformation SOP3.
 +
# Analyse analytical gel by UV SOP2.
 +
#Cut DNA from purification gel;  freeze at -18°C for next day or purify right away SOP2.  
 +
-
10:30 -- Begin work on the project
+
20:00 -- Social Dinner at India Palace (buffet), Address: 13 H.C. Andersens Boulevard, 1553 Copenhagen V.
-
1.  Prepare PCR reaction mix (2 PCR reaction pr team) SOP1
+
-
2.   Prepare USER cloning reaction mix SOP 3 + handout note (1 positive and 1 negative reaction per team)
+
-
Step 1 and 2 can both be stored several hours at 4°C
+
-
12:00 -- Lunch (Pizza)
 
-
 
-
13:00 -- Lecture: Tips and Tricks in the lab (TBD)
 
-
Practical advice from previous iGEMmers on what techniques worked well; what pitfalls they encountered, and how to avoid them. 
 
-
 
-
13:30 -- Lecture: Advice on project management and time management (Julie Rank)
 
-
 
-
14:00 -- Continue work on project in the lab (Transform cells and plate, incubate overnight)
 
-
 
-
1. Prepare 1 analytical gel for each team  + 2 purification gels SOP2 2.
 
-
2. While waiting for the gel, prepare samples for analytical gel + purification electrophorese SOP2
 
-
3. Prepare transformation of USER cloning SOP3
 
-
4. While waiting for the transformation: Load analytical gel + purification gel electrophorese SOP2
 
-
4. Heatshock of transformation and plating of transformation SOP3
 
-
5. Analyse analytical gel by UV SOP2
 
-
6. Cut DNA from purification gel;  freeze at -18°C for next day or purify right away SOP2
 
-
 
-
20:00 -- Social Dinner at India Palace (buffet)
+
'''Sunday March 10th'''
-
Adress:
+
-
13 H.C. Andersens Boulevard
+
-
1553 Copenhagen V
+
-
Sunday March 10th
+
9:00 -- Continue work on project in the lab (Using pre-prepared cultures, digest and run on a gel).
-
Location:  
+
# Purify plasmids SOP4.
 +
# Prepare restriction enzyme mix for purified plasmids SOP4.
 +
# Analyse transformation plate and count number of colonies of transformation plates from Saturday. Pick 3 colonies from positive plate for further cultivation and purification SOP4.
-
9:00 -- Continue work on project in the lab (Using pre-prepared cultures, digest and run on a gel)
+
12:00 -- Lunch
-
1. Purify plasmids SOP4
+
-
2. Prepare restriction enzyme mix for purified plasmids SOP4
+
-
3. Analyse transformation plate and count number of colonies of transformation plates from Saturday. Pick 3 colonies from positive plate for further cultivation and purification SOP4
+
-
12:00 -- Lunch (Pizza?)
+
13:00 -- Continue Lab work.
 +
# Purify DNA from cutout of gel from Saturday SOP2.
-
13:00 -- Continue Lab work
+
13:30 -- Lecture: How to get gold in iGEM (Chris Workman).
-
4. Purify DNA from cutout of gel from Saturday SOP2
+
-
13:30 -- Lecture: How to get gold in iGEM (Chris Workman)
 
Discuss some of the frequently overlooked aspects of iGEM such as human practices and characterization of Biobricks that are necessary to achieve a gold medal.  
Discuss some of the frequently overlooked aspects of iGEM such as human practices and characterization of Biobricks that are necessary to achieve a gold medal.  
-
14:30 -- Finish lab work
+
14:30 -- Finish lab work.
-
5. Prepare restriction enzyme reaction samples for gel electrophoresis SOP2
+
# Prepare restriction enzyme reaction samples for gel electrophoresis SOP2.
-
6. Load on gel SOP2
+
# Load on gel SOP2.
-
16:00 -- Wrap up, Thanks (Chris Workman)
+
16:00 -- Wrap up, Thanks (Chris Workman).
{{:Team:DTU-Denmark/Templates/EndPage|BioBrick_Workshop}}
{{:Team:DTU-Denmark/Templates/EndPage|BioBrick_Workshop}}

Latest revision as of 20:59, 4 October 2013

BioBrick Workshop

The idea

We planned and hosted a three-day BioBrick workshop to introduce ourselves and the other iGEM teams from Denmark (SDU, KU) to the lab skills necessary to complete our projects. The workshop consisted of a mix of lectures, lab work and social events. Lectures were on the BioBrick standards, BioBricks registry, project and time management, biosafety considerations, and the methods used over the lab experiments of the workshop, such as: USER cloning, PCR reactions and purification of plasmids, etc.

