Difference between revisions of "DNA Extraction Schizophyllum commune CTAB-PEG"
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# Prepare fresh mycelia from [[IPDA]] plates. Dry the mycelia on filter paper. The recommendated amount of sample is 0.09–0.12 g (dry weight) for each operation. | # Prepare fresh mycelia from [[IPDA]] plates. Dry the mycelia on filter paper. The recommendated amount of sample is 0.09–0.12 g (dry weight) for each operation. | ||
# Freeze the dried mycelium in [[liquid nitrogen]] and grind it to a powder in a mortar prechilled with liquid nitrogen. | # Freeze the dried mycelium in [[liquid nitrogen]] and grind it to a powder in a mortar prechilled with liquid nitrogen. | ||
− | # Add 4 mL of [#4% CTAB extraction buffer (pH 8.0)] to the mortar. | + | # Add 4.5 mL of [#4% CTAB extraction buffer (pH 8.0)] to the mortar. |
# Incubate the digest for 40–60 min at 65°C. The mortar should be sealed to prevent contamination during digestion. | # Incubate the digest for 40–60 min at 65°C. The mortar should be sealed to prevent contamination during digestion. | ||
# Mix the digest well. | # Mix the digest well. | ||
# Transfer 4 mL of the lysis suspension to a fresh 15ml Falcon tube. | # Transfer 4 mL of the lysis suspension to a fresh 15ml Falcon tube. | ||
− | # Preheated [[#CTAB/NaCl | + | # Preheated [[#CTAB/NaCl (10% w/v CTAB, 0.7 M NaCl) | CTAB/NaCl solution]] to 65°С. This step cannot be omitted. Without heating up the CTAB/NaCl, the solution is sticky, and cannot be pipetted easily. |
− | # Add | + | # Add 1 mL of 96% ethanol and 440 μL of 5 M [[#Potassium acetate 5M CH3COOK | Potassium acetate (CH<sub>3</sub>COOK)]] to each tube (ethanol:CH<sub>3</sub>COOK = 25:11, v/v), and mix contents of the tube by vortexing for 1 min. |
+ | # Incubate the tubes for 30 min at 4°C in the fridge. | ||
# Allow the tubes to warm up to room temperature for ~3 min. | # Allow the tubes to warm up to room temperature for ~3 min. | ||
− | # Add | + | # Add 4 mL [[#chloroform:isoamyl alcohol (24:1 v/v) | chloroform:isoamyl alcohol (24:1 v/v)]] to each tube, and mix the organic and aqueous phases by vortexing for 1 minute. |
− | # Separate the mixture into three phases by centrifuging at 10,000 xg for 15 min at 20°C. Transfer the upper aqueous phase to | + | # Separate the mixture into three phases by centrifuging at 10,000 xg for 15 min at 20°C. |
− | # Add | + | # Transfer 4.5 ml of the upper aqueous phase to a fresh tube. |
− | # Add | + | # Add 733 μL of [[5M NaCl]] and mix by inversion. The final concentration NaCl should be 0.7 M. |
+ | # Add 594 μL of CTAB/NaCl solution (pH 8.0, preheated for >10min at step 4 ) and mix well by inverting multiple times. | ||
# Incubate the tubes for 15 min at 65°C. | # Incubate the tubes for 15 min at 65°C. | ||
− | # | + | # Add 5 μL of DNase-free RNase A (100 mg/ml). |
# Incubate the mixture for 30 min at 50°C. | # Incubate the mixture for 30 min at 50°C. | ||
# Transfer each 900 μL of the mixture to a fresh microfuge tube. Add an equal volume of chloroform: isoamyl alcohol (24 : 1, v/v) to each tube, and mix the organic and aqueous phases by vortexing for 1 min. | # Transfer each 900 μL of the mixture to a fresh microfuge tube. Add an equal volume of chloroform: isoamyl alcohol (24 : 1, v/v) to each tube, and mix the organic and aqueous phases by vortexing for 1 min. | ||
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*2ml 1M EDTA, pH 8.0 | *2ml 1M EDTA, pH 8.0 | ||
