From 2014.igem.org

(Difference between revisions)

Revision as of 15:06, 16 October 2014

Kits

Kit	Supplier	Catalog Number
MinElute® PCR Purification Kit (250)	QIAGEN	28006
Plasmid Plus Maxi Kit (25)	QIAGEN	12963
Plasmid Plus Midi Kit (25)	QIAGEN	12943
QIAEX II® Gel Extraction Kit (500)	QIAGEN	20051
QIAGEN® Plasmid Plus Midi Kit (100)	QIAGEN	12945
QIAquick® Gel Extraction Kit (250)	QIAGEN	28706
QIAquick® PCR Purification Kit (250)	QIAGEN	28106
QIAprep® Spin Miniprep Kit (250)	QIAGEN	27106
QIAprep® Spin Miniprep Columns	QIAGEN	27115
EnzChek® Ultra Xylanase Assay Kit	Life Technologies	E33650

Marker

Marker	Supplier	Catalog Number
Quick-Load® 2-Log DNA Ladder (0.1-10.0 kb)	New England BioLabs	N3200S
Quick-Load® 1 kb DNA Ladder	New England BioLabs	N0468S
50 bp DNA Ladder	New England BioLabs	N3236S
Gel loading solution	Sigma-Aldrich Chemie GmbH	G2526-5ML
MagicMark XP Western Protein Standard	Life Technologies	LC5602
Novex® Sharp Pre-stained Protein Standard	Invitrogen	LC5800

Enzymes

Enzyme	Supplier	Catalog Number
DreamTaq Green PCR Master Mix (2X)	Thermo Fisher Scientific Biosciences GmbH	K1081
DreamTaq PCR MM	Fermentas Life Sciences	K1071
Gibson Assembly® Master Mix	New England Biolabs	E2611 S
Lysozyme from Chicken Egg White	Sigma-Aldrich Chemie GmbH	L4919-500MG
Phusion® Flash High-Fidelity PCR Master Mix	Biozym Scientific GmbH	F-548L
Phusion® High-Fidelity PCR Master Mix	New England Biolabs	M0531 L
T4 DNA Ligase	New England Biolabs GmbH	M0202 S
2x PCR Master mix Solution (iTaq)	HISS DIAGNOSTICS GmbH	25028

Antibodies

Antibody	Supplier	Catalog Number
Penta·His Antibody, BSA-free	QIAGEN	34660
Anti-GFP	Roche	11814460001
mRFP
Goat anti Mouse IgG	HRPO Dianova GmbH	115-035-003
secondary rat

Restriction Enzymes

Enzyme	Supplier	Catalog Number
BamI	New England Biolabs	R3136 S
BgIII	New England Biolabs	R0144 S
DpnI	New England Biolabs	R0176 S
EcoRI	New England BioLabs	R0101S
EcoRI-HF	New England Biolabs	R3101
HindIII-HF	New England Biolabs	R3104 S
KpnI-HF	New England Biolabs	R3142 S
MfeI-HF	New England Biolabs	R3589 S
NheI-HF	New England BioLabs	R3131 S
NotI-HF	New England BioLabs	R3189 S
PacI	New England Biolabs	R0547 S
PstI-HF	New England Biolabs	R3140 S
PvuI-HF	New England BioLabs	R3150S
SalI-HF	New England Biolabs	R3138 S
SpeI-HF	New England BioLabs	R3133 S
XbaI	New England BioLabs	R0145 S

Bacterial Strains

Strain	Supplier	Catalog Number
Delftia acidovorans DSM-39	DSMZ	DSM 50251
Delftia acidovorans SPH-1	DSMZ	DSM 14801
E. coli DH10ß	New England Biolabs	C3019
E. coli Top10	invitrogen	C404010
Photorhabdus laumondii luminescens	DSMZ	DSM 15139
Streptomyces lavendulae lavendulae	DSMZ	DSM 40708
Streptomyces mobaraensis	DSMZ	DSM 40903

