I'm doing ChIP on a TF that is expressed in cell types with low density and am struggling to get reproducible results. My protocol works fine for other TFs. I crosslink my material in 1% formaldehyde by vacuum infiltration before I freeze/grind the material to extract nuclei. Some people actually freeze and grind their material first and then do the crosslinking. Has anyone ever compared both methods and is willing to share insights?
...a friend of mine published a nice method paper about chip in arabidopsis. maybe you can have a look there!
enjoy and good luck....
Methods Mol Biol. 2009;479:261-72. doi: 10.1007/978-1-59745-289-2_17.
Chromatin immunoprecipitation experiments to investigate in vivo binding of Arabidopsis transcription factors to target sequences.
Fode B, Gatz C.
I haven't compared the two but have always done cross-linking before grinding the tissue. Usually I cross-link using 0.1% formaldehyde by vacuum infiltration for 15 to 20 minutes. This method worked for me for different grasses. Some plant tissue work well at low formaldehyde concentration, may be you can try optimizing using less or more formaldehyde.
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