Daniel:Protocols/CProbeLigate: Difference between revisions
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[[Daniel Jacobsen|Back to Notebook]] | [[Daniel Jacobsen|Back to Notebook]] | ||
This page describes the protocol for hybridizing C probes as used in PLAYR Design (as from [http://www. | This page describes the protocol for hybridizing C probes as used in PLAYR Design (as from [http://www.nature.com/nmeth/journal/v13/n3/abs/nmeth.3742.html Nolan lab paper]). | ||
==Protocol== | ==Protocol== | ||
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<li>Hybridization</li> | <li>Hybridization</li> | ||
<ol type-"A"> | <ol type-"A"> | ||
<li> | <li>Pellet cells via centrifugation at 600g for 3 min</li> | ||
<li>Heat C probes to 90C for 5 min; Chill probes on ice to quench</li> | |||
<li>Add probes to cells for final concentration of 100 nM</li> | |||
<li>Incubate probes at 40C for 1 hour with vigorous agitation</li> | |||
<li>Wash three times with wash buffer and pelleting at 600xg for 3 min</li> | |||
<li>Incubate cells for 20 min at 40C in stringent wash buffer</li> | |||
</ol> | </ol> | ||
</ol> | </ol> | ||
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*0.1% Tween | *0.1% Tween | ||
*4 U/mL RNasin | *4 U/mL RNasin | ||
'''Stringent Wash Buffer''' | |||
*PBS | |||
*4X SSC | |||
*40 U/mL RNasin | |||
'''Hybridization Buffer''' | |||
*1X SSC | |||
*2.5% vol/vol polyvinylsulfonic acid | |||
*20 mM ribonucleoside vanadyl complex | |||
*40 U/mL RNasin | |||
*0.1% Tween | |||
*100 ug/mL salmon sperm |
Revision as of 23:41, 5 May 2016
C Probe Hybridization
This page describes the protocol for hybridizing C probes as used in PLAYR Design (as from Nolan lab paper).
Protocol
Resuspend oligos in nuclease free water to concentration of 100 uM
- Fix cells
- Pellet cells at 600g for 3 min and resuspend at concentration of ~1,000,000/mL
- Fix cells in medium with 1.6% paraformaldehyde for 10 min at RT
- Wash cells with wash buffer
- Pellet cells and permeabilize with ice-cold methanol for 10 min on ice Once in methanol cells may be stored long term
- Hybridization
- Pellet cells via centrifugation at 600g for 3 min
- Heat C probes to 90C for 5 min; Chill probes on ice to quench
- Add probes to cells for final concentration of 100 nM
- Incubate probes at 40C for 1 hour with vigorous agitation
- Wash three times with wash buffer and pelleting at 600xg for 3 min
- Incubate cells for 20 min at 40C in stringent wash buffer
Wash Buffer
- PBS
- 0.1% Tween
- 4 U/mL RNasin
Stringent Wash Buffer
- PBS
- 4X SSC
- 40 U/mL RNasin
Hybridization Buffer
- 1X SSC
- 2.5% vol/vol polyvinylsulfonic acid
- 20 mM ribonucleoside vanadyl complex
- 40 U/mL RNasin
- 0.1% Tween
- 100 ug/mL salmon sperm