Antibiotics and Media Supplements

Antibiotic	Supplier	Catalog Number	Concentration stock solution	Dilution	Solvent
Ampicillin Anhydrous Crystalline	Sigma-Aldrich Chemie GmbH	A9393-5G	100 mg/ml	1:1000	H₂O
Ampicillin Sodium Crystalline	Sigma-Aldrich Chemie GmbH	A9518-5G	100 mg/ml	1:1000	H₂O
Chloramphenicol Crystalline	Sigma-Aldrich Chemie GmbH	C0378-5G	30 mg/ml	1:3000	Ethanol
Kanamycinsulfat Mixture of Componenta	Sigma-Aldrich Chemie GmbH	60615-5G	50 mg/ml	1:1000	H₂O
Tetracycline	Sigma-Aldrich Chemie GmbH	T7660	10 mg/ml	1:1000	Ethanol
Propionic Acid Sodium Insect Cell*Culture	Sigma-Aldrich Chemie GmbH	P5436-100G	100mM	10mM	H₂O
Bacitracin	Sigma-Aldrich Chemie GmbH	B0125-50KU	-	-

Media

Medium	Supplier	Catalog Number
SOC Outgrowth Medium	New England Biolabs GmbH	B9020 S
LB BROTH BASE	Th. Geyer GmbH & Co KG	SA/L3022/001000
LB Broth Powder	Sigma-Aldrich Chemie GmbH	L3022-1KG
M9 Minimal Salts	SERVA	48505.01

Buffers

Buffer	Supplier	Catalog Number
NEBuffer Pack #4 (green)	New England Biolabs GmbH	B7004 S
NEBuffer Pack #1 (yellow)	New England Biolabs GmbH	B7001 S
NEBuffer Pack for T4 DNA Ligase	New England Biolabs GmbH	B0202 S
NEBuffer Pack #2 (blue)	New England Biolabs GmbH	B7002 S
NEBuffer Pack #3 (red)	New England Biolabs GmbH	B7003 S
TAE - Buffer (50X) for Molecular Biology	VWR International GmbH	A4686.1000
Gel Loading Buffer	Sigma-Aldrich	G2526-5ML
Tris Acetate-EDTA Buffer	Sigma-Aldrich	T9650-1L

Other Chemicals

Chemical	Supplier	Catalog Number
Isopropyl B-D-Thiogalactopyranoside 1 piece	Sigma-Aldrich Chemie GmbH	I5502-1G
Dimethyl Sulfoxide PCR Reagent	Sigma-Aldrich Chemie GmbH	D9170-1VL
Glycerol Sigma Grade	Sigma-Aldrich Chemie GmbH	G9012-100ML
5-Bromo-4-Chloro-3-Indolyl B-D-*Galactop	Sigma-Aldrich Chemie GmbH	B4252-100MG
Bacteriological Agar	Sigma-Aldrich Chemie GmbH	A5306-250G
L-Plus-Arabinose Crystalline	Sigma-Aldrich Chemie GmbH	A3256-25G
Calciumchlorid Dihydrat	Th. Geyer GmbH & Co KG	SA/00223506/000500
Malt Extract from Starch Digestion	Sigma-Aldrich Chemie GmbH	M0383-100G
D(+)-Saccharose, ACS, for Micro-Biology	Sigma-Aldrich Chemie GmbH	84100-1KG
Dimethyl Sulfoxide Plant Cell Culture*TE		D4540-100ML
Sodium Hydroxide Anhydrous Pellets	Th. Geyer GmbH & Co.KG	SA/S5881/000500
TRIZMA(R) Hydrochloride PH 3.5-5.0	Sigma-Aldrich Chemie GmbH	T6666-50G
L-Glutamine 200 MM Sterile	Sigma-Aldrich Chemie GmbH	G7513-20ML
Ethanol 96% Denatured	Carl Roth GmbH & Co.KG	T171.3
Propanol-2	Sigma-Aldrich Chemie GmbH	59309-1L
Natriumdodecylsulfat,SDS,99%, Ultra Pure		13904
Gold(III)-Chloride	Carl Roth GmbH & Co.KG	5624.1
Pro-Leu	Sigma-Aldrich Chemie GmbH	P1130-1G
Nitric Acid 65% p.a. Iso	Carl Roth GmbH & Co.KG	X943.1
Mops, Sodium	Sigma-Aldrich Chemie GmbH	M9024-25G
L-Glutamine	Sigma-Aldrich Chemie GmbH	G7513-100ML
Chelating Resin	Sigma-Aldrich Chemie GmbH	C7901-50G
Potassium Hydroxide in Platellets		6751.3
Hydrochloric Acid 37%		4625.1
Pyruvic Acid	Sigma-Aldrich Chemie GmbH	107360-25G
Fmoc-Orn(BOC)-OH 96.0 %		47560-5G-F
Glycerol >99.5%	Sigma-Aldrich Chemie GmbH	G9012-1L
Water Molecular Biology Reagent	Sigma-Aldrich Chemie GmbH	W4502-1L
Acetonitrile	Sigma-Aldrich Chemie GmbH	34967-1L
Ascorbic Acid 99%	Sigma-Aldrich Chemie GmbH	A92902-100G

