Nitrogen Cavitation - Revision history

Admin: /* Procedure */

2021-11-25T14:18:22Z

Procedure

← Older revision		Revision as of 14:18, 25 November 2021
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	# Culture 1 x 10<sup>7</sup> of desired cells and wash cells with PBS twice.		# Culture 1 x 10<sup>7</sup> of desired cells and wash cells with PBS twice.
	# Resuspend cells at 1 x 10<sup>7</sup> cells/mL in disruption buffer and put sample into nitrogen cavitator.		# Resuspend cells at 1 x 10<sup>7</sup> cells/mL in disruption buffer and put sample into nitrogen cavitator.
	~~# Add magnetic stir bar into cavitator.~~		# Pressurize nitrogen cavitator and incubate sample in 250 PSI for 20 minutes at 4C.
	# Pressurize nitrogen cavitator and incubate sample in 250 PSI for 20 minutes at 4C ~~with stirring~~.
	# Release the sample dropwise into a 15mL conical tube.		# Release the sample dropwise into a 15mL conical tube.
	# Spin tube at 1000 g for 10 minutes (Nuclei pellet), collect supernatant in separate tube (Cytoplasmic fraction).		# Spin tube at 1000 g for 10 minutes (Nuclei pellet), collect supernatant in separate tube (Cytoplasmic fraction).

	== Citations ==		== Citations ==

Admin at 14:40, 16 November 2021

2021-11-16T14:40:31Z

← Older revision		Revision as of 14:40, 16 November 2021
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	# Release the sample dropwise into a 15mL conical tube.		# Release the sample dropwise into a 15mL conical tube.
	# Spin tube at 1000 g for 10 minutes (Nuclei pellet), collect supernatant in separate tube (Cytoplasmic fraction).		# Spin tube at 1000 g for 10 minutes (Nuclei pellet), collect supernatant in separate tube (Cytoplasmic fraction).

			== Citations ==

Admin: /* Protocol 1 - Phagosomes/Efferosomes */

2021-11-16T14:40:03Z

Protocol 1 - Phagosomes/Efferosomes

← Older revision		Revision as of 14:40, 16 November 2021
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	== Protocol 1 - Phagosomes/Efferosomes ==		== Protocol 1 - Phagosomes/Efferosomes ==
	This protocol was optimized for isolation of phagosomes and efferosomes containing magnetic (solid) mimic particles. This protocol may not be suitable for organelle recovery, or for recovery of phagosomes/efferosomes containing organic targets.		This protocol was optimized for isolation of phagosomes and efferosomes containing magnetic (solid) mimic particles. This protocol may not be suitable for organelle recovery, or for recovery of phagosomes/efferosomes containing organic targets. This protocol is published<ref>Charles Yin, Yohan Kim, Dean Argintaru, Bryan Heit. <u>Rab17 mediates differential antigen sorting following efferocytosis and phagocytosis.</u> ''Cell Death and Disease''. 2016 Dec 22;7(12):e2529. doi: [https://doi.org/10.1038/cddis.2016.431 10.1038/cddis.2016.431.]

			</ref>.

	=== Recipes ===		=== Recipes ===

Admin: /* Lysis Buffer */

2021-11-16T14:35:20Z

Lysis Buffer

← Older revision		Revision as of 14:35, 16 November 2021
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	=== Recipes ===		=== Recipes ===

	==== ''Wash Buffer'' ====		==== Wash Buffer ====
	*0.25M sucrose (856mg/10ml)		*0.25M sucrose (856mg/10ml)
	*10mM HEPES (24mg/10ml)		*10mM HEPES (24mg/10ml)
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	*1mM NaVO4 (100ul of 1M) - add immediately before use		*1mM NaVO4 (100ul of 1M) - add immediately before use

	==== ~~'''''~~Lysis Buffer~~'''''~~ ====		==== Lysis Buffer ====
	*1ml wash buffer		*1ml wash buffer
	*0.25mM PMSF (6.25ul of 200mM in ethanol)		*0.25mM PMSF (6.25ul of 200mM in ethanol)

Admin: Created page with "Nitrogen caviatation is a gentle way of lysing cells, and can be used to recover intact organelles, efferosomes, phagosomes, etc. We have two protocols, optimized for differen..."

2021-11-16T14:34:51Z

Created page with "Nitrogen caviatation is a gentle way of lysing cells, and can be used to recover intact organelles, efferosomes, phagosomes, etc. We have two protocols, optimized for differen..."

