{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"submitter":["Masamichi Kamihira"],"study_type":["transcription profiling by array"],"organism":["Homo sapiens"],"species":["Homo sapiens"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-15803"],"description":["We developed a heat-inducible hepatic cell line (hi-Hep) in which BRCA1-associated protein-1 (BAP1) was introduced under the control of a TRE/PCMVmin promoter, in addition to the existing eight liver-enriched transcription factor (LETF) genes (HNF-1α, HNF-1β, HNF-3β, HNF-4α, HNF-6, C/EBP-α, C/EBP-β and C/EBP-γ). The synthetic heat-inducible promoter system utilizes a tetracycline-responsive transactivator (tTA) with a transcriptional positive-feedback loop and EGFP reporter, enabling stringent induction of transgenes upon transient heat treatment (43 °C, 30 min). Following induction, hi-Hep cells exhibit enhanced hepatic functions including ammonia detoxification, albumin secretion, and cytochrome P450 activity compared to parental HepG2 and HepG2/8F_HS cells. Transcriptome profiling was performed using Agilent SurePrint G3 Human GE 8×60K v3 arrays to compare hi-Hep cells with or without heat treatment, in monolayer and spheroid culture formats, under both serum-containing and optimized serum-free conditions, alongside parental HepG2/8F_HS controls."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Sample Collection - Samples were collected at 24 and 72 h after heat induction (HS[+]) or without heat treatment (HS[−]) for all culture conditions. Total RNA was extracted from each condition (n = 1 group; see sample list) for transcriptome analysis.","Hybridization - Cy3-labelled cRNA was hybridized to a 60K 60-mer oligomicroarray (SurePrint G3 Human GE Microarray 8x60K v3.0 (G4858A#72363); Agilent Technologies) according to the manufacturer's instructions.","Labeling - Cy3-labeled cRNA was prepared from 50 ng total RNA using a Low input Quick Amp Labelling Kit (Agilent Technologies) according to the manufacturer's instructions, followed by RNeasy column purification (Qiagen).","Nucleic Acid Extraction - Total RNA was extracted using TRIzol Reagent (Thermo Fisher Scientific). Samples were submitted to Cell Innovator (Fukuoka, Japan) for microarray analysis. RNA quality was confirmed using an Agilent 2200 TapeStation (Agilent Technologies, Santa Clara, CA, USA) to ensure RIN ≥7.0, 28S/18S ≥2.0, and yield ≥1 µg.","Growth Protocol - hi-Hep cells were maintained in high-glucose DMEM supplemented with 10% FBS for serum-containing conditions or in Williams’ E-based serum-free functional medium (FM) supplemented with ITS-X, B27, EGF, forskolin, dexamethasone, DAPT, and triiodothyronine for serum-free conditions. Monolayer cultures were maintained on collagen-coated dishes, while spheroids were generated in EZSPHERE plates. Heat induction was performed by immersing culture dishes in a 43 °C water bath for 30 min, followed by changing medium and recovery at 37°C in a 5%(v/v) CO2 incubator.","Scaning - The hybridized microarray slides were scanned on the Agilent scanner using one color scan setting (Scan resolution 5 μm)."],"figure_sub":["MIAME Score","Raw Data","Organization","Assays and Data","Processed Data","MAGE-TAB Files","Array Designs"],"pubmed_authors":["Masamichi Kamihira"],"data_protocol":["Data Transformation - The scanned images were analyzed with Feature Extraction Software 9.5.1.1 (Agilent) using default parameters to obtain background-subtracted and spatially detrended processed signal intensities. Raw signal intensities and probe flags were calculated from hybridization intensities and spot information according to the procedures recommended by Agilent Technologies, using the flag criteria in GeneSpring Software. Raw signal intensities of all samples were normalized using the quantile normalization algorithm implemented in Bioconductor."],"additional_accession":[]},"is_claimable":false,"name":"Gene expression profiles for genetically engineered human hepatoma hi-Hep cells with or without heat treatment, cultured as monolayer or spheroids using serum-containing or serum-free functional media","description":"We developed a heat-inducible hepatic cell line (hi-Hep) in which BRCA1-associated protein-1 (BAP1) was introduced under the control of a TRE/PCMVmin promoter, in addition to the existing eight liver-enriched transcription factor (LETF) genes (HNF-1α, HNF-1β, HNF-3β, HNF-4α, HNF-6, C/EBP-α, C/EBP-β and C/EBP-γ). The synthetic heat-inducible promoter system utilizes a tetracycline-responsive transactivator (tTA) with a transcriptional positive-feedback loop and EGFP reporter, enabling stringent induction of transgenes upon transient heat treatment (43 °C, 30 min). Following induction, hi-Hep cells exhibit enhanced hepatic functions including ammonia detoxification, albumin secretion, and cytochrome P450 activity compared to parental HepG2 and HepG2/8F_HS cells. Transcriptome profiling was performed using Agilent SurePrint G3 Human GE 8×60K v3 arrays to compare hi-Hep cells with or without heat treatment, in monolayer and spheroid culture formats, under both serum-containing and optimized serum-free conditions, alongside parental HepG2/8F_HS controls.","dates":{"release":"2026-01-01T00:00:00Z","modification":"2026-05-27T14:38:24.124Z","creation":"2025-10-22T17:41:56.598Z"},"accession":"E-MTAB-15803","cross_references":{"Biostudies":["E-MTAB-11486"],"EFO":["EFO_0002768","EFO_0002944","EFO_0003814","EFO_0003813","EFO_0003789","EFO_0005518","EFO_0003816","EFO_0003815"]}}