Electrophoresis

Reagent	Supplier	Catalog Number	Concentration	Solvent
Agarose Molecular Biology Reagent	Th. Geyer GmbH & Co KG	SA/A9539/000050	0.5%	H₂O
Agarose for Routine Use	Sigma-Aldrich Chemie GmbH	A9539-100G	-	-

Primers and Oligos

Identifier	Order date	Note	Sequence

Plasmids

Name	Date	Brief Description	Genotype	Plasmid Map	GenBank-File

Instruments

Instrument	Type	Manufacturer
Table Centrifuge	Microfuge® 18 Centrifuge	Beckman CoulterTM
Table Centrifuge	Microfuge® 22R Centrifuge	Beckman CoulterTM
Centrifuge	Allegra X-12R	Beckman CoulterTM
Shaker	VORTEXGENIE 2	Scientific Industries, SITM
Heating plate (magnet stirrer)	MR Hei-Standard	Heidolph
Heatblock	QBD4	Grant
Heatblock (shakeing function)	Thermomixer comfort	Eppendorf
PCR-Machine	MyCyclerTM thermo cycler	BioRad
PCR-Machine	T100 Therma Cycler	BioRad
UV-Chamber	Transluminator	Vilber Lourmat
Scale (fine)	PioneerTM PA114C	OHAUS
Scale	PioneerTM PA4101C	OHAUS
FACS	Cytomics FC 500 MPL	Beckman Coulter
Fridge	KTP 1750 Premium	Liebherr
Freezer	GP 1366 Premium	Liebherr
Hood	Tischabzug	Wesemann® Laboreinrichtung
Draw-Off Pump	Vacuhand control	Vacubrand
Incubator	HT Multitron Version 2	INFORS
Plate Reader	Infinite M200	Tecan
Computer		Sun Microsystems
UV/VIS Spectrometer	Ultrospec 3300 pro	Amersham Biosciences
Photometer	NanoDrop® ND-1000 Spectrophotometer	peQLab Biotechnologie GmbH
Photometer	NanoVue	General Electric
Ice Machine	MF22	SCOTSMAN®
Gel Electrophoresis Chamber	Mupid®-One	Advance
Mini-PROTEAN Tetra Cell	165-8001	BioRad
Cell Density Meter	Ultrospec10	Amersham Biosciences
PH-Meter	PH-Meter 765 Calimatic	Knick
Incubator	Heraeus	Thermo Scientific
Lyophilizer	Gefriertrocknungsanlage ALPHA 1-2 LD Plus Best. Nr. 101521	Christ
Ultra Sonification Stick	Sonoplus Gm 2070 (2002)	Bandelin
Vacuum Manifold	Qiavac 24 Plus	QIAGEN
Gas Cartridge Ventil CV470	Burner	13883
NuPAGE(R) Novex 3-8% Tris-Acetate Gel 1	SDS-Gel	Life Technologies GmbH

