Assay for transposase-accessible chromatin-sequencing (ATAC-seq) of liver samples from  Ythdc1flox/flox and Ythdc1-HKO mice, respectively.
The goal of this study is to determine whether hepatic deletion of Ythdc1 affects chromatin accessibility. Overall design: To assess chromatin accessibility in the liver casued by hepatic deletion of Ythdc1, ATAC-seq analysis of liver samples in Ythdc1flox/flox and hepatocyte-specific Ythdc1 knockout (Ythdc1-HKO) mice was performed. Each liver sample was pooled from four Ythdc1-HKO and Ythdc1flox/flox mice, respectively. Nuclei was extracted from liver samples, and the nuclei pellet was resuspended in the Tn5 transposase reaction mix. The transposition reaction was incubated at 37°C for 30 min. Equimolar Adapter1 and Adatper 2 were added after transposition, PCR was then performed to amplify the library. After the PCR reaction, libraries were purified with the AMPure beads and library quality was assessed with Qubit. The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumina) according to the manufactuer's instructions. After cluster generation, the library preparations were sequenced on an Illumina NovaSeq 6000 platform and 150 bp paired-end reads were generated. ATAC-seq analysis was performed using a standard protocol. The chromatin accessibility in the livers of Ythdc1flox/flox and Ythdc1-HKO mice were characterized.