Team:LMU-Munich/Lab Notebook/Protocols

From 2012.igem.org

(Difference between revisions)
 
(50 intermediate revisions not shown)
Line 1: Line 1:
{{:Team:LMU-Munich/Templates/Page Header|File:Team-LMU_Photo10.jpg}}
{{:Team:LMU-Munich/Templates/Page Header|File:Team-LMU_Photo10.jpg}}
 +
[[File:Protocols banner.resized WORDS.JPG|620px|link=]]
-
==Protocols==
 
On this page, we offer our unique protocols to the public.
On this page, we offer our unique protocols to the public.
-
Because ''Bacillus subtilis'' is our choice organism, we have focused on protocols specifically for ''Bacillus''.
 
 +
'''Because ''Bacillus subtilis'' is our choice organism, we have focused on protocols specifically for ''Bacillus''.'''
-
1. [https://static.igem.org/mediawiki/2012/5/56/LMU-Munich_2012_Media_for_Bacillus_subtilis.pdf Media and components for ''Bacillus subtilis'']
 
-
This protocol gives the recipes for various media and the antibiotic concentrations used for ''B. subtilis''.
+
However [[Team:LMU-Munich/Lab Notebook/Protocols#Other protocols we used|below]], you will also find other standard protocols we use.
-
2. [https://static.igem.org/mediawiki/2012/4/41/LMU-Munich_2012_Transformation_of_Bacillus_subtilis.pdf Transformation of ''Bacillus subtilis'']
+
<div class="box" style= "background-color:#e4f1d7">
 +
===Protocols for the work with ''B. subtilis''===
 +
</div>
-
Protocol how to transform ''B. subtilis''.
+
<div class="box">
 +
'''1.''' [https://static.igem.org/mediawiki/2012/5/56/LMU-Munich_2012_Media_for_Bacillus_subtilis.pdf Growth, storage, media and components for ''Bacillus subtilis'']
 +
This protocol gives the basic growth- and storage conditions, and the recipes for various media and the antibiotic concentrations used for ''B. subtilis''.
 +
</div>
-
3. [https://static.igem.org/mediawiki/2012/0/00/LMU-Munich_2012_Isolation_of_chromosomal_DNA_from_Bacillus_subtilis_for_transformation.pdf Isolation of chromosomal DNA from ''Bacillus subtilis'' for transformation]
+
<div class="box">
 +
'''2.''' [https://static.igem.org/mediawiki/2012/4/41/LMU-Munich_2012_Transformation_of_Bacillus_subtilis.pdf Transformation of ''Bacillus subtilis'']
-
A quick protocol how to isolate genomic DNA from ''B.subtilis'' to transform it to a different strain. By this mean you can very easily combine different B. subtilis genotypes. transformation of genomic DNA is much more efficient than plasmids. Isolated DNA with this protocol is not clean!
+
Protocol for the transformation of ''B. subtilis''.
 +
</div>
 +
<div class="box">
 +
'''3.''' [https://static.igem.org/mediawiki/2012/0/00/LMU-Munich_2012_Isolation_of_chromosomal_DNA_from_Bacillus_subtilis_for_transformation.pdf Isolation of chromosomal DNA from ''Bacillus subtilis'' for transformation]
-
4. [https://static.igem.org/mediawiki/2012/6/6b/LMU-Munich_2012_Isolation_of_genomic_DNA_from_Bacillus_%28for_PCR....%29.pdf Isolation of chromosomal DNA from ''Bacillus subtilis'' (for PCR....)]
+
A quick protocol for how to isolate genomic DNA from ''B. subtilis'' to transform it to a different strain. By this means, you can very easily combine different ''B. subtilis'' genotypes. Transformation of genomic DNA is much more efficient than plasmids. Isolated DNA with this protocol is not clean!
 +
</div>
-
Isolation of pure genomic DNA from ''B. subtilis''.
+
<div class="box">
 +
4. [https://2012.igem.org/Team:LMU-Munich/Bacillus_BioBricks/vector_use ''Bacillus subtilis'' vectors]
 +
How to work with integrative ''B. subtilis'' vectors and how to verify the integration.
 +
</div>
-
5. [https://static.igem.org/mediawiki/2012/7/7a/LMU-Munich_2012_Long-Flanking_Homology_PCR.pdf Long Flanking Homology PCR]
+
<div class="box">
 +
5. [https://static.igem.org/mediawiki/2012/6/6b/LMU-Munich_2012_Isolation_of_genomic_DNA_from_Bacillus_%28for_PCR....%29.pdf Isolation of chromosomal DNA from ''Bacillus subtilis'' (for PCR....)]
 +
 
 +
Isolation of pure genomic DNA from ''B. subtilis''.
 +
</div>
 +
 
 +
<div class="box">
 +
6. [https://static.igem.org/mediawiki/2012/7/7a/LMU-Munich_2012_Long-Flanking_Homology_PCR.pdf Long Flanking Homology PCR]
PCR protocol for long flanking homology PCR. You might need those PCR products for interrupting genes with resistance cassettes.
PCR protocol for long flanking homology PCR. You might need those PCR products for interrupting genes with resistance cassettes.
-
 
