Bioinformatics Training and Education Program

BTEP Question Forum

BTEP maintains several Question and Answer Forums of interest to the NCI/CCR community.
Currently, there are forums on these topics listed below:

If you wish to ask a question go to the Ask Question Page and submit your question.

 Back to Questions

Control Types: What is the difference between input and naked DNA?

What is the difference between in put and naked DNA?

1 Answer:

Input samples have the same three-dimensional chromosome structure as ChIP samples when doing the chromosome fragmentation stage (usually by sonication). Everything through that step should be completed in parallel with the ChIP sample. In fact, the optimal input is an aliquot of the sonicated sample that is then processed independently of the ChIP (and has no antibody or pull-down step). Naked DNA is what is used for most DNA-seq experiments. It has no fixation step and the proteins are removed from the DNA prior to fragmentation. - answered by Tovah Markowitz, Paul Schaughency, Vishal Koparde

Answered on June 5th, 2020 by