Lab Materials

Material	Name	Manufacturer
Bottle 50 ml, 100 ml, 200 ml, 500 ml, 1000 ml
Beaker 50 ml, 100 ml, 200 ml, 500 ml 1000 ml
Conical Flask 500 ml, 1000 ml, 100 ml
Conical Flask 300 ml
Single Channel Pipette	Pipetman® P2, P20, P200, P1000	Gilson
Multichannel Pipette
Multistep Pipette
Pipette
0.2 ml PCR Tube, Flat Cap, Natural	I1402-8200	Starlab GmbH
Microcentrifuge Tubes
Centrifugetubes
PCR 8-Strips
Gloves Nitril Gr. L	Starlab powderfree	Starlab
Gloves Nitril Gr. M	Starlab powderfree	Starlab
Gloves Nitril Gr. S	Starlab powderfree	Starlab
Filtertips
Inoculating Loop
Disposal Bags
Flasks
Plate
Petri Dishes	P5731-500EA	Sigma-Aldrich Chemie GmbH
Petri Dishes	N221.2	Carl Roth GmbH & Co.KG
Petri Dishes	10558071	Fischer Scientific
TipOne® Pipette Tip	S1110-1700	Starlab GmbH
TipOne® Pipette Tip, 1000μl, Graduated	S1111-2721	Starlab GmbH
NeoBox-81 6er Set, je 1 x Transparent, g	22916
NeoLab-Marker for Reaction-Flaks	19079
Gene Pulser/MicroPulser Cuvettes, 0.1 cm	165-2089
NeoLab-Paper Scissors, 23 cm Long, Even	23272
TipOne® Pipette Tip, 200μl	S1110-1700	Starlab GmbH
TipOne® Pipette Tip, 10μl, Graduated, Re	S1111-3700	Starlab GmbH
Pipette, 5 ml	606180	Greiner bio-one GmbH
Micro Plates, 96 well	655101	Greiner bio-one GmbH
Ring out of Plumbum with Vinyl Coating, 57 mm In	310161013	NEOLAB GmbH
Reaction Tube,S.L.1.5 ml,Colorless.	12682	Eppendorf, Fisher Scientific GmbH
Reaction Tube,S.L.,2 ml, Colorless	12776	Eppendorf
NeoTape-Writing Tape, 13 mm, Gray	280126114	NEOLAB GMBH
NeoTape-Writing Tape, 25 mm, Salmon-Colored	280126229	NEOLAB GMBH
10 ml Serological Pipette, Filter, Sterile	E4860-1011	Starlab GmbH
Gloves Latex + Alovera L	14089
Gloves Latex + Alovera M	14088
Gloves Latex + Alovera S	14087
CYTOONE 96W F-BTM TC PLT	CC7682-7596	Starlab Gmbh
PH-Stripes	WHAT10362000	PANPEHA PLUS
PCR Plates 96 well	GK96HIGH	Kisker Biotec
100 Run24Barcode	20110099-100	GATC Biotech AG
Adhesive PCR Film	82-0558-A	Peqlab GmbH
Tube Conical, Polypropylen, 50 ml	352070	NEOLAB GMBH
Gene Pulser/MicroPulser Cuvettes, 0.1 cm	165-2089	Bio-Rad Laboratories GmbH
0.2 ml 8-Tube Strips Without Caps, Nature	TBS-0201	Bio-Rad Laboratories GmbH
Round-Bottom Tubule, Polypropylen, 14 ml	352059	NEOLAB GMBH
Optical Flat 8-Cap Strips	TCS-0803	Bio-Rad Laboratories GmbH
Inoculation Loop 10 μl, Blue, Sterile	2900254437
Corning Serological Pipette 50 ml	14303
Weighing Dish 500 ST	1884.1	Carl Roth GmbH & Co.KG
Filter Paper	Z274836-1PAK	Sigma-Aldrich Chemie GmbH
Inoculation Loop 10 µl	2900254437	NEOLAB GMBH
Immobilon-PSQ Membran, PVDF	ISEQ00010	Merck Milipore

Further Recipies and Stocks

Ampicillin Stock Solution

Stock	Ampicillin 100 mg / ml
Amount	50 ml
Storage	-24°C freezer
Notes	Use in 1:1000 dilution

Chloramphenicol Stock Solution

Stock	Chloramphenicol 30 mg / ml
Amount	10 ml
Storage	-24°C freezer
Notes	Solved in 100% ethanol. Use in 1:3000 dilution

E.Coli BAP 1 Glycerol Stock

Stock	E. coli BAP1 glycerol stock
Amount	2 x 1.3 ml
Storage	-80°C freezer

E.Coli BAP1, Competent

Stock	E. coli BAP1
Amount	18 x 100 µl
Storage	-80°C freezer
Notes	Grows extremely fast. Be careful with miniPreps, at least in cultures with ampicillin it tends to degrade all available ampicillin and then lose the respective plasmid.

