I am a newbie in the field of Chip-Seq and would like to gain some knowledge from the experts,I am planning to do Chip seq experiments for the Histone marks,H3k4 mono methyl and K27 Acetyl.
I am a bit confused about the validation,using PCR or qPCR.
What should be my positive and negative controls.Which all gene specific primers can I use,I am not able to understand,due to the confusion.I want to run a pre check,before sequencing,about the modification specificity.Whether the DNA pooled is related to the Histone marks,and they can be distinguished using PCR.
Suggestions and comments are welcome.
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written
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Rc •
1 answer
Advice, not an answer....
If you are just getting into this field, I HIGHLY recommend that you find a local resource (a person) who has experience with chip-seq. If you do not have access to someone locally, then I suggest contacting a lab that has some expertise and set up a short teleconference to discuss your project and plans. There are significant experimental design issues and controls that should be discussed before getting going. You should also enlist a bioinformatics collaborator to work with you on the project before you start (if you are not a bioinformaticist yourself).
Hope that helps.
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Strictly speaking, this is not a bioinformatics question as its theme is PCR. Thus, you may not see many if any responses here.
which taxon, which tissue. do you have transcription data from these cells? these are enhancer marks? I think the question has bioinformatical issues: if very little is known, already available data (e.g. encode) could help her identifying positive and negative controls.
I agree with Larry this is not a bioinformatics/comp biol question. I've closed this on but will re-open on request from the community.
If a question has relevance for bioinformatics is it still not a bioinformatics question? Why do we have to be so narrow in allowing what can be discussed? Informaticists are often faced with issues of experimental design and controls - so this question is extremely relevant to bioinformatics in my view. I know a lot of people who are ignorant of such issues and can waste analysis time on data sets generated without controls. It would be better if they were aware of, or exposed to the issues.