-
6. [https://static.igem.org/mediawiki/2012/6/6d/LMU-Munich_2012_Clean_deletions_in_Bacillus_subtilis.pdf Clean deletion of genomic fragments in ''Bacillus subtilis'']
+
[https://static.igem.org/mediawiki/2012/6/67/LMU-Munich_2012_Removal_of_germination_genes.pdf Example: Using LFH PCR to replace germination genes with resistance cassettes]
-
Protocol for the production of markerless gene deletions. You will need the [http://www.ncbi.nlm.nih.gov/pubmed/15528558 pMAD] plasmid. This method is more time consuming than inserting resistance cassettes but offers better cell perfomance.
+
An explanation of how we used this protocol for how we knocked out our germination genes using LFH.
 +
</div>
 +
<div class="box">
 +
7. [https://static.igem.org/mediawiki/2012/6/6d/LMU-Munich_2012_Clean_deletions_in_Bacillus_subtilis.pdf Clean deletion of genomic fragments in ''Bacillus subtilis'']
-
7. [https://static.igem.org/mediawiki/2012/6/66/LMU-Munich_2012_Spore_germination_assay.pdf Spore germination assay]
+
Protocol for the production of markerless gene deletions. You will need the [http://www.ncbi.nlm.nih.gov/pubmed/15528558 pMAD] plasmid. This method is more time consuming than inserting resistance cassettes but offers better cell perfomance.
 +
</div>
 +
 
 +
<div class="box">
 +
8. [https://static.igem.org/mediawiki/2012/6/66/LMU-Munich_2012_Spore_germination_assay.pdf Spore germination assay]
Protocol to count efficiency of sporulation and germination.
Protocol to count efficiency of sporulation and germination.
 +
</div>
 +
<div class="box">
 +
9. [https://static.igem.org/mediawiki/2012/e/e9/LMU-Munich_2012_Protocol_for_enhancement_of_mature_spore_numbers.pdf Enhancement of mature spore numbers]
-
8. [https://static.igem.org/mediawiki/2012/7/70/LMU-Munich_2012_%C3%9F-Galactosidase_Assay_B._subtilis.pdf ß-Galactosidase Assay ''B. subtilis'']
+
Protocol to enrich the spore numbers and purification from vegetative cells.
 +
</div>
 +
 
 +
<div class="box">
 +
10. [https://static.igem.org/mediawiki/2012/7/70/LMU-Munich_2012_%C3%9F-Galactosidase_Assay_B._subtilis.pdf ß-Galactosidase Assay ''B. subtilis'']
Protocol how to measure ''lacZ'' gene activity in ''B. subtilis''
Protocol how to measure ''lacZ'' gene activity in ''B. subtilis''
 +
</div>
 +
 +
<div class="box">
 +
11. [https://static.igem.org/mediawiki/2012/e/e6/LMU-Munich_2012_Protocol_Plate_Reader.pdf Luminescence measurement]
 +
 +
This protocol explains how cultures were treated in advance of a plate reader assay.
 +
</div>
 +
 +
 +
 +
<div class="box" style= "background-color:#e4f1d7">
 +
===Other protocols we used===
 +
</div>
 +
 +
<div class="box">
 +
[http://partsregistry.org/Help:Protocols/Competent_Cells Competent Cells]
 +
 +
''E.coli'' competent cells and transformation. We used the [http://ecoliwiki.net/colipedia/index.php/XL-1_Blue XL1 blue strain].
 +
</div>
 +
 +
<div class="box">
 +
[https://static.igem.org/mediawiki/2012/1/1f/LMU-Munich_2012_Alkaline_Lysis_Plasmid_Preparation.pdf Alkaline Lysis Plasmid Preparation]
 +
 +
Alkaline Lysis Plasmid Preparation for ''E. coli''
 +
</div>
 +
 +
<div class="box">
 +
[http://openwetware.org/wiki/Silver:_Restriction_Digest Restriction digest]
 +
[http://openwetware.org/wiki/Silver:_Ligation Ligation]
 +
Standard restriction digest and ligation. We often used longer incubation times (up to over night) and did not dephosphorylate the backbones, if they had incompatible sticky ends.
 +
</div>
 +
<div class="box">
 +
[https://static.igem.org/mediawiki/2012/b/bb/LMU-Munich_2012_%C3%9F-Galactosidase_Assay_E._coli.pdf β-Galactosidase Assay in ''E. coli'']
 +
Quantitative ''lacZ''-assay in ''E.coli''.
 +
</div>
{{:Team:LMU-Munich/Templates/Page Footer}}
{{:Team:LMU-Munich/Templates/Page Footer}}

Latest revision as of 02:00, 27 September 2012

iGEM Ludwig-Maximilians-Universität München Beadzillus

Team-LMU Photo10.jpg

The LMU-Munich team is exuberantly happy about the great success at the World Championship Jamboree in Boston. Our project Beadzillus finished 4th and won the prize for the "Best Wiki" (with Slovenia) and "Best New Application Project".

IGEM HQ LMU prize.jpg

[ more news ]

Sporenfreunde

Retrieved from "http://2012.igem.org/Team:LMU-Munich/Lab_Notebook/Protocols"