HepG2 WT vs CEBPB KO
HepG2 WT vs CEBPB KO
HepG2 cultured cells RNA-seq was performed as previously described.81 Three or four biological replicates were processed per condition. FastQC was used to inspect the quality of raw sequence reads. The clean sequence reads were aligned to human genome using HISAT2. FeatureCounts was applied to quantify the number of reads mapped to each gene and then Transcripts Per Million (TPM) of each gene was calculated. Differential gene expression analysis was performed using DESeq2 package. Gene set enrichment analysis (GSEA) were conducted using clusterProfile package.  TRIZOL reagent. RNA-seq was performed as previously described.81 Three or four biological replicates were processed per condition. FastQC was used to inspect the quality of raw sequence reads. The clean sequence reads were aligned to human genome using HISAT2. FeatureCounts was applied to quantify the number of reads mapped to each gene and then Transcripts Per Million (TPM) of each gene was calculated. Differential gene expression analysis was performed using DESeq2 package. Gene set enrichment analysis (GSEA) were conducted using clusterProfile package.  mRNA was obtained primarily through two methods: first, by leveraging the structural feature that most eukaryotic mRNAs possess a polyA tail, enabling enrichment of polyA-tailed mRNA using Oligo(dT) beads; second, by removing ribosomal RNA from total RNA to obtain mRNA. The mRNA was then randomly fragmented in fragmentation buffer using divalent cations. Library construction was carried out following either a standard library preparation protocol or a strand-specific library construction method (Parkhomchuk et al., 2009). 