Team:Heidelberg/Notebook/material

From 2008.igem.org

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===Kits===
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{| class="wikitable"
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|- bgcolor=grey
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! height=20px, width=350px | Kit || width=350px | supplier
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|-style="height:20px"
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|  ||
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|-align="center"
 +
| style="font-weight:bold;" |CompactPrep Plasmid Maxi Kit || Qiagen
 +
|-align="center"
 +
| style="font-weight:bold;" |HISpeed Plasmid Maxi Kit || Qiagen
 +
|-align="center"
 +
| style="font-weight:bold;" |MaxPlax™ Lambda Packaging Extracts || EPICENTRE Biotechnologies
 +
|-align="center"
 +
| style="font-weight:bold;" |QIAEX II Gel Extraction Kit || Qiagen
 +
|-align="center"
 +
| style="font-weight:bold;" |QIAGEN Lambda Mini Kit || Qiagen
 +
|-align="center"
 +
| style="font-weight:bold;" |QIAprep Spin Mini Kit  || Qiagen
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|-align="center"
 +
| style="font-weight:bold;" |QIAquick Gel Extraction Kit || Qiagen
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|-align="center"
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| style="font-weight:bold;" |QIAquick PCR Purification Kit || Qiagen
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|-
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|}
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 +
===Marker===
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{| class="wikitable"
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|- bgcolor=grey
 +
! height=20px, width=350px | Marker || width=350px | supplier
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|-style="height:20px"
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|  ||
 +
|-align="center"
 +
| style="font-weight:bold;" |GeneRulerTM High Range DNA Ladder || MBI Fermentas
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|-align="center"
 +
| style="font-weight:bold;" |GeneRulerTM 1kb DNA Ladder Mix || MBI Fermentas
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|-align="center"
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| style="font-weight:bold;" |GeneRulerTM 1kb Plus DNA Ladder Mix || MBI Fermentas
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|-
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|}
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===Enzymes===
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{| class="wikitable"
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|- bgcolor=grey
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! height=20px, width=350px | Enzym || width=350px | supplier
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|-style="height:20px"
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|  ||
 +
|-align="center"
 +
| style="font-weight:bold;" |Pfu DNA polymerase || Stratagene
 +
|-align="center"
 +
| style="font-weight:bold;" |Pfu turbo DNA polymerase || Stratagene
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|-align="center"
 +
| style="font-weight:bold;" |Phusion DNA polymerase || Finnzymes
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|-align="center"
 +
| style="font-weight:bold;" |Taq DNA polymerase || MBI Fermentas
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|-align="center"
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| style="font-weight:bold;" |T4 DNA ligase || MBI Fermentas / New England Biolabs
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|-style="height:20px"
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|  ||
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|-align="center"
 +
| style="font-weight:bold;" |AgeI || New England Biolabs
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|-align="center"
 +
| style="font-weight:bold;" |BamHI || New England Biolabs
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|-align="center"
 +
| style="font-weight:bold;" |BglI || MBI Fermentas
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|-align="center"
 +
| style="font-weight:bold;" |BseJI || MBI Fermentas
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|-align="center"
 +
| style="font-weight:bold;" |BspEI || New England Biolabs
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|-align="center"
 +
| style="font-weight:bold;" |DpnI || Roche Diagnostics / New England Biolabs
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|-align="center"
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| style="font-weight:bold;" |DraI || New England Biolabs
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|-align="center"
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| style="font-weight:bold;" |EcoRI || New England Biolabs
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|-align="center"
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| style="font-weight:bold;" |EcoRV || New England Biolabs
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|-align="center"
 +
| style="font-weight:bold;" |HindIII || New England Biolabs
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|-align="center"
 +
| style="font-weight:bold;" |KpnI || New England Biolabs
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|-align="center"
 +
| style="font-weight:bold;" |NcoI || New England Biolabs
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|-align="center"
 +
| style="font-weight:bold;" |NdeI || New England Biolabs
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|-align="center"
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| style="font-weight:bold;" |NotI || New England Biolabs
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|-align="center"
 +
| style="font-weight:bold;" |PstI || New England Biolabs
 +
|-align="center"
 +
| style="font-weight:bold;" |SacI || New England Biolabs
 +
|-align="center"
 +
| style="font-weight:bold;" |SalI || MBI Fermentas
 +
|-align="center"
 +
| style="font-weight:bold;" |ScaI || New England Biolabs
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|-align="center"
 +
| style="font-weight:bold;" |SfcI || New England Biolabs
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|-align="center"
 +
| style="font-weight:bold;" |SmiI || MBI Fermentas
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|-align="center"
 +
| style="font-weight:bold;" |SpeI || New England Biolabs
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|-align="center"
 +
| style="font-weight:bold;" |SpeI || New England Biolabs
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|-align="center"
 +
| style="font-weight:bold;" |XbaI || New England Biolabs
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|-align="center"
 +
| style="font-weight:bold;" |XhoI || MBI Fermentas
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|-align="center"
 +
| style="font-weight:bold;" |XmaI || New England Biolabs
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|-
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|}
 +
 +
===Plasmidvectors===
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{| class="wikitable"
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|- bgcolor=grey
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! height=20px, width=200px | Name || width=250px | application || width=250px | reference
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|-style="height:20px"
 +
|  ||  ||
 +
|-align="center"
 +
| style="font-weight:bold;" |BBa_B0015 || terminator || http://partsregistry.org
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|-align="center"
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| style="font-weight:bold;" |BBa_F1610 || LuxI || http://partsregistry.org
 +
|-align="center"
 +
| style="font-weight:bold;" |BBa_I15030 || AI-1 amplifier || http://partsregistry.org
