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Http://2014.igem.org/Team:Heidelberg/pages/Notebook/Materials
From 2014.igem.org
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 |
| 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 |
Mass Spectrometry and Neonate Screening
| 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) |
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 |
| 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 |
| Ring out of Plumbum with Vinyl Coating, 57 mm In | 310161013 | NEOLAB GmbH |
| TipOne® Pipette Tip 10μl, Graduated, Rac | S1111-3800 | Starlab 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 | |
| PH-Stripes | WHAT10362000 | PANPEHA PLUS |
| 100 Run24Barcode | 20110099-100 | GATC Biotech AG |
| 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 |
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 (Ampr) |
| 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 (Ampr) |
| 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 (Ampr, Cmr) |
| 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. |
E. Coli TOP10-BBa I746200/pSB1AK3 Glycerol Stock
| Stock | E. coli TOP10-(BBa I746200 in pSB1AK3) (Ampr, Kanr) |
| 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 (Cmr) |
| Amount | 1 x 1.3 ml |
| Storage | -80°C freezer |
E. Coli TOP10-pIK1 Glycerol Stock
| Stock | E. coli TOP10-pIK1 glycerol stock (Cmr) |
| Amount | 1 x 1.3 ml |
| Storage | -80°C freezer |
E. Coli TOP10-pKD46 Glycerol Stock
| Stock | E. coli TOP10-pKD46 glycerol stock (Ampr) |
| 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 (Kanr) |
| 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
