McClean: Dry Ice-Ethanol Bath - Revision history

Megan N McClean: /* Contact */

2012-06-29T22:50:06Z

Contact

←Older revision		Revision as of 22:50, 29 June 2012
Line 44:		Line 44:
	[[Category:Yeast]]		[[Category:Yeast]]
	-->		-->
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-	~~1. Find a suitable container to hold the bath (see Hint #1).~~
-
-	~~2. Break the Dry Ice into easily transferable pieces (see Hint #2).~~
-
-	~~3. Add several pieces of Dry Ice to the bath.~~
-
-	~~4. Carefully add the Ethanol Solution to the Dry Ice until it covers the Dry Ice in the bath (see Hint #3).~~
-
-	~~5. After the Ethanol has cooled down, the solution will "boil" more slowly. As the "boiling" slows, add more Ethanol and / or Dry Ice as necessary.~~
-
-	~~Solutions~~
-	~~Title \| Overview \| Procedure \| Solutions \| BioChemicals \| Hints \| Printable Version~~
-	~~Ethanol Solution Prepared in ddH2O~~
-	70% (v/v) Ethanol*
-	~~See Hint #4~~
-
-	~~BioReagents and Chemicals~~
-	~~Title \| Overview \| Procedure \| Solutions \| BioChemicals \| Hints \| Printable Version~~
-	~~Ethanol~~
-	~~Dry Ice~~
-
-	~~Protocol Hints~~
-	~~Title \| Overview \| Procedure \| Solutions \| BioChemicals \| Hints \| Printable Version~~
-	1. The container is usually made of stainless steel or a rubber ice bucket and not plastic. Plastics can crack, causing super cooled Ethanol to leak. Although some high performance plastics can be used as a bath, the plastic will eventually degrade and crack. Find a container with a depth that is appropriate for your application.
-
-	~~2. Be sure to use gloves when handling Dry Ice.~~
-
-	~~3. Be careful, the Ethanol may splatter and burn you.~~
-
-	4. For general applications, use 70% (v/v) Ethanol, although other concentrations of Ethanol can be used. Remember that as you lower the concentration of Ethanol in the bath, you decrease the overall temperature of the bath solution. If you use 70% Ethanol, tissue sections will freeze evenly but more slowly than if you use 100% Ethanol. When precipitating RNA, DNA, or proteins, the Ethanol Solution can contain 70% to 100% Ethanol.

Megan N McClean at 22:49, 29 June 2012

2012-06-29T22:49:35Z

←Older revision		Revision as of 22:49, 29 June 2012
Line 5:		Line 5:

	==Materials==		==Materials==
		+	* Ice bucket or similar
		+	* Dry ice (available as pellets downstairs near the loading dock)
		+	* 70% (v/v) Ethanol (see notes)

-	* 1M LiAC
-	* 100mM LiAC
-	* 50% w/v PEG MW 3350 (Sigma P3640)
-	* Sterile H20
-	* Single-stranded carrier DNA (Sigma D1626, 2.0 mg/ml in TE buffer pH 8.0)
-	* Appropriate selective plates (SC-URA, YPD+G418, etc)
-	* Sterile 4mm glass-beads for plating (Fisher 11-312B)

-	==~~Stock Solutions~~==	+	==Procedure==
		+	# Find a suitable container, such as an ice bucket, to hold the bath. Don't use something that will crack due to the extreme temperatures.
		+	# Add several pieces of dry ice to the bath (see Hint #1).
		+	# Carefully add the Ethanol Solution to the Dry Ice until it covers the Dry Ice in the bath (see Hint #3).
		+	# After the Ethanol has cooled down, the solution will "boil" more slowly. As the "boiling" slows, add more Ethanol and / or Dry Ice as necessary.

