{"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-16207"],"description":["To gain insight into the gene signatures directly mediated by LAP (CEBPB) for cancer cell progression, we performed RNA-seq in LAP-HepG2 versus control cells."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Sequencing - Differential gene expression analysis was performed using DESeq2 package. RNA-seq was performed as previously described. Three 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 - 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.","Nucleic Acid Extraction - Trizol reagent. RNA-seq was performed as previously described. Three 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 - Ctrl or LAP (CEBPB) overexpressed HepG2 cells RNA-seq was performed as previously described. Three 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."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Data Transformation - RNA-seq was performed as previously described. Three 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":"RNA seq of HepG2 cells Ctrl vs LAP (CEBPB) OE","description":"To gain insight into the gene signatures directly mediated by LAP (CEBPB) for cancer cell progression, we performed RNA-seq in LAP-HepG2 versus control cells.","dates":{"release":"2026-06-14T00:00:00Z","modification":"2026-06-14T15:40:52.789Z","creation":"2025-11-13T16:26:00.037Z"},"accession":"E-MTAB-16207","cross_references":{"ENA":["ERP184390"],"EFO":["EFO_0002944","EFO_0004170","EFO_0005518","EFO_0003816","EFO_0003738","EFO_0004184"]}}