{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Yifan Luo"],"organism":["Homo sapiens"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-16228"],"description":["WT HepG2 cells vs CEBPB knockout HepG2. CEBPB knockout HepG2 was generated from a single clone by CRISPR KO."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Nucleic Acid Extraction - 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.","Sample Collection - 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.","Library Construction - 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).","Sequencing - Following successful library quality control, qualified libraries are pooled in appropriate ratios based on their effective concentrations and the desired sequencing data volume for Illumina sequencing. The fundamental principle of the sequencing method is Sequencing by Synthesis (SBS). During the sequencing process on the flow cell, four fluorescently labelled dNTPs, DNA polymerase, and adapter primers are introduced for amplification. As the complementary strand within each sequencing cluster is extended, the incorporation of each fluorescently labelled dNTP releases a corresponding fluorescent signal. The sequencer captures these fluorescence signals, and dedicated computer software converts the optical signals into sequencing peaks, thereby determining the nucleotide sequence of the target fragments. The sequencing process is illustrated in the figure below."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Data Transformation - 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."],"omics_type":["Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["Illumina NovaSeq X"],"study_type":["RNA-seq of coding RNA"],"species":["Homo sapiens"],"pubmed_authors":["Yifan Luo"],"additional_accession":[]},"is_claimable":false,"name":"HepG2 WT vs CEBPB KO","description":"WT HepG2 cells vs CEBPB knockout HepG2. CEBPB knockout HepG2 was generated from a single clone by CRISPR KO.","dates":{"release":"2026-06-14T00:00:00Z","modification":"2026-06-14T15:40:02.423Z","creation":"2025-11-13T16:33:25.232Z"},"accession":"E-MTAB-16228","cross_references":{"ENA":["ERP184391"],"EFO":["EFO_0002944","EFO_0004170","EFO_0005518","EFO_0003816","EFO_0003738","EFO_0004184"]}}