-	~~'''Polyethylene glycol PEG 50% w/v (Sigma P3640)'''~~
-
-	* Make up 50% w/v with H<sub>2</sub>O and filter-sterilize with a 0.45uM filter unit (Nalgene 295-4545 or similar). It will take a long time for the PEG to work it's way through the filter, be patient. We don't autoclave the PEG. Store in a tightly capped container to avoid evaporation.
-
-	~~'''Single-stranded carrier DNA (Sigma D1626)'''~~
-	# Weight out 200mg of the DNA into 100ml of TE buffer. Disperse the Dna into solution by drawing it p and dwn repeatedly in a 10-ml pipette. Mix vigorosly on a magnetic stirrer for 2-3 hours or until fully dissolved. Alternatively, leave the covered solution mixing at this stage overnight in a cold rom.
-	~~# Aliquot the DNA into 100μL portions and store at -20°C.~~
-	~~# Prior to use, the aliquot should be boiled and then quickly cooled on ice. We use a thermocycler to heat the DNA to 95°C for 25 minutes and then rapidly cool it on ice.~~
-
-	~~Once the salmon sperm has been boiled it can be freeze-thawed 3 or 4 times before transformation efficiencies begin to decrease. In practice, we boil the DNA before every transformation.~~
-
-	~~'''TE Buffer (pH 8.0)'''~~
-	*10 mM Tris-HCL (pH 8.0)
-	*1.0 mM EDTA
-
-	~~'''1.0M Lithium acetate stock solution (LiAc)'''~~
-
-	* Prepare as a 1.0 M stock in distilled deionized H<sub>2</sub>O; filter-sterilize. The final pH should be between 8.4 and 8.9
-
-	~~'''Glass-beads for plating (Fisher 11-312B)'''~~
-	*Pour beads into a small glass bottle (typically wide-mouthed 100ml or 250ml bottles work well) and autoclave on a 15 minute dry cycle to sterilize
-
-	~~==''Day 1''==~~
-	~~# Inoculate the strain to transform from a single colony into 5mls of YPD in a test tube. Put on the roller drum at room temperature overnight.~~
-
-	~~==''Day 2''==~~
-	# Inoculate 50 ml of YPD with 500 μL of the YPD overnight culture in a 250 ml flask. The 500 µl volume is approximate, and depends on the density of the strain you inoculate (you want to aim for diluting your culture down to 5x10^6 cells).
-	~~# Grow in shaking incubator at room temperature for about 3-5 hours.~~
-	# Adjust water bath to 37°C (for heat-shock) if it is not already on. REMEMBER: Don't leave the water bath set to 42°C! You can also put a beaker of water in the 37°C warm room (and let it equilibriate to 37°C!) so that you don't have to bother with adjusting the water bath.
-	# Harvest the cells by centrifuging in Eppendorf centrifuge model 5810R at 4000rpm (3130 xg) for 5 min. Resuspend pellet in 25 ml of sterile water by vortexing briefly. Pellet again and then resuspend in 1 ml of 100 mM LiAc.
-	~~# Transfer cell suspension to a 1.5 ml eppendorf tube, centrifuge at 3,000 xg for 2 min in an Eppendorf 5418 centrifuge and discard supernatant by removing it with a pipette.~~
-	# Add 400 µl 100 mM LiAc and resuspend cells by pipetting up and down. Aliquot 50 μL into 1.5 ml tubes (1 for each transformation). Pellet cells (3,000 xg for 2 min) and remove supernatant by aspiration.
-	~~# Add 300 μL T mix to each eppendorf tube of cells. Per one transformation reaction add '''IN ORDER''':~~
-	~~#*240 μL 50% PEG 3350~~
-	~~#*35 μL 1.0 M lithium acetate~~
-	~~#*25 μL 2 mg/ml sssDNA~~
-	~~#*50 μL sterile H20 and 20 μL of DNA (Note: You are aiming for a final concentration between 0.1-10 μg for plasmid DNA. Adjust your DNA and water amounts to add 70 μL of volume total)~~
-	~~# Vortex to resuspend cells.~~
-	~~# Incubate for 30 minutes at room temperature.~~
-	~~# Incubate tubes in a water bath at 37°C for 45 minutes. The time may need to optimized for your strain and transformation conditions.~~
-	# Microfuge at 3,000 xg for 15s, and remove transformation mix with a micropipette. (NOTE: If you are transforming cells with a drug resistance marker such as KanMX, NatMX, HygMX or selecting for 5-FOA resistance, '''DO NOT''' plate your cells now, you need to do a recovery step. See below.)
-	~~# Add 200 µL of sterile water to each tube and resuspend cells by pipetting it up and down as gently as possible if high efficiency is important.~~
-	# Plate your cells using glass beads to spread the cells. Add 3-4 glass beads to each plate that you will be using, add about 200μL of cells + water, and spread by shaking the plate horizontally. To ensure single colonies:
-	~~#* Plate 150 µl of sterile water and add 20 µl cell suspension in one selection plate #1.~~
-	~~#* Plate the remaining 180 µl in selection plate #2~~
-	~~#Incubate at room temperature. Colonies should appear after 2-4 days.~~
-
-	~~==Recovery step for drug resistance markers and 5-FOA==~~
-	*If you are plating your cells onto plates with G418, clonNat, hygromycin, or 5-FOA (basically if you are trying to select for anything BUT the ability to grow without a particular amino acid) you need to give your cells some time to recover and express the resistance marker after you've transformed them. This is done after you have removed the transformation mix but ''before'' you plate the cells. You have two options for recovery:
-	# Gently resuspend cells in 1ml of YPD. Put this tube at room temperature for 1-4 hours (with a tube clamp to keep the eppendorf from popping open). After recovery, spin down the cells, resuspend in sterile water, and plate as above.
-	# Gently resuspend cells in 1ml of YPD. Plate 200μL cuture onto a YPD plate. In the morning, replica plate this lawn of cells onto a selection plate. You should see colonies in 2-4 days. We usually save the rest of the cells resuspended in YPD overnight at room temperature (with a tube clamp to keep the eppendorf from popping open) and plate about 200μL of this onto a selection plate in the morning just as a back-up.
-
-	*We have found that plating onto YPD and replica plating the next day gives the best results. For 5-FOA transformations it seems crucial to do it this way, as allowing the cells to grow in liquid YPD for any amount of time allows cells with mutations in URA3 to arise and these are able to grow on 5-FOA.