New page

Nitrogen caviatation is a gentle way of lysing cells, and can be used to recover intact organelles, efferosomes, phagosomes, etc. We have two protocols, optimized for different isolations, established in the lab:

== Protocol 1 - Phagosomes/Efferosomes ==
This protocol was optimized for isolation of phagosomes and efferosomes containing magnetic (solid) mimic particles. This protocol may not be suitable for organelle recovery, or for recovery of phagosomes/efferosomes containing organic targets.

=== Recipes ===

==== ''Wash Buffer'' ====
*0.25M sucrose (856mg/10ml)
*10mM HEPES (24mg/10ml)
*3mM MgCl (3ul/10ml of a 1M stock)
*1mM NaVO4 (100ul of 1M) - add immediately before use

==== '''''Lysis Buffer''''' ====
*1ml wash buffer
*0.25mM PMSF (6.25ul of 200mM in ethanol)
*200nM Okadaic acid (1ul of 1mM in DMSO)
*10mM NaF (100ul of 500mM)
*Commercial protease and phosphatase inhibitors at the recommended concentration
*1:50 dilution of DNAse I (10mg/ml stock)

=== Procedure ===
#Pre-suspend phagocytic/efferocytic target beads in the total volume of media required to cover the plate(s), cool to 10C.
#Wash cells 2X in 10C HEPES-buffered serum-containing media, then place in 10C fridge and allow to cool completely (~10 min). Use a large volume of media for these washes to ensure rapid cooling of cells.
#Once cells are cooled, replace media with bead-containing media (1ml for 5cm plates, 300ul for 35mm wells). Is possible use 100xG, 1min centrifugation to spin magnetic target particles onto phagocytes as described in [http://wiki.phagocytes.ca/index.php/Synchronised_Phagocytosis synchronized phagocytosis]. Otherwise, add an additional 5 min to the incubation (step 4)
#Incubate at 10C for 20 min to allow binding of particles, then was 2X in 37C serum-containing media to remove unbound particles and initiate phagocytosis. Large volumes (75% of max well volume) of warmed media should be used for this step to aid in rapid warming of the cells.  Do not wash vigorously.
#Place in 37C incubator for the desired length of time, then wash 2X with ice-cold media and palce on-ice to cool.
#Add lysis buffer (~0.3ml per 35mm, ~1ml per 5cm plate, ~3ml for 10cm plate) and scrape cells into buffer.  If using multiple wells per condition, transfer buffer from well-to-well instead of using additional buffer for each well.
#Pressurize lysate in pre-cooled nitrogen bomb to 300PSI. Let sit 10 min, then recover drop-wise into a parafilm-covered 1.5ml tube.
#Check a small sample on a slide for lysis; repeat step 9 if lysis is incomplete.
#Let sit on-ice for 10 min to allow DNAse to degrade DNA.
#On-ice, place tube in magnetic column and allow magnetic beads to accumulate on magent, approximately 10 min.  If solution is still viscous add additional DNAse and retry recovery.
#Wash recovered beads in 1ml wash buffer. Recover with magnetic column; 5 min.
#Repeat step 11 an additional 1-2 times.
#After the last wash, carefully remove all of the supernatant being careful to not disturb the beads.
#Pellet beads by spinning tube, maximum speed, for 3 min in the minifuge.
#For immunoblotting or mass spectometry, solubilize phagosomes in lammelli's buffer with protease and phosphatase inhibitors and run on gel as per normal.
#For other experiments, treat isoalted phagosomes as required.

== Protocol 2 - Nuclei (and other organelles) ==

=== Recipes ===

==== Disruption Buffer ====

* 0.075 M KCl
* 0.065 M NaCl
* 2.5 mM MgCL2
* 0.01 M HEPES
* Protease inhibitors added fresh before use

''pH to 7.4''

=== Procedure ===

# Culture 1 x 107 of desired cells and wash cells with PBS twice.
# Resuspend cells at 1 x 107 cells/mL in disruption buffer and put sample into nitrogen cavitator.
# Add magnetic stir bar into cavitator.
# Pressurize nitrogen cavitator and incubate sample in 250 PSI for 20 minutes at 4C with stirring.
# Release the sample dropwise into a 15mL conical tube.
# Spin tube at 1000 g for 10 minutes (Nuclei pellet), collect supernatant in separate tube (Cytoplasmic fraction).