Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

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

ABSTRACT: 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.

ORGANISM(S): Homo sapiens

SUBMITTER: Masamichi Kamihira

PROVIDER: E-MTAB-15803 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Gene expression profiles for genetically engineered human hepatoma HepG2/8F_HS cells with or without heat treatment, cultured as monolayer or spheroids

Project description:We developed genetically engineered HepG2/8F_HS cells, in which eight liver-enriched transcription factor (LETF) genes—hepatocyte nuclear factor (HNF)-1α, HNF-1β, HNF-3β, HNF-4α, HNF-6, CCAAT/enhancer binding protein (C/EBP)-α, C/EBP-β and C/EBP-γ— under the control of TRE/PCMVmin promoter were introduced into a previously developed human hepatoma cell line (HepG2-HSP). The heat-inducible synthetic promoter system was introduced into HepG2 cells and tetracycline-responsive transactivator (tTA) and enhanced green fluorescent protein (EGFP) were expressed via positive feedback of tTA transcription in response to heat treatment. HepG2/8F_HS cells can induce high liver functions by heat treatment via overexpression of LETF genes.

2022-04-04 | E-MTAB-11486 | biostudies-arrayexpress

Gene expression profiles for genetically engineered murine hepatoma Hepa8F5 cells treated with or without doxycycline, cultured as monolayer or spheroids

Project description:We developed genetically engineered Hepa/8F5 cells (available from RIKEN BioResource Center [RCB4661]), in which genes of eight liver-enriched transcription factors (LETFs)—hepatocyte nuclear factor (HNF)-1α, HNF-1β, HNF-3β [FOXA2], HNF-4α, HNF-6, CCAAT/enhancer binding protein (C/EBP)-α, C/EBP-β and C/EBP-γ—were transduced into murine hepatoma Hepa1-6 cells as drug-inducible expression cassettes [Biochem. Eng. J., 60, 67–73 (2012)]. Hepa/8F5 cells can induce high liver functions by the addition of an inducer drug (doxycycline; Dox) via overexpression of LETF genes.

2017-11-15 | E-MTAB-5770 | biostudies-arrayexpress

shRNA profiling of human hepatocyte HepG2 cells knocked down for HNF4 to investigate its role in inflammatory response

Project description:To obtain a genomic view of hepatocyte nuclear factor-4Î± (HNF-4Î±) in the regulation of the inflammatory response, microarray analysis was used to probe the expression profile of an inflammatory response induced by cytokines in a model of knock-down HNF-4Î± HepG2 cells. The results indicate an extensive role for HNF-4Î± plays in the regulation of a large number of the liver-specific genes. Majority of genes (71%) affected by cytokine treatment are also affected by HNF-4Î± knock-down. This significant overlap suggests that HNF-4Î± may play a role in regulating the cytokine-induced inflammatory response. Experiment Overall Design: The different treated HepG2 cells were grouped into 4 groups (four replicates in each group): Group1, Control; Group2, HNF-4Î± shRNA treated cells; Group3, cytokine treated group; Group4, HNF-4Î± shRNA and cytokine treatments. RNA extraction and hybridization on Affymetrix microarrays were processed. The expression profiles between different groups were analyzed and compared. In order to explore the function of HNF-4Î± in the inflammatory response, a set of 170 genes annotated as inflammatory response was obtained from GO (geneotology.org), the enrichments of these inflammatory genes were analyzed in different treated groups.

2009-05-16 | E-GEOD-15991 | biostudies-arrayexpress

HepG2 Cell: Control vs. HGF treated

Project description:Transcription profile of HepG2 cells treated with hepatocyte growth factor and control cells Two condition experiment, Hep G2 vs. Hep G2-HGF. Biological replicates: 1 control and 1 HGF-treated (no replication)

2012-02-23 | E-GEOD-35994 | biostudies-arrayexpress

Heat inactivation of foetal bovine serum performed after EV-depletion influences the proteome of cell-derived extracellular vesicles