	==Notes==		==Notes==
Line 75:		Line 22:
	#You can also link to FAQs/tips provided by other sources such as the manufacturer or other websites.		#You can also link to FAQs/tips provided by other sources such as the manufacturer or other websites.
	#Anecdotal observations that might be of use to others can also be posted here.		#Anecdotal observations that might be of use to others can also be posted here.
		+	*[[User:Megan N McClean\|Megan N McClean]] 18:49, 29 June 2012 (EDT) You need to be careful when handling the dry ice and especially when the bath is boiling. Wear gloves when handling the dry ice, a lab coat, and goggles (to protect your eyes in case of splashing ethanol)
		+	*[[User:Megan N McClean\|Megan N McClean]] 18:49, 29 June 2012 (EDT)For general applications, use 70% (v/v) Ethanol, although other concentrations of ethanol can be used. We generally use 95% ethanol for the Bust n' Grab protocol.
		+

	Please sign your name to your note by adding <font face="courier"><nowiki>'''*~~~~''':</nowiki></font> to the beginning of your tip.		Please sign your name to your note by adding <font face="courier"><nowiki>'''*~~~~''':</nowiki></font> to the beginning of your tip.
Line 87:		Line 37:

	<!-- You can tag this protocol with various categories. See the [[Categories]] page for more information. -->		<!-- You can tag this protocol with various categories. See the [[Categories]] page for more information. -->
-		+	[[Category:Protocol]]
	<!-- Move the relevant categories above this line to tag your protocol with the label		<!-- Move the relevant categories above this line to tag your protocol with the label
-	~~[[Category:Protocol]]~~

