Cistrome profiles of Retinoids x Receptor alpha (RXRα) , Retinoic Acid Receptor alpha (RARα), and Retinoic Acid Receptor beta (RARβ) in livers of mice treated by control and retionic acid-containing diet. Mus musculus

Comparison between ChIP-Seq data of RARα and RARβ, between RAR and RXR, as well as between control and retinoic acid-treatment for each investigated nuclear receptors. Overall design: Mouse were treated by control diet and RA-diet for 1 days. After treatment, livers were used to do ChIP using antibodies of RXRα, RARα, and RARβ. An aliquote of total chromatin without pull-down process by any antibodies was used as input control. A single-end read of 35bp sequencing was performed on each of ChIPed DNA and input. Sequencing data of RARα and RARβ were compared to each other. In addtional, each of RARα and RARβ data were compared with RXRα data. For each nuclear receptor, ChIP-Seq data prior or after RA-treatment were also compared with each other.

本数据集针对各研究涉及的核受体，开展三类对比分析：视黄酸受体α（Retinoic Acid Receptor α, RARα）与视黄酸受体β（Retinoic Acid Receptor β, RARβ）的染色质免疫共沉淀测序（Chromatin Immunoprecipitation Sequencing, ChIP-Seq）数据对比、视黄酸受体（RAR）与类视黄醇X受体（Retinoid X Receptor, RXR）的相关数据对比，以及对照组与视黄酸（retinoic acid, RA）处理组的ChIP-Seq数据对比。

整体实验设计：将小鼠分为普通饮食对照组与视黄酸饮食处理组，处理时长为1天。处理结束后，提取肝脏组织，使用RXRα、RARα及RARβ抗体进行染色质免疫共沉淀（ChIP）实验。同时设置输入对照：取未经过任何抗体下拉富集步骤的总染色质等分试样。对所有ChIP富集的DNA样本及输入对照样本，均开展35bp单端读长测序。

数据分析层面，将RARα与RARβ的测序数据进行相互比较；此外，将RARα、RARβ各自的测序数据分别与RXRα的数据进行对比；针对每种核受体，同时比较其视黄酸处理前后的ChIP-Seq数据。