Question

Experimental design for mutiple groups of paired samples

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Wu, Xiwei ▴ 350

@wu-xiwei-1102

Last seen 9.6 years ago

Dear list, I have eight samples with following structure: Control input Control enriched Treatment A input Treatment A enriched Treatment B input Treatment B enriched Treatment C input Treatment C enriched Note that each input is paired with an enriched sample. These are chromatin immunoprecipitation samples. My interest is to compare the different enrichment between each of the treated samples and controls. I am also potentially interested in enrichment differences among A, B and C. I have to use two-colored array due to experimental nature. Assuming that obtaining enough biological replicated samples is not an issue, what is the best hybridization approach? I am thinking about hybridizing each of the enriched sample vs. its control, and then using a loop design (which needs 4 arrays, or a saturated design which needs 6 arrays) to connect all the enriched samples. I am not sure whether that is a good approach. Any suggestion will be highly appreciated, XiweiXiwei Wu, MD, PhD Director, Affymetrix and Data Analysis Core Facility Assistant Research Scientist Department of Biomedical Informatics Beckman Research Institute City of Hope National Medical Center Duarte, CA 91010 Phone: (626) 359-8111 ext. 65071 "EMF <coh.org>" made the following annotations. ---------------------------------------------------------------------- -------- SECURITY/CONFIDENTIALITY WARNING: This message and any atta...{{dropped}}

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ADD COMMENT • link written 17.8 years ago by Wu, Xiwei ▴ 350

Gordon Smyth · Answer 1 · 2016-09-20

ChIP is commonly used in the study of transcriptional factor binding site or protein modification site. With the development of NGS, the combination of CHIP and NGS, Chromatin Immunoprecipitation Sequencing (ChIP-Seq), is now able to screen and identify the protein binding sites on the entire chromosomal scale with high efficiency and accuracy. Briefly, in vivo protein-DNA interaction complex is fixed and digested into small fragments and then immunoprecipitated by an antibody against the DNA-binding protein. This way, the protein-binding DNA fragments are enriched and can be analyzed by NGS so the protein binding sites in the entire genome can be mapped and characterized. ChIP-Seq is a valuable tool for discerning and quantifying the specific DNA sequences where proteins bind or epigenetic modifications exist.