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DNA loading for chromatin check

chromatin check concentration agarose gel

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#1 Desert



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Posted 06 February 2012 - 02:48 AM

Hi all,

I have a relatively basic question. I am starting to do IPs and I have for this to prepare chromatin and qualtiy check it.

After reverese-crosslinking, I am obtaining a descent concentration on the nanodrop i.e: 2371 ng/µl.

after loading 600 ng for the quality check of my sheared chromatin, the bands are very faint although it seems that I have a good shearing. Others show very strong bands using the same amounts !!! The ladder in my case looks fine too.

In order to obtain the 600 ng, I diluted an aliquot of my sample to 1:1 with water so ending with a concentration of 1185 ng/µl from which I took 0.5 µl. To this I added 1.5 µl of Orange G and 8 µl of water to load 10 µl final ...

I am using 1% agarose gel where I load...

Any hint so why I am having a very faint band while 600 ng corresponds to a lot of DNA ?

Many thanks for your suggestions,

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