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|-align="center"
 +
| style="font-weight:bold;" |BBa_I20260 || GFP || http://partsregistry.org
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|-align="center"
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| style="font-weight:bold;" |BBa_J01003 || oriT || http://partsregistry.org
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|-align="center"
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| style="font-weight:bold;" |BBa_J16002 || cloning vector || http://partsregistry.org
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|-align="center"
 +
| style="font-weight:bold;" |BBa_J23107 || constitutive promotor || http://partsregistry.org
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|-align="center"
 +
| style="font-weight:bold;" |BBa_T9002 || AI-1 GFP receiver || http://partsregistry.org
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|-align="center"
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| style="font-weight:bold;" |CheY-mCherry || cloning vector || V. Sourjik, ZMBH
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|-align="center"
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| style="font-weight:bold;" |ColE1 || colicin E1 || DSMZ
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|-align="center"
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| style="font-weight:bold;" |ColE9-J || colicin E9 || C. Kleanthous, University of York
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|-align="center"
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| style="font-weight:bold;" |pBad18 || cloning vector || V. Sourjik, ZMBH
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|-align="center"
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| style="font-weight:bold;" |pBad33 || cloning vector || V. Sourjik, ZMBH
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|-align="center"
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| style="font-weight:bold;" |pBluescript II SK (+) || cloning vector || V. Sourjik, ZMBH
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|-align="center"
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| style="font-weight:bold;" |pDest15  || cloning vector || DKFZ Library
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|-align="center"
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| style="font-weight:bold;" |pDK4 || visualization || V. Sourjik, ZMBH
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|-align="center"
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| style="font-weight:bold;" |pDK48 || cloning vector || V. Sourjik, ZMBH
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|-align="center"
 +
| style="font-weight:bold;" |pDK58 || cloning vector || V. Sourjik, ZMBH
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|-align="center"
 +
| style="font-weight:bold;" |pDK6 || visualization || V. Sourjik, ZMBH
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|-align="center"
 +
| style="font-weight:bold;" |pED374 || oriT || K. Derbyshire, Wadsworth
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|-align="center"
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| style="font-weight:bold;" |pES16 || cloning vector || V. Sourjik, ZMBH
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|-align="center"
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| style="font-weight:bold;" |pMMB863 || oriT || M. Bagdasarian, MSU
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|-align="center"
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| style="font-weight:bold;" |pQE-30 || cloning vector || Invitrogen
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|-align="center"
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| style="font-weight:bold;" |pSB1A2 || cloning vector || http://partsregistry.org
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|-align="center"
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| style="font-weight:bold;" |pSB2K3 || cloning vector || http://partsregistry.org
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|-align="center"
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| style="font-weight:bold;" |pTrc99a || cloning vector || V. Sourjik, ZMBH
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|-align="center"
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| style="font-weight:bold;" |pUB307 || helper plasmid || E. Lanka, BfR
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|-align="center"
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| style="font-weight:bold;" |RP4 || helper plasmid || M. Bagdasarian, MSU
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|-
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|}
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===Synthetic oligonucleotides===
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===Phages===
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===Bacteria===
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{| class="wikitable"
 +
|- bgcolor=grey
 +
! height=20px, width=200px | E.coli strain || width=250px | usage || width=250px | reference
 +
|-style="height:20px"
 +
|  ||  ||
 +
|-align="center"
 +
| style="font-weight:bold;" |DH5a || amplification of plasmids || Invitrogen
 +
|-align="center"
 +
| style="font-weight:bold;" |HCB33 || swarm assays || V. Sourjik, ZMBH
 +
|-align="center"
 +
| style="font-weight:bold;" |MG1655 || swarm assays || V. Sourjik, ZMBH
 +
|-align="center"
 +
| style="font-weight:bold;" |TOP10 || amplification of plasmids || Invitrogen
 +
|-align="center"
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| style="font-weight:bold;" |UU1250 || chemotaxis receptor knock out || V. Sourjik, ZMBH
 +
|-
 +
|}
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 +
===Bacteria Growth Media===
 +
{| class="wikitable"
 +
|- bgcolor=grey
 +
! height=20px, width=200px | E.coli strain || width=250px | usage || width=250px | reference
 +
|-style="height:20px"
 +
|  ||  ||
 +
|-align="center"
 +
| style="font-weight:bold;" |DH5a || amplification of plasmids || Invitrogen
 +
|-align="center"
 +
| style="font-weight:bold;" |HCB33 || swarm assays || V. Sourjik, ZMBH
 +
|-align="center"
 +
| style="font-weight:bold;" |MG1655 || swarm assays || V. Sourjik, ZMBH
 +
|-align="center"
 +
| style="font-weight:bold;" |TOP10 || amplification of plasmids || Invitrogen
 +
|-align="center"
 +
| style="font-weight:bold;" |UU1250 || chemotaxis receptor knock out || V. Sourjik, ZMBH
 +
|-
 +
|}
 +
 +
 +
For cultivation of phages the media were supplied with 0.2 % maltose and 10 mM MgSO4. For preparation of agar plates 15 g/l agar, for preparation of top agar 7 g/l agar was added prior the autoclaving. For selection of resistant bacteria following antibiotics were added during cooling of at agar at about 50 °C:
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{| class="wikitable"
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|- bgcolor=grey
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! height=20px, width=200px | Antibiotic || width=250px | concentration
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|-style="height:20px"
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|  ||
 +
|-align="center"
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| style="font-weight:bold;" |Ampicillin || 100 µg/ml
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|-align="center"
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| style="font-weight:bold;" |Chloramphenicol || 35 µg/ml
 +
|-align="center"
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| style="font-weight:bold;" |Kanamycin || 50 µg/ml
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|-
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|}
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The same concentrations of antibiotics were used for selection of resistant in media.

