Dear colleagues, please help me find answers to a few questions. 1. Why does the size of sonicated chromatin differ between the input and ChIP samples? In the input, the DNA smear has a size between 200-500 bp, but in the ChIP, the DNA size is below 100 bp. 2. Is there any point in checking the DNA size after ChIP for subsequent ChIP-seq analysis ? I would like to note that the DNA concentration after ChIP is very low (1-2 ng/µl in a volume of 30 µl).
Hello! On first glance it seems that the sonication was slightly overzealous for your ChIP samples and the input is no Ab so you can get smaller/larger fragment sizes as the DNA is unprotected. Please have a look at the ENCODE standards for ChIP-seq, especially the antibody validation measures. Also the fancy sonicator is pretty much essential. Good luck!! https://genome.cshlp.org/content/22/9/1813.full.pdf
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