ChIP Troubleshoot - (Feb/13/2008 )
I'm having problem with my ChIP bound samples. I did a ChIP using mouse left ventricle and the input and unbound amplified beautifully at cycle 19 using RT-PCR but my bound samples came up with squiggly lines, can someone tell me why????
I also nanodropped the samples, once again, input and unbound were very clean with an A260/280 reading of 1.9 whereas the bound were only 0.5. Can someone tell me how to improve this???
The input, unbound and bound samples were all phenol chloroform extracted and ethanol ppt the same way, how come the bound samples did not amplify???? Help~~~~
-chippychip-
QUOTE (chippychip @ Feb 14 2008, 06:44 AM)
I'm having problem with my ChIP bound samples. I did a ChIP using mouse left ventricle and the input and unbound amplified beautifully at cycle 19 using RT-PCR but my bound samples came up with squiggly lines, can someone tell me why????
I also nanodropped the samples, once again, input and unbound were very clean with an A260/280 reading of 1.9 whereas the bound were only 0.5. Can someone tell me how to improve this???
The input, unbound and bound samples were all phenol chloroform extracted and ethanol ppt the same way, how come the bound samples did not amplify???? Help~~~~
I also nanodropped the samples, once again, input and unbound were very clean with an A260/280 reading of 1.9 whereas the bound were only 0.5. Can someone tell me how to improve this???
The input, unbound and bound samples were all phenol chloroform extracted and ethanol ppt the same way, how come the bound samples did not amplify???? Help~~~~
How many cells are you using per IP? I use about 4 million and after ChIP I don't have enough DNA to nanodrop accurately. I also prefer to clean up my ChIP products with a column. Perhaps I am crap at EtOH ppt, because my curves were never as nice compared to column purified samples!
-Clare-