Sequencing and analysis

JC Jie Cui
JL Jiatao Liu
LF Lulu Fan
YZ Yue Zhu
BZ Bei Zhou
YW Yu Wang
WH Wei Hua
WW Wei Wei
GS Guoping Sun
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For Chromatin immunoprecipitation-sequencing (CHIP-Seq) and RNA-sequencing (RNA-Seq), samples were prepared and sent to Guangzhou Eipbiotec Co., Ltd. (Guangzhou, China). CHIP-Seq was performed by Active Motif (Carlsbad, TX, USA), as described [21]. In brief, 1 × 107 HepG2 cells were first cross-linked and fixed in a 1% formaldehyde solution, followed by the addition of 125 μmol/L glycine. Cells were then washed twice in ice-cold PBS and flash frozen at −80 °C. The histone mark H3K27ac (ab4729, Abcam, Cambridge, MA, USA) was used, which distinguish active enhancer [22]. Total RNA was extracted from HepG2 cell treated with TM (2.5 mM, 24 h) or with the vehicle control, using the RNeasy Mini Kit from Qiagen (cat no;74104). To determine the top enriched DNA-Binding Motifs, the Homer findPeaks tool (http://homer.ucsd.edu/homer/ngs/peakMotifs.html) was used with default parameters. Motifs were ranked according to adjusted P-value.

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