E. coli BAP1-pKD46 Glycerol Stock

What	E. coli BAP1-pKD46 glycerol stock (Amp^r)
Amount	2 x 1.3 ml
Storage	-80°C freezer
Notes	Grow at 30°C only! Growth at 37°C will lead to loss of pKD46 plasmid.

E.Coli BAP1-pLF03 Glycerol Stock

Stock	E. coli BAP1-pLF03 glycerol stock (Amp^r)
Amount	1 x 1.3 ml
Storage	-80°C freezer
Notes	Might have low amount of plasmid-carrying bacteria due to long culturing time (all Amp in medium cleaved)

E. Coli DH5α-pCP20 Glycerol Stock

Stock	E. coli DH5α-pCP20 glycerol stock (Amp^r, Cm^r)
Amount	2 x 1.3 ml
Storage	-80°C freezer
Notes	Grow at 30°C only! Growth at 37°C will lead to loss of pCP20 plasmid.

Heat-Shock Competent E. Coli TOP10

Stock	E. coli TOP10, Heat-shock competent
Amount	200 x 100 µl
Storage	-80°C freezer
Notes	Verified on 2013-06-07.

Figure 3 Control transformation of competent TOP10 cells with 80 ng pSB4K5 with insert J04450 (IPTG-inducible mRFP production). Left: transformation with plasmid; right: transformation with water.

E. Coli TOP10-BBa I746200/pSB1AK3 Glycerol Stock

Stock	E. coli TOP10-(BBa I746200 in pSB1AK3) (Amp^r, Kan^r)
Amount	1 x 1.3 ml
Storage	-80°C freezer

E. Coli TOP10-BBa J04450/pSB3C5 Glycerol Stock

Stock	E. coli TOP10-(BBa_J04450 in pSB3C5) glycerol stock (Cm^r)
Amount	1 x 1.3 ml
Storage	-80°C freezer

E. Coli TOP10-pIK1 Glycerol Stock

Stock	E. coli TOP10-pIK1 glycerol stock (Cm^r)
Amount	1 x 1.3 ml
Storage	-80°C freezer

E. Coli TOP10-pKD46 Glycerol Stock

Stock	E. coli TOP10-pKD46 glycerol stock (Amp^r)
Amount	2 x 1.3 ml
Storage	-80°C freezer
Notes	Grow at 30°C only! Growth at 37°C will lead to loss of pKD46 plasmid.

E. Coli TOP10-pMM65 Glycerol Stock

Stock	E. coli TOP10-pMM65 glycerol stock (Kan^r)
Amount	1 x 1.3 ml
Storage	-80°C freezer

IPTG Stock Solution

Stock	IPTG 23.8 mg / ml
Amount	10 ml
Storage	-20°C freezer
Notes	Use 0.1 to 1 mM

Kanamycin Stock Solution

Stock	Kanamycin 50 mg / ml
Amount	10 ml
Storage	-24°C freezer
Notes	Use in 1:1000 dilution

M9 Medium

Name	M9 Minimal Salts 5x, Powder
Amount	1 l
Storage	room temperature
Notes	close tightly, hygroscopic

Add 200 ml of sterile M9 salt solution to 750 ml sterile, distilled H₂O (45-50°C)
Add sterile 20 ml 20% Glucose-solution, 2 ml 1 M MgSO₄ and (optionally) 1 M CaCal