Revision as of 14:57, 28 October 2008

Contents

Material

Buffers & Solution

SM 50 mM Tris, pH 7.5
20 mM MgSO4
50 mM NaCl
0.01 % gelatine
Tethering buffer, pH 7.0 10 mM potassium phosphate
(K2HPO4 : KH2PO4 = 1 :1 )
100 µM EDTA
1 µM L-Methionine
10 mM lactic acid
M63 salt 3 g/l KH2PO4
9 g/l K2HPO4
4 g/l (NH4)2SO4
0.5 g/l FeSO4
Amino acid mix 5 g/l L-threonine
5 g/l L-histidin
5 g/l L-leucine
5 g/l L-methionine
M9 salts 64 g/l Na2HPO4 x 7H2O
15 g/l KH2PO4
2.5 g/l NaCl
5 g/l NH4Cl

Kits

Kit supplier
CompactPrep Plasmid Maxi Kit Qiagen
HISpeed Plasmid Maxi Kit Qiagen
MaxPlax™ Lambda Packaging Extracts EPICENTRE Biotechnologies
QIAEX II Gel Extraction Kit Qiagen
QIAGEN Lambda Mini Kit Qiagen
QIAprep Spin Mini Kit Qiagen
QIAquick Gel Extraction Kit Qiagen
QIAquick PCR Purification Kit Qiagen