Purpose

The purpose of this workshop was to serve as an assembly tutorial to cover lab techniques independent of organism and project. We combined 5 parts using USER cloning in E. coli, and validated that the transformation was successful.

And of course, also to have fun!!

Agenda

Preparation (Done at DTU, by DTU team earlier in the week).

Prepare plates (4 per team).

Prepare colonies to use for validating that the transformation has worked.


Friday March 8th

13:00 -- Welcome, Introductions (Chris Workman).

13:30 -- Lecture: Introduction to working with Biobricks (Thomas Trolle).

Discussion of the Biobrick standard.

Overview of the lab process.

14:30 -- Lecture: What is the biobrick registry, and how to find parts (Damian Plichta).

Work through an example of finding parts to reach a particular goal.

15:00 -- Lecture: Introduction to the weekend project and USER cloning (Mathilde Lund).

What is USER cloning?

USER cloning with Biobricks.

16:30 -- Lecture: PHUSER (Hans Jasper Genee).

17:00 -- Tour of the lab.

Introduction to the equipment and techniques that will be over the weekend.

18:00 -- Social dinner in CBS kitchen.


Saturday March 9th

9:00 -- Introduction to labwork (Mathilde Lund).

Safety considerations when working in the lab.

How to run PCR.

10:30 -- Begin work on the project.

  1. Prepare PCR reaction mix (2 PCR reaction pr team) SOP1.
  2. Prepare USER cloning reaction mix SOP 3 + handout note (1 positive and 1 negative reaction per team).

Step 1 and 2 can both be stored several hours at 4°C.

12:00 -- Lunch

13:30 -- Lecture: Advice on project management and time management (Julie Rank).

14:00 -- Continue work on project in the lab (Transform cells and plate, incubate overnight).

  1. Prepare 1 analytical gel for each team + 2 purification gels SOP2 2.
  2. While waiting for the gel, prepare samples for analytical gel + purification electrophorese SOP2.
  3. Prepare transformation of USER cloning SOP3.
  4. While waiting for the transformation: Load analytical gel + purification gel electrophorese SOP2.
  5. Heatshock of transformation and plating of transformation SOP3.
  6. Analyse analytical gel by UV SOP2.
  7. Cut DNA from purification gel; freeze at -18°C for next day or purify right away SOP2.


20:00 -- Social Dinner at India Palace (buffet), Address: 13 H.C. Andersens Boulevard, 1553 Copenhagen V.


Sunday March 10th

9:00 -- Continue work on project in the lab (Using pre-prepared cultures, digest and run on a gel).

  1. Purify plasmids SOP4.
  2. Prepare restriction enzyme mix for purified plasmids SOP4.
  3. Analyse transformation plate and count number of colonies of transformation plates from Saturday. Pick 3 colonies from positive plate for further cultivation and purification SOP4.

12:00 -- Lunch

13:00 -- Continue Lab work.

  1. Purify DNA from cutout of gel from Saturday SOP2.

13:30 -- Lecture: How to get gold in iGEM (Chris Workman).

Discuss some of the frequently overlooked aspects of iGEM such as human practices and characterization of Biobricks that are necessary to achieve a gold medal.

14:30 -- Finish lab work.

  1. Prepare restriction enzyme reaction samples for gel electrophoresis SOP2.
  2. Load on gel SOP2.

16:00 -- Wrap up, Thanks (Chris Workman).


Retrieved from "http://2013.igem.org/Team:DTU-Denmark/Biobrick_Workshop"