pre-clearing problem - (Aug/09/2005 )
im doing chip analysis for the first time, and im using upstate chip protocol.
when im doing preclearing with 80 ul of salmon sperm DNA/protein A agarose slurry i have to agitate for 30 minutes and then to pellet agarose by brief centrifugation (1000 rpm for 1').
my problem is that i dont have any pellet after the centrifugation......may be my centrifugation is too gentle?
dont know what my problem is...
I use 1000rpm for 1 min to spin down agarose bead (G-PLUS agarose bead from santa cruz), no problem.
You can try 3000rpm for 1 min.