Marker

Marker supplier
GeneRulerTM High Range DNA Ladder MBI Fermentas
GeneRulerTM 1kb DNA Ladder Mix MBI Fermentas
GeneRulerTM 1kb Plus DNA Ladder Mix MBI Fermentas

Enzymes

Enzym supplier
Pfu DNA polymerase Stratagene
Pfu turbo DNA polymerase Stratagene
Phusion DNA polymerase Finnzymes
Taq DNA polymerase MBI Fermentas
T4 DNA ligase MBI Fermentas / New England Biolabs
AgeI New England Biolabs
BamHI New England Biolabs
BglI MBI Fermentas
BseJI MBI Fermentas
BspEI New England Biolabs
DpnI Roche Diagnostics / New England Biolabs
DraI New England Biolabs
EcoRI New England Biolabs
EcoRV New England Biolabs
HindIII New England Biolabs
KpnI New England Biolabs
NcoI New England Biolabs
NdeI New England Biolabs
NotI New England Biolabs
PstI New England Biolabs
SacI New England Biolabs
SalI MBI Fermentas
ScaI New England Biolabs
SfcI New England Biolabs
SmiI MBI Fermentas
SpeI New England Biolabs
SpeI New England Biolabs
XbaI New England Biolabs
XhoI MBI Fermentas
XmaI New England Biolabs

Plasmidvectors

Name application reference
BBa_B0015 terminator http://partsregistry.org
BBa_F1610 LuxI http://partsregistry.org
BBa_I15030 AI-1 amplifier http://partsregistry.org
BBa_I20260 GFP http://partsregistry.org
BBa_J01003 oriT http://partsregistry.org
BBa_J16002 cloning vector http://partsregistry.org
BBa_J23107 constitutive promotor http://partsregistry.org
BBa_T9002 AI-1 GFP receiver http://partsregistry.org
CheY-mCherry cloning vector V. Sourjik, ZMBH
ColE1 colicin E1 DSMZ
ColE9-J colicin E9 C. Kleanthous, University of York
pBad18 cloning vector V. Sourjik, ZMBH
pBad33 cloning vector V. Sourjik, ZMBH
pBluescript II SK (+) cloning vector V. Sourjik, ZMBH
pDest15 cloning vector DKFZ Library
pDK4 visualization V. Sourjik, ZMBH
pDK48 cloning vector V. Sourjik, ZMBH
pDK58 cloning vector V. Sourjik, ZMBH
pDK6 visualization V. Sourjik, ZMBH
pED374 oriT K. Derbyshire, Wadsworth
pES16 cloning vector V. Sourjik, ZMBH
pMMB863 oriT M. Bagdasarian, MSU
pQE-30 cloning vector Invitrogen
pSB1A2 cloning vector http://partsregistry.org
pSB2K3 cloning vector http://partsregistry.org
pTrc99a cloning vector V. Sourjik, ZMBH
pUB307 helper plasmid E. Lanka, BfR
RP4 helper plasmid M. Bagdasarian, MSU

Synthetic oligonucleotides

Phages

Bacteria

E.coli strain usage reference
DH5a amplification of plasmids Invitrogen
HCB33 swarm assays V. Sourjik, ZMBH
MG1655 swarm assays V. Sourjik, ZMBH
TOP10 amplification of plasmids Invitrogen
UU1250 chemotaxis receptor knock out V. Sourjik, ZMBH

Bacteria Growth Media

E.coli strain usage reference
DH5a amplification of plasmids Invitrogen
HCB33 swarm assays V. Sourjik, ZMBH
MG1655 swarm assays V. Sourjik, ZMBH
TOP10 amplification of plasmids Invitrogen
UU1250 chemotaxis receptor knock out V. Sourjik, ZMBH


For cultivation of phages the media were supplied with 0.2 % maltose and 10 mM MgSO4. For preparation of agar plates 15 g/l agar, for preparation of top agar 7 g/l agar was added prior the autoclaving. For selection of resistant bacteria following antibiotics were added during cooling of at agar at about 50 °C:


Antibiotic concentration
Ampicillin 100 µg/ml
Chloramphenicol 35 µg/ml
Kanamycin 50 µg/ml

The same concentrations of antibiotics were used for selection of resistant in media.

Retrieved from "http://2008.igem.org/Team:Heidelberg/Notebook/material"