	[[Category:Media]]		[[Category:Media]]

Megan N McClean: /* Contact */

2012-06-29T22:43:44Z

Contact

←Older revision		Revision as of 22:43, 29 June 2012
Line 98:		Line 98:


-	~~General Laboratory Method~~
-
-	~~Preparation and Use of a Dry Ice / Ethanol Bath~~



-	~~Overview~~
-	~~Title \| Overview \| Procedure \| Solutions \| BioChemicals \| Hints \| Printable Version~~

-
-	~~Procedure~~
-	~~Title \| Overview \| Procedure \| Solutions \| BioChemicals \| Hints \| Printable Version~~
	1. Find a suitable container to hold the bath (see Hint #1).		1. Find a suitable container to hold the bath (see Hint #1).

Megan N McClean at 22:42, 29 June 2012

2012-06-29T22:42:51Z

←Older revision		Revision as of 22:42, 29 June 2012
Line 2:		Line 2:

	==Overview==		==Overview==
-	Dry Ice-Ethanol baths are used to rapidly cool solutions to below freezing temperatures. In the lab, we most often use this for the genomic DNA preparation protocol. This protocol was adapted from the protocol of the Malaysian Cocoa Board (no joke!). See references below.	+	Dry Ice-Ethanol baths are used to rapidly cool solutions to below freezing temperatures. In the lab, we most often use this for the [[McClean: Genomic DNA Prep (Bust 'n' Grab Protocol)\| Bust n' Grab]] genomic DNA preparation protocol. This protocol was adapted from the protocol of the Malaysian Cocoa Board (no joke!). See references below.

	==Materials==		==Materials==

Megan N McClean: /* References */

2012-06-29T22:41:45Z

References

←Older revision		Revision as of 22:41, 29 June 2012
Line 79:		Line 79:

	==References==		==References==
-	[[http://www.koko.gov.my Malaysian Cocoa Board Protocol]]	+	[http://www.koko.gov.my Malaysian Cocoa Board Protocol]

	==Contact==		==Contact==

Megan N McClean: New page: ==Overview== Dry Ice-Ethanol baths are used to rapidly cool solutions to below freezing temperatures. In the lab, we most ...

2012-06-29T22:41:28Z

New page:  ==Overview== Dry Ice-Ethanol baths are used to rapidly cool solutions to below freezing temperatures. In the lab, we most ...

New page

==Overview==
Dry Ice-Ethanol baths are used to rapidly cool solutions to below freezing temperatures. In the lab, we most often use this for the genomic DNA preparation protocol. This protocol was adapted from the protocol of the Malaysian Cocoa Board (no joke!). See references below.

==Materials==

* 1M LiAC
* 100mM LiAC
* 50% w/v PEG MW 3350 (Sigma P3640)
* Sterile H20
* Single-stranded carrier DNA (Sigma D1626, 2.0 mg/ml in TE buffer pH 8.0)
* Appropriate selective plates (SC-URA, YPD+G418, etc)
* Sterile 4mm glass-beads for plating (Fisher 11-312B)

==Stock Solutions==

'''Polyethylene glycol PEG 50% w/v (Sigma P3640)'''

* Make up 50% w/v with H2O and filter-sterilize with a 0.45uM filter unit (Nalgene 295-4545 or similar). It will take a long time for the PEG to work it's way through the filter, be patient. We don't autoclave the PEG. Store in a tightly capped container to avoid evaporation.

'''Single-stranded carrier DNA (Sigma D1626)'''
# Weight out 200mg of the DNA into 100ml of TE buffer. Disperse the Dna into solution by drawing it p and dwn repeatedly in a 10-ml pipette. Mix vigorosly on a magnetic stirrer for 2-3 hours or until fully dissolved. Alternatively, leave the covered solution mixing at this stage overnight in a cold rom.
# Aliquot the DNA into 100μL portions and store at -20°C.
# Prior to use, the aliquot should be boiled and then quickly cooled on ice. We use a thermocycler to heat the DNA to 95°C for 25 minutes and then rapidly cool it on ice.

