I have isolated cells from a single mouse testis and assume that the number should be around 7-8 million. I want to do ChIP on them consisting of three immunoprecipitations (IPs). I need advice on how to do three IPs with such a low number of cells.
Has anyone tried protocols of microChIP which talk about ChIP with cell count ranging between 100-100,000? Can I use these protocols in my case? An example of such protocol is : http://www.nature.com/nprot/journal/v3/n6/full/nprot.2008.68.html
I am also looking to do ChIP with a small number of cells. I am still troubleshooting so I can't give you a protocol that will definitely work, but I found this Jove article which might be helpful:
http://www.jove.com/video/50064/efficient-chromatin-immunoprecipitation-using-limiting-amounts
Bradley: I will get back to you also if I am able to optimise the ChIP protocol
First, dont use kits for this, the ChIP technique requires careful work up for each target and the kits tend to be optimised for one particular target. The answer whenever using small amounts of cells or tissues is to either add cells or chromatin from a distinct species from the one you are working on, this bulks out the total material you are working with and minimises loss of material on plastics etc. Then you use species-specific PCR or sequencing to identify the targets from your cells of interest.
Protocol described in the following paper should help you to work with few number of cells:
Dahl JA, Collas P. Q2ChIP, a quick and quantitative chromatin
immunoprecipitation assay, unravels epigenetic dynamics of developmentally
regulated genes in human carcinoma cells. Stem Cells. 2007 Apr;25(4):1037-46.
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