Reactivation Medium

for 1L

5.0 g Peptone
3.0 g Meat extract
1000.0 ml Distilled water

Adjust pH to 7.0

@@ Line 352: / Line 352: @@
 |-
 |Gel Electrophoresis Chamber || Mupid®-One || 	Advance
+|-
+|Mini-PROTEAN Tetra Cell || 165-8001 || BioRad
 |-
 |Cell Density Meter|| Ultrospec10 || Amersham Biosciences
@@ Line 368: / Line 370: @@
 |-
 |NuPAGE(R) Novex 3-8% Tris-Acetate Gel 1|| SDS-Gel || Life Technologies GmbH
-|}
-<br/>
-=Mass Spectrometry and Neonate Screening=
-{|class="wikitable sortable"
-|-
-! Instrument !! Type !! Manufacturer !! Order number
-|-
-| Micro Filter Plates || Multiscreen 96 well || Merck Millipore || MSHVN4550
-|-
-| Microtiter Plates|| 96 well Mikrotiter plates made of Polypropylen (F-Form)  ||Greiner|| 655201
-|-
-| Microtiter Plates Locks|| ||Micromats ||
-|-
-| Aluminium Foil|| || ||
-|-
-| Mass Spectrometer || Quattro Ultima (ESI-MS/MS)|| Micromass (today: Waters)||
-|-
-| Methanol || (20837.320 METHANOL HIPERSOLV HPLC ISOCRATIC GRADE) || ||
-|-
 |}
 <br/>
@@ Line 441: / Line 422: @@
 |-
 | Petri Dishes || N221.2 || Carl Roth GmbH & Co.KG
+|-
+| Petri Dishes || 10558071 || Fischer Scientific
 |-
 | TipOne® Pipette Tip || S1110-1700 || Starlab GmbH
@@ Line 460: / Line 443: @@
 | Pipette, 5 ml || 606180 || Greiner bio-one GmbH
 |-
-| Ring out of Plumbum with Vinyl Coating, 57 mm In || 310161013 || NEOLAB GmbH
+| Micro Plates, 96 well || 655101 || Greiner bio-one GmbH
 |-
-| TipOne® Pipette Tip 10μl, Graduated, Rac || S1111-3800 ||Starlab GmbH
+| Ring out of Plumbum with Vinyl Coating, 57 mm In || 310161013 || NEOLAB GmbH
 |-
 | Reaction Tube,S.L.1.5 ml,Colorless. || 12682 || Eppendorf, Fisher Scientific GmbH
@@ Line 479: / Line 462: @@
 |-
 | Gloves Latex + Alovera S || 14087 ||
+|-
+| CYTOONE 96W F-BTM TC PLT || CC7682-7596 || Starlab Gmbh
 |-
 | PH-Stripes || WHAT10362000 || PANPEHA PLUS
+|-
+| PCR Plates 96 well || GK96HIGH || Kisker Biotec
 |-
 | 100 Run24Barcode || 20110099-100 || GATC Biotech AG
+|-
+| Adhesive PCR Film || 82-0558-A || Peqlab GmbH
 |-
 | Tube Conical, Polypropylen, 50 ml || 352070 || NEOLAB GMBH
@@ Line 503: / Line 492: @@
 |-
 | Inoculation Loop 10 µl|| 2900254437 || NEOLAB GMBH
+|-
+| Immobilon-PSQ Membran, PVDF || ISEQ00010 || Merck Milipore
 |}
 <br/>

Http://2014.igem.org/Team:Heidelberg/pages/Notebook/Materials

From 2014.igem.org

Revision as of 15:06, 16 October 2014

Contents

Kits

Marker

Enzymes

Antibodies

Restriction Enzymes

Bacterial Strains

Antibiotics and Media Supplements

Media

Buffers

Other Chemicals

Electrophoresis

Primers and Oligos

Plasmids

Instruments

Lab Materials

Further Recipies and Stocks

Ampicillin Stock Solution

Chloramphenicol Stock Solution

E.Coli BAP 1 Glycerol Stock

E.Coli BAP1, Competent

E. coli BAP1-pKD46 Glycerol Stock

E.Coli BAP1-pLF03 Glycerol Stock

E. Coli DH5α-pCP20 Glycerol Stock

Heat-Shock Competent E. Coli TOP10

E. Coli TOP10-BBa I746200/pSB1AK3 Glycerol Stock

E. Coli TOP10-BBa J04450/pSB3C5 Glycerol Stock

E. Coli TOP10-pIK1 Glycerol Stock

E. Coli TOP10-pKD46 Glycerol Stock

E. Coli TOP10-pMM65 Glycerol Stock

IPTG Stock Solution

Kanamycin Stock Solution

M9 Medium

Reactivation Medium

for 1L