Identification of mRNAs associated with YTHDC1 in primary hepatocytes
The goal of this study is to identify mRNAs associated with YTHDC1 in primary hepatocytes. Overall design: Primary hepatocytes were infected with Ad-FLAG-YTHDC1 adenovirus overnight. RNA immunoprecipitation sequence (RIP-seq) assay was performed to identify mRNAs associated with YTHDC1 in primary hepatocytes. Then, immunoprecipitated RNA or Input was used for library construction with NEB NextR Ultra™ RNA Library Prep Kit (New England Biolabs). Library quality was assessed on the Agilent Bioanalyzer 2100 system. The libraries were sequenced on an Illumina Novaseq 6000 platform with a paired-end read length of 150 bp according to the standard protocols. Raw data (raw reads) of fastq format were firstly processed using fastp software. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low- quality reads from raw data. At the same time, Q20, Q30 and GC content of the clean data were calculated. All the downstream analyses were based on the clean data with high quality. Index of the reference genome ( GRCm38/mm10) was built using BWA (v 0.7.12) and clean reads were aligned to the reference genome using BWA mem (v 0.7.12). mRNAs associated with YTHDC1 in primary hepatocytes were characterized.