Project description:The release of extracellular vesicles (EVs) in cell cultures as well as their molecular cargo can be influenced by cell culture conditions such as the presence of foetal bovine serum (FBS). Although several studies have evaluated the effect of removing FBS-derived EVs by ultracentrifugation (UC), less is known about the influence of FBS heat inactivation (HI) on the cell-derived EVs. To assess this, three protocols based on different combinations of EV depletion by UC and HI were evaluated, including FBS ultracentrifuged but not heat inactivated (no-HI FBS), FBS heat inactivated before EV depletion (HI-before EV-depl FBS), and FBS heat inactivated after EV depletion (HI-after EV-depl FBS). We isolated large (L-EVs) and small EVs (S-EVs) from FBS treated in the three different ways, and we found that the S-EV pellet from HI-after EV-depl FBS was larger than the S-EV pellet from no-HI FBS and HI-before EV-depl FBS. Transmission electron microscopy, protein quantification, and particle number evaluation showed that HI-after EV-depl significantly increased the protein amount of S-EVs but had no significant effect on L-EVs. Consequently, the protein quantity of S-EVs isolated from three cell lines cultured in media supplemented with HI-after EV-depl FBS was significantly increased. Quantitative mass spectrometry analysis of FBS-derived S-EVs showed that the EV protein content was different when FBS was HI after EV depletion compared to EVs isolated from no-HI FBS and HI-before EV-depl FBS. Moreover, we show that several quantified proteins could be ascribed to human origin demonstrating that FBS bovine proteins can mistakenly be attributed to human cell-derived EVs. We conclude that HI of FBS performed after EV depletion results in changes in the proteome, with molecules that co-isolate with EVs and can contaminate EVs when used in subsequent cell cultures. Our recommendation is therefore to always perform HI of FBS prior to EV depletion.

2024-01-26 | PXD047505 | Pride

Expression profile analysis of inflammatory response regulated by hepatocyte nuclear factor 4α

Project description:To obtain a genomic view of hepatocyte nuclear factor-4α (HNF-4α) in the regulation of the inflammatory response, microarray analysis was used to probe the expression profile of an inflammatory response induced by cytokines in a model of knock-down HNF-4α HepG2 cells. The results indicate an extensive role for HNF-4α plays in the regulation of a large number of the liver-specific genes. Majority of genes (71%) affected by cytokine treatment are also affected by HNF-4α knock-down. This significant overlap suggests that HNF-4α may play a role in regulating the cytokine-induced inflammatory response.

2009-05-06 | GSE15991 | GEO

HepG2 Hi-C

Project description:HepG2 Hi-C

| PRJNA451031 | ENA

Towards epigenetic understanding and therapy of insulin resistance by intranuclear insulin [DNA methylation]

Project description:There is evidence indicating the involvement of DNA methylation memory in maintaining gene expression patterns associated with insulin resistance. Although the exact mechanism remains unknown, it has been proved that insulin resistance is correlated to low heat shock protein (HSP) expression. We reveal that intranuclear insulin can reduce HSP DNA methylation level to up-regulate HSP protein expression and result in long term cure of hyperglycemia. Insulin resistance HepG2 cell were selected in our experiments.Two conditions were compared with three replicates each. These are:(1) Insulin resistance HepG2(R-HepG2) and (2) Biomineralized insulin treated HepG2 (BI).

2014-05-23 | E-GEOD-57894 | biostudies-arrayexpress

m6A mapping in human RNA (with treatments)

Project description:We developed a novel approach, m6A-seq, for high-resolution mapping of the transcriptome-wide m6A landscape, based on antibody-mediated capture followed by massively parallel sequencing. Identification of m6A modified sequences in HepG2 cells. HepG2 cells were incubated with either IFNg (200ng/ml) or HGF/SF (10 ng/ml) over night. Stress effects were tested in HepG2 cells by either 30 minutes incubation at 43M-BM-:C (heat shock) or UV irradiation of 0.04 J/cm2 followed by 4 hours of recovery in normal growing conditions prior to harvesting using Trypsin.

2012-04-25 | E-GEOD-37002 | biostudies-arrayexpress

Transcriptomics analysis of the Bordetella holmesii response to human serum exposure

Project description:We performed RNA-Seq transcriptomics analyses of the Bordetella holmesii type strain ATCC 51541T under in vitro growth conditions that mimic exposure to the human bloodstream. We sequenced 3 biological replicates of each of the following conditions of exposure to heat-inactivated human serum: 5% serum, 0.5% serum, and a no serum control. RNA-Seq was performed on the Bordetella holmesii type strain ATCC 51541T grown under three conditions: 5% heat-inactivated human serum, 0.5% heat-inactivated human serum, and a no serum control.

2014-03-28 | E-GEOD-56290 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data