*fill to 100ml with demiwater | *fill to 100ml with demiwater | ||
+ | Store at RT in drawer under fume hood | ||
+ | '''Note that CTAB needs to be disposed of properly.''' | ||
+ | |||
+ | ===CTAB/NaCl (10% w/v CTAB, 0.7 M NaCl)=== | ||
+ | For 100 ml: | ||
+ | * 10 g CTAB | ||
+ | * 4.1 g NaCl | ||
+ | * 5ml 1M Tris-HCl, pH 8.0 | ||
+ | * 2ml 1M EDTA, pH 8.0 | ||
+ | * fill to 100ml with demiwater | ||
+ | Store at RT in drawer under fume hood | ||
+ | '''Note that CTAB needs to be disposed of properly.''' | ||
===1.4 M NaCl=== | ===1.4 M NaCl=== | ||
For 100 ml | For 100 ml | ||
− | Dissolve 8.2 g NaCl in demiwater | + | Dissolve 8.2 g NaCl in 100 ml demiwater |
Sterilize by autoclaving | Sterilize by autoclaving | ||
+ | |||
+ | ===5 M NaCl=== | ||
+ | For 100 ml | ||
+ | Dissolve 29.2 g NaCl in 100 ml demiwater | ||
+ | Sterilize by autoclaving and store at RT | ||
===Potassium acetate 5M CH3COOK=== | ===Potassium acetate 5M CH3COOK=== | ||
+ | For 100 ml | ||
+ | Dissolve 49.1 g CH3COOK in 100 ml demiwater | ||
+ | Sterilize by autoclaving and store at RT | ||
===chloroform:isoamyl alcohol (24:1 v/v)=== | ===chloroform:isoamyl alcohol (24:1 v/v)=== | ||
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* 96 ml Chloroform | * 96 ml Chloroform | ||
* 4 ml Isoamyl alcohol | * 4 ml Isoamyl alcohol | ||
+ | Store at RT in drawer under fume hood | ||
'''Note that chloroform:isoamyl alcohol needs to be disposed of properly.''' | '''Note that chloroform:isoamyl alcohol needs to be disposed of properly.''' | ||
− | |||
− | |||
− | |||
− | |||
− | |||
− | |||
− | |||
− | |||
===20% PEG 8000 solution (1.2 M NaCl)=== | ===20% PEG 8000 solution (1.2 M NaCl)=== | ||
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* 7 g NaCl | * 7 g NaCl | ||
* fill to 100ml with demiwater | * fill to 100ml with demiwater | ||
+ | Store at 4°C |
Revision as of 16:58, 17 June 2020
Extraction protocol for high-quality, high-molecular-weight genomic DNA
This protocol is based on paper Huang et al. “CTAB-PEG DNA Extraction from Fungi with High Contents of Polysaccharides.” Molecular Biology 52, no. 4 (July 1, 2018): 621–28. the errata in that protocol can be found here.
- Prepare fresh mycelia from IPDA plates. Dry the mycelia on filter paper. The recommendated amount of sample is 0.09–0.12 g (dry weight) for each operation.
- Freeze the dried mycelium in liquid nitrogen and grind it to a powder in a mortar prechilled with liquid nitrogen.
- Add 4.5 mL of [#4% CTAB extraction buffer (pH 8.0)] to the mortar.
- Incubate the digest for 40–60 min at 65°C. The mortar should be sealed to prevent contamination during digestion.
- Mix the digest well.
- Transfer 4 mL of the lysis suspension to a fresh 15ml Falcon tube.
- Preheated CTAB/NaCl solution to 65°С. This step cannot be omitted. Without heating up the CTAB/NaCl, the solution is sticky, and cannot be pipetted easily.
- Add 1 mL of 96% ethanol and 440 μL of 5 M Potassium acetate (CH3COOK) to each tube (ethanol:CH3COOK = 25:11, v/v), and mix contents of the tube by vortexing for 1 min.
