Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

14 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

MRNA microarray analysis on HepG2 cells exposed to amorphous Silica Nanoparticles (SiO2-NP)

ABSTRACT: In order to evaluate the identification of genes and pathways, the global gene expression profiles were assessed in response to amorphous Silica nanoparticles on Human hepatoma (HepG2) cells. We performed whole genome DNA microarray experiments using HepG2 cells exposed to for 24h. We used whole genome microarrays to screen for global changed in HepG2 transcription profiles and with subsequent quantitative analysis conducted on selected genes. 24h SiO2-NP (100 mg/L) exposed HepG2 cells were used for total RNA extraction and hybridization on Affymetrix microarrays.

ORGANISM(S): Homo sapiens

SUBMITTER: jinhee choi

PROVIDER: E-GEOD-51276 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

mRNA microarray analysis on HepG2 cells exposed to amorphous Silica Nanoparticles (SiO2-NP)

Project description:In order to evaluate the identification of genes and pathways, the global gene expression profiles were assessed in response to amorphous Silica nanoparticles on Human hepatoma (HepG2) cells. We performed whole genome DNA microarray experiments using HepG2 cells exposed to for 24h. We used whole genome microarrays to screen for global changed in HepG2 transcription profiles and with subsequent quantitative analysis conducted on selected genes.

2013-10-01 | GSE51276 | GEO

mRNA microarray analysis on HepG2 cells exposed to Grpahene oxide (GO) and reduced graphene oxide (rGO) Nanomaterials

Project description:In order to evaluate the identification of genes and pathways, the global gene expression profiles were assessed in response to GO and rGO on Human hepatoma (HepG2) cells. We performed whole genome DNA microarray experiments using HepG2 cells exposed to GO and rGO for 24h. We used whole genome microarrays to screen for global changed in HepG2 transcription profiles and with subsequent quantitative analysis conducted on selected genes. 24h GO and rGO exposed HepG2 cells were used for total RNA extraction and hybridization on Affymetrix microarrays.

2013-08-21 | E-GEOD-50039 | biostudies-arrayexpress

Transcriptional profiling of A549 cells exposed to silica nanoparticles coated by bovine serum albumin

Project description:A549 cells were treated with 130 microgram/ml BSA-coated SiO2 nanoparticles for 24 h.

2012-05-01 | E-MEXP-3600 | biostudies-arrayexpress

Silica-cSilica-coated-magnetic-nanoparticle-induced cytotoxicity is reduced in microglia by glutathione and citrate discovered using integrated omics analysisoated-magnetic-nanoparticle-induced cytotoxicity is reduced in microglia by glutathione and citrate discovered using integrated omics analysis

Project description:Exposure to nanoparticles leads to their accumulation in the brain, but drug development to counteract this nanotoxicity remains challenging. Here we assessed the effect of silica-coated-magnetic nanoparticles containing the rhodamine B isothiocyanate dye [MNPs@SiO2(RITC)] on microglia through integration of transcriptomics, proteomics, and metabolomics. Intracellular reactive oxygen species production, an inflammatory response, and morphological activation of cells were greater, but glucose uptake was lower in MNPs@SiO2(RITC)-treated BV2 microglia and primary rat microglia. Expression of 121 genes, and levels of 45 proteins and 17 metabolites related to the above phenomena changed in MNPs@SiO2(RITC)-treated microglia. We integrated the three omics datasets and generated a single network using a machine learning algorithm. We screened 19 compounds and predicted their effects on nanotoxicity within the triple-omics network. A combination of glutathione and citrate attenuated nanotoxicity induced by MNPs@SiO2(RITC) and ten other nanoparticles in vitro and in the murine brain, protecting mostly the hippocampus and thalamus.

2022-02-15 | PXD020225 | Pride

Global proteomics to study silica nanoparticle-induced cytotoxicity and its mechanisms in HepG2 cells

Project description:Silica nanoparticles (SiO2 NPs) are commonly used in medical and pharmaceutical fields. Research into the cytotoxicity and overall proteomic changes occurring during initial exposure to SiO2 NPs is limited. We investigated the mechanism of toxicity in human liver cells according to exposure time [0, 4, 10, and 16 hours (h)] to SiO2 NPs through proteomic analysis using mass spectrometry. SiO2 NP-induced cytotoxicity through various pathways in HepG2 cells. Interestingly, when cells were exposed to SiO2 NPs for 4 h, the morphology of the cells remained intact, while the expression of proteins involved in mRNA splicing, cell cycle, and mitochondrial function was significantly downregulated. These results show that the toxicity of the nanoparticles affects protein expression even if there is no change in cell morphology at the beginning of exposure to SiO2 NPs. The levels of reactive oxygen species changed significantly after 10 h of exposure to SiO2 NPs, and the expression of proteins associated with oxidative phosphorylation, and the immune system was upregulated. Eventually, these changes in protein expression induced HepG2 cell death. This study provides insights into cytotoxicity evaluation at early stages of exposure to SiO2 NPs through in vitro experiments.

2021-09-10 | PXD024206 | Pride

Nano-silica particles synergistically IgE-mediated mast cell activation

Project description:To deeply investigate the details of the nano-SiO2 effects, we examined the gene expression profile alterations after nano-SiO2 treatment in BMMCs. The difference analysis between the groups showed that 285 genes were significantly expressed after treatment with nano-SiO2. Compared with the blank group, both nano-SiO2 exposure and DNP-HSA stimulation increased the expression of genes related to the MAPK signaling pathway in mast cells to varying degrees.

2022-07-05 | GSE206630 | GEO

Homo sapiens

Project description:mRNA microarray analysis on HepG2 cells exposed to amorphous Silica Nanoparticles (SiO2-NP)

| PRJNA222285 | ENA

Impact on Arabidopsis thaliana transcriptome of multifunctional silica nanoparticles based on metal atom clusters

Project description:au14-09_silice - clustop transcriptomics. - Understand and categorize plant mechanisms implicated in the interaction with nanoparticles, both in the phenomena responsible for toxicity as in accommodation, see detoxication. - Phytotoxicity of Cs2[Mo6Br14]@SiO2 nanoparticles and their components, i.e. Cs2[Mo6Br14] clusters and SiO2 nanoparticles, has been studied usign Arabidopsis thaliana cell suspension culture. Cs2[Mo6Br14]@SiO2 nanoparticles used here are composed of 7,5% clusters and 92,5% SiO2. Thus, to compare to the impