STARR-seq based mutagenesis of transcription factor binding sites

We performed a STARR-seq based, massively parallel reporter assay on reference genome and mutation-containing oligonucleotide sequences from regions associated with a large number of transcription factor ChIP-seq peaks or DHS-footprinted motifs. Overall design: The data set includes a plasmid DNA oligo library reference sample and 6 replicate RNA samples isolated from the HepG2 cell line. 92,000 170bp oligonucleotides were cloned in parallel into the STARR-seq reporter vector and transfected into HepG2 in 6 replicates. RNA was harvested from these 6 replicates after 48 hours and oligonucleotide expression levels were compared to their representation in the original plasmid DNA pool.

本研究针对参考基因组，以及来自大量转录因子染色质免疫共沉淀测序（ChIP-seq）峰或DNase I超敏位点足迹基序（DHS-footprinted motifs）相关区域的携带突变的寡核苷酸序列，开展了基于STARR-seq的大规模平行报告基因检测实验。整体实验设计如下：本数据集包含质粒DNA寡核苷酸文库对照样本，以及从HepG2细胞系中分离获得的6份生物学重复RNA样本。研究人员将92000条长度为170bp的寡核苷酸并行克隆至STARR-seq报告载体中，并以6次生物学重复的方式转染至HepG2细胞内。转染48小时后，收集该6份重复样本的总RNA，将寡核苷酸的表达水平与其在原始质粒DNA文库池中的丰度占比进行对比分析。