- Incubate the tubes for 30 min at 4°C in the fridge.
- Allow the tubes to warm up to room temperature for ~3 min.
- Add 4 mL chloroform:isoamyl alcohol (24:1 v/v) to each tube, and mix the organic and aqueous phases by vortexing for 1 minute.
- Separate the mixture into three phases by centrifuging at 10,000 xg for 15 min at 20°C.
- Transfer 4.5 ml of the upper aqueous phase to a fresh tube.
- Add 733 μL of 5M NaCl and mix by inversion. The final concentration NaCl should be 0.7 M.
- Add 594 μL of CTAB/NaCl solution (pH 8.0, preheated for >10min at step 4 ) and mix well by inverting multiple times.
- Incubate the tubes for 15 min at 65°C.
- Add 5 μL of DNase-free RNase A (100 mg/ml).
- Incubate the mixture for 30 min at 50°C.
- Transfer each 900 μL of the mixture to a fresh microfuge tube. Add an equal volume of chloroform: isoamyl alcohol (24 : 1, v/v) to each tube, and mix the organic and aqueous phases by vortexing for 1 min.
- Separate the mixture into three phases by centrifuging at 10,000 xg for 15 min at 20°C. Transfer the upper aqueous phase to fresh tubes.
- Repeat steps XXXXX
- Transfer the upper aqueous phase to a fresh microfuge tube.
- Collect the DNA by precipitation with an equal volume of 20% PEG-8000 (pH 8.0, contains 20% PEG-8000 w/v, 1.2M NaCl) for 1–2 h at –20°C or at 4°C overnight.
- Precipitate the nucleic acids by centrifugation at 10,000 xg for 10 min at 4°C in the Cooling centrifuge.
- Remove the supernatant by aspiration.
- Rinse the pellet with 200 μL of 70% ethanol.
- Centrifuge the tubes at 10,000 xg for 1 min at room temperature in a microfuge.
- Rinse the pellet once more with 200 μL 70% ethanol.
- Centrifuge again at 10,000 xg for 1 min at room temperature.
- Combine the precipitates from all tubes into 1–2 tubes. It can increase the concentration of DNA.
- Remove the supernatant by aspiration and allow the pellet to dry in the air for 1–2 min. Redissolve the pellet in 20–40 μL of DNase-free H2O.
Reagents and solutions
Buffers and solutions used for DNA isolation from mycelium of Schizophyllum commune.
4% CTAB extraction buffer:
For 100 ml:
- 4g CTAB
- 5ml 1M Tris-HCl, pH 8.0
- 2ml 1M EDTA, pH 8.0
- fill to 100ml with demiwater
Store at RT in drawer under fume hood Note that CTAB needs to be disposed of properly.
CTAB/NaCl (10% w/v CTAB, 0.7 M NaCl)
For 100 ml:
- 10 g CTAB
- 4.1 g NaCl
- 5ml 1M Tris-HCl, pH 8.0
- 2ml 1M EDTA, pH 8.0
- fill to 100ml with demiwater
Store at RT in drawer under fume hood Note that CTAB needs to be disposed of properly.
1.4 M NaCl
For 100 ml Dissolve 8.2 g NaCl in 100 ml demiwater Sterilize by autoclaving
5 M NaCl
For 100 ml Dissolve 29.2 g NaCl in 100 ml demiwater Sterilize by autoclaving and store at RT
Potassium acetate 5M CH3COOK
For 100 ml Dissolve 49.1 g CH3COOK in 100 ml demiwater Sterilize by autoclaving and store at RT
chloroform:isoamyl alcohol (24:1 v/v)
In a fume hood, mix in a 250 ml Greiner bottle:
- 96 ml Chloroform
- 4 ml Isoamyl alcohol
Store at RT in drawer under fume hood Note that chloroform:isoamyl alcohol needs to be disposed of properly.
20% PEG 8000 solution (1.2 M NaCl)
For 100 ml:
- 20 g PEG-8000
- 7 g NaCl
- fill to 100ml with demiwater
Store at 4°C