Once the salmon sperm has been boiled it can be freeze-thawed 3 or 4 times before transformation efficiencies begin to decrease. In practice, we boil the DNA before every transformation.

'''TE Buffer (pH 8.0)'''
*10 mM Tris-HCL (pH 8.0)
*1.0 mM EDTA

'''1.0M Lithium acetate stock solution (LiAc)'''

* Prepare as a 1.0 M stock in distilled deionized H2O; filter-sterilize. The final pH should be between 8.4 and 8.9

'''Glass-beads for plating (Fisher 11-312B)'''
*Pour beads into a small glass bottle (typically wide-mouthed 100ml or 250ml bottles work well) and autoclave on a 15 minute dry cycle to sterilize

==''Day 1''==
# Inoculate the strain to transform from a single colony into 5mls of YPD in a test tube. Put on the roller drum at room temperature overnight.

==''Day 2''==
# Inoculate 50 ml of YPD with 500 μL of the YPD overnight culture in a 250 ml flask. The 500 µl volume is approximate, and depends on the density of the strain you inoculate (you want to aim for diluting your culture down to 5x10^6 cells).
# Grow in shaking incubator at room temperature for about 3-5 hours.
# Adjust water bath to 37°C (for heat-shock) if it is not already on. REMEMBER: Don't leave the water bath set to 42°C! You can also put a beaker of water in the 37°C warm room (and let it equilibriate to 37°C!) so that you don't have to bother with adjusting the water bath.
# Harvest the cells by centrifuging in Eppendorf centrifuge model 5810R at 4000rpm (3130 xg) for 5 min. Resuspend pellet in 25 ml of sterile water by vortexing briefly. Pellet again and then resuspend in 1 ml of 100 mM LiAc.
# Transfer cell suspension to a 1.5 ml eppendorf tube, centrifuge at 3,000 xg for 2 min in an Eppendorf 5418 centrifuge and discard supernatant by removing it with a pipette.
# Add 400 µl 100 mM LiAc and resuspend cells by pipetting up and down. Aliquot 50 μL into 1.5 ml tubes (1 for each transformation). Pellet cells (3,000 xg for 2 min) and remove supernatant by aspiration.
# Add 300 μL T mix to each eppendorf tube of cells. Per one transformation reaction add '''IN ORDER''':
#*240 μL 50% PEG 3350
#*35 μL 1.0 M lithium acetate
#*25 μL 2 mg/ml sssDNA
#*50 μL sterile H20 and 20 μL of DNA (Note: You are aiming for a final concentration between 0.1-10 μg for plasmid DNA. Adjust your DNA and water amounts to add 70 μL of volume total)
# Vortex to resuspend cells.
# Incubate for 30 minutes at room temperature.
# Incubate tubes in a water bath at 37°C for 45 minutes. The time may need to optimized for your strain and transformation conditions.
# Microfuge at 3,000 xg for 15s, and remove transformation mix with a micropipette. (NOTE: If you are transforming cells with a drug resistance marker such as KanMX, NatMX, HygMX or selecting for 5-FOA resistance, '''DO NOT''' plate your cells now, you need to do a recovery step. See below.)
# Add 200 µL of sterile water to each tube and resuspend cells by pipetting it up and down as gently as possible if high efficiency is important.
# Plate your cells using glass beads to spread the cells. Add 3-4 glass beads to each plate that you will be using, add about 200μL of cells + water, and spread by shaking the plate horizontally. To ensure single colonies:
#* Plate 150 µl of sterile water and add 20 µl cell suspension in one selection plate #1.
#* Plate the remaining 180 µl in selection plate #2
#Incubate at room temperature. Colonies should appear after 2-4 days.

