Team:KIT-Kyoto/Notebook/Protocol
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Revision as of 19:29, 21 September 2014
Protocol
LB Broth/ LB Medium
Materials
Tryptone | final concentration: 1%(w/v) |
Yeast extract | final concentration: 0.5%(w/v) |
Sodium chloride F.W. =58.44 | final concentration: 1%(w/v) |
5M Sodium hydroxide solution |
Procedure
- Dissolve tryptone (1.0 g), yeast extract (500 mg) and sodium chloride (1.0 g) in distilled water (90 ml)
- Adjust pH to 7.0 by adding 20μL of 5M sodium chloride
- Dilute solution with distilled water and bring volume to 100 ml
- Autoclave
Note
- Add antibiotics to medium at 1/1000
LB Agar
Materials
Agar powder | final concentration: 1.5 %(w/v) |
LB medium |
Procedure
- Add agar powder (6.0 g) to LB medium (400 ml)
- Dissolve it by autoclaving
- Stir up with magnetic stirrer
- Cool it down to the room temperature in order to make it to gel form
YPD Broth/YPD Medium
Materials
Peptone | final concentration: 2%(w/v) |
Yeast extract | final concentration: 1%(w/v) |
Glucose | final concentration: 2%(w/v) |
Procedure
- Dissolve peptone (2.0 g), yeast extract (1.0 g) and glucose (2.0 g) to distilled water (90 ml)
- Dilute solution with distilled water and bring up volume to 100 ml
- Sterilize by autoclave
Note
- To make agar plate, add agar powder (final concentration: 1.5%) at procedure 1.
Main Culture
Materials
LB medium | 100ml |
IPTG | 10μL |
Sample | 500μL |
Procedure
- Add samples to LB medium, cultivate at 37°C in shaken culture (120 rpm) until reaching a cell density of OD600 0.5A
- Add IPTG (10 μL) to the sample (25 ml)
- Cultivate at 37°C in shaken culture (120 rpm) for 3 hours
Note
Transformation (E.coli)
Materials
Sample | 10μL |
Competent cell | 20μL |
Procedure
- Thaw the competent cells on ice
- Add 10 μL of sample into thawed competent cells
- Cool an Eppendorf tube, which contains competent cells and samples, with ice for one hour, then Heat shock the cells by immersion in pre-hearted water bath at 41°C for 30 seconds
- Place the tube on ice for 2 minutes to cool it down
- At a clean bench, add 1.0 ml of LB medium into the tube and suspend it
- Incubate the tube at 37°C for 35 minutes
- Harvest the cells by centrifuge
- Seed the transformed competent cells onto the agar plate and incubate it at 37°C overnight
Pre-culture
Materials
Sample | |
Medium | 20ml |
Procedure
- Scrape samples from the agar plate and inoculate them on medium
- Cultivate at 37°C in a shaken culture overnight
Protein Extraction (E.coli)
Materials
Sample | |
Fast Break Cell Lysis Reagent, 10X (Promega) | |
50mM potassium phosphate buffer (=pH6.8) | |
SDS sample buffer |
Procedure
- Separate samples into two and harvest by centrifuge
- Add potassium phosphate buffer, then mix and remove medium completely
- Add Fast Break Cell Lysis Reagent, 10X at the ratio of Fast Break Buffer Cell Lysis Readent,10X: Samples=1:9 and extract protein for 15 minutes at room temperature
Colony Sweep
Materials
Sample | |
Phe-Chl | |
Cracking solution |
Procedure
- Dispense cracking solution (50 μL) each into Eppendorf tubes
- Collect the sample and suspend it into cracking solution
- Incubate at 65°C for 10 minutes
- Add Phe-Chl and BPB pigment and vortex
- Centrifuge at 14,000 rpm for 5 minutes
- Check the bands by agar gel electrophoresis
AGE
Materials
{Sample} | 5μL |
Agarose gel | |
2X Loading Buffer Triple Dye (NIPPON GENE) | 5μL |
1X TAE Buffer |
Procedure
- Set an agarose gel on an electrophoresis chamber
- Add 1X TAE buffer to the electrophoresis chamber
Note: Do not generate bubbles under the gel - Add 2X loading buffer to electrophoresis samples
- Apply samples on agarose gel wells
- Set an appropriate voltage and run the electrophoresis
- Stop the electrophoresis when the BPB reaches 2/3 of the gel
- Soak the gel in ethidium bromide and dye it for 20 minutes
- Place plastic cooking wrap on the trans-illuminator and irradiate UV to the gel on the wrap
- Take photographs of the gel by using a trans-illuminator
PCR
Materials
Buffer for KOD-FX-NEO | |
---|---|
dNTP | 20μL |
Primer mix | 1μL |
KOD-FX-NEO | 2μL |
H2O | 26.5μL |
Total | 50μL |
Procedure
- Bring the volume up forward primer to 100 pmol/μL with sterile dH2O
- Add 10 μL of this primer solution and 80 μL of H2O into another tube
Make 10 times dilution - Use 1 μL primer mix for PCR
Reaction composition is below
Ligation
Materials
DNA sample (cut out from the gel) | |
Distilled water | 5μL |
DNA ligase | 5μL |
Procedure
- Add DNA sample, distilled water and DNA ligase into a micro test tube and vortex
- Ligation for 5minutes at room temperature
<>Western Blotting
Materials
BufferⅠ | |
BufferⅡ | |
BufferⅢ | |
Distilled water | 2ml |
PBS | |
PBS-S | |
PBS-T | |
PBS-TS | |
PonceauS | |
PVDF membrane | 1 sheet |
Whatman paper | 6 sheets |
Hybridization bag | 1 |
Peroxidase Stain Kit | one drop for each |
antiglutathione S - transferase (和光純薬工業株式会社製) | 1μL |
Procedure
- Cut the gel in appropriate size
- Add BufferⅢ and gel then shake it gently
- Soak the membrane on ethanol then soak it in BufferⅢ and percolate
- 2, 1, 3 Whatman papers (all in the same size) on BufferⅠ, BufferⅡ, BufferⅢ respectively. wet the surface of the blotter
- Blot at the constant current of membrane's area ×2.5 mA
- Dye the membrane with Ponceau S for 5 minutes rinse it with distilled water and scan it
- Shake and wash with PBS-TS (3 minutes ×3 times)
- Put the membrane in a hybridization bag add PBS-S antiglutathione S-transferase and shake it for one hour at room temperature
- Shake and wash with PBS-T twice (5 min/10 min)
- Shake and wash with PBS twice (5 min/5 min)
- Add one drip of 3 Peroxidase Stain Kits and distilled water
- Scan it
Reagent
- BufferⅠ: bring to 300 ml with Tris base 10.9g, MetOH60ml/H2O
- BufferⅡ: bring to 300 ml with Tris base 0.9g, MetOH60ml/H2O
- BufferⅢ: bring to 300 ml with Tris base 0.91g, Boric acid10.5mg, MetOH60ml/H2O
- PBS-S: PBS with 1% SkimMilk
- PBS-T: PBS with 0.05% Tween20
- PBS-TS: PBS with 0.05% Tween20+1% SkimMilk