title: GSM9382814: Nala_3, HepG2 cells, Nala treated, 48 h; Homo sapiens; RNA-Seq
library_construction_protocol: For RNA-seq assay, total RNA was extracted using the RNAiso Plus reagent (Takara Bio, Shiga, Japan, catalog no. 9109) according to the manufacturer's protocol. For ChIP-seq assay, HepG2 cells were cross-linked with 37% formaldehyde solution (final concentration 1%) for 10 minutes. The cross-linking reaction was quenched with 2.5 M glycine (final concentration 125 mM) for 5 minutes. Cells were washed with cold PBS, and the pellets were resuspended in SDS lysis buffer containing 100× PMSF (final concentration 1×) and 100× PIC (final concentration 1×). The samples were sheared by sonication at 80% amplitude in 1% SDS lysis buffer to generate chromatin fragments of 200–400 bp. For ATAC-seq assay, after treatment, 5 × 104 cells were treated with cell lysis buffer, and the nuclei were collected by centrifugation at 500 × g for 5 minutes. RNA-seq library preparation is performed using Optimal Dual-mode mRNA Library Prep Kit (BGI-Shenzhen, China). ChIP-seq libraries were prepared using the VAHTS Universal DNA Library Prep Kit for Illumina V3 (Catalog No. ND607, Vazyme) and then sequenced on the DNBSEQ-T7 sequencer (MGI Tech Co., Ltd., China) with the PE150 model. For ATAC-seq library construction protocol, transposition and high-throughput DNA sequencing libraries were generated using the TruePrep DNA Library Prep Kit V2 for Illumina (Catalog No. TD501, Vazyme), and the libraries were sequenced on the DNBSEQ-T7 sequencer (MGI Tech Co., Ltd., China) using the PE150 model.