==Recovery step for drug resistance markers and 5-FOA==
*If you are plating your cells onto plates with G418, clonNat, hygromycin, or 5-FOA (basically if you are trying to select for anything BUT the ability to grow without a particular amino acid) you need to give your cells some time to recover and express the resistance marker after you've transformed them. This is done after you have removed the transformation mix but ''before'' you plate the cells. You have two options for recovery:
# Gently resuspend cells in 1ml of YPD. Put this tube at room temperature for 1-4 hours (with a tube clamp to keep the eppendorf from popping open). After recovery, spin down the cells, resuspend in sterile water, and plate as above.
# Gently resuspend cells in 1ml of YPD. Plate 200μL cuture onto a YPD plate. In the morning, replica plate this lawn of cells onto a selection plate. You should see colonies in 2-4 days. We usually save the rest of the cells resuspended in YPD overnight at room temperature (with a tube clamp to keep the eppendorf from popping open) and plate about 200μL of this onto a selection plate in the morning just as a back-up.

*We have found that plating onto YPD and replica plating the next day gives the best results. For 5-FOA transformations it seems crucial to do it this way, as allowing the cells to grow in liquid YPD for any amount of time allows cells with mutations in URA3 to arise and these are able to grow on 5-FOA.

==Notes==
Please feel free to post comments, questions, or improvements to this protocol. Happy to have your input!
#List troubleshooting tips here.
#You can also link to FAQs/tips provided by other sources such as the manufacturer or other websites.
#Anecdotal observations that might be of use to others can also be posted here.

Please sign your name to your note by adding <nowiki>'''*~~~~''':</nowiki> to the beginning of your tip.

==References==
[[http://www.koko.gov.my Malaysian Cocoa Board Protocol]]

==Contact==
*'''[[User:Megan N McClean|Megan N McClean]] 14:01, 20 July 2011 (EDT)'''

or instead, [[Talk:{{PAGENAME}}|discuss this protocol]].





General Laboratory Method

Preparation and Use of a Dry Ice / Ethanol Bath

Overview
Title | Overview | Procedure | Solutions | BioChemicals | Hints | Printable Version

Procedure
Title | Overview | Procedure | Solutions | BioChemicals | Hints | Printable Version
1. Find a suitable container to hold the bath (see Hint #1).

2. Break the Dry Ice into easily transferable pieces (see Hint #2).

3. Add several pieces of Dry Ice to the bath.

4. Carefully add the Ethanol Solution to the Dry Ice until it covers the Dry Ice in the bath (see Hint #3).

5. After the Ethanol has cooled down, the solution will "boil" more slowly. As the "boiling" slows, add more Ethanol and / or Dry Ice as necessary.

Solutions
Title | Overview | Procedure | Solutions | BioChemicals | Hints | Printable Version
Ethanol Solution Prepared in ddH2O
70% (v/v) Ethanol*
See Hint #4

BioReagents and Chemicals
Title | Overview | Procedure | Solutions | BioChemicals | Hints | Printable Version
Ethanol
Dry Ice

Protocol Hints
Title | Overview | Procedure | Solutions | BioChemicals | Hints | Printable Version
1. The container is usually made of stainless steel or a rubber ice bucket and not plastic. Plastics can crack, causing super cooled Ethanol to leak. Although some high performance plastics can be used as a bath, the plastic will eventually degrade and crack. Find a container with a depth that is appropriate for your application.

2. Be sure to use gloves when handling Dry Ice.

3. Be careful, the Ethanol may splatter and burn you.

4. For general applications, use 70% (v/v) Ethanol, although other concentrations of Ethanol can be used. Remember that as you lower the concentration of Ethanol in the bath, you decrease the overall temperature of the bath solution. If you use 70% Ethanol, tissue sections will freeze evenly but more slowly than if you use 100% Ethanol. When precipitating RNA, DNA, or proteins, the Ethanol Solution can contain 70% to 100% Ethanol.