ChIP-seq: Analysis of CTCF occupancy in unaffected and DM1 patient lymphoblastoid cell lines.

We performed CTCF ChIP-seq to determine the extent of CTCF occupancy alterations in two DM1 patient lymphoblastoid cell lines (LCLs) compared to an unaffected control LCL. Our results show that there were no large-scale changes in CTCF occupancy in the DM1 patient cells either genome-wide or in a 2 Mb region centered around the expanded repeats of DMPK. Overall design: We performed CTCF ChIP-seq using a CTCF antibody (Diagenode) in the unaffected LCL GM04604 (UN-B) and two DM1 patient-derived LCLs GM06077 (DM1-A) and GM04648 (DM1-B). Each CTCF ChIP-seq library was prepared in triplicate.

我们通过CCCTC结合因子（CCCTC-binding factor, CTCF）染色质免疫共沉淀测序（Chromatin Immunoprecipitation sequencing, ChIP-seq），旨在探究相较于未受影响的对照淋巴母细胞系（Lymphoblastoid Cell Line, LCL），两株肌强直性营养不良1型（Myotonic Dystrophy Type 1, DM1）患者来源的淋巴母细胞系中CTCF结合占有率的变化幅度。研究结果显示，无论全基因组范围，还是以肌强直性营养不良蛋白激酶（Dystrophia Myotonica Protein Kinase, DMPK）基因扩增重复序列为中心的2 Mb区域内，DM1患者细胞中的CTCF结合占有率均未出现大规模变化。
实验总体设计：我们使用CTCF抗体（迪阿根诺（Diagenode）品牌），对未受影响的LCL GM04604（标记为UN-B）以及两株DM1患者来源的LCL GM06077（标记为DM1-A）和GM04648（标记为DM1-B）开展CTCF ChIP-seq实验。每份CTCF ChIP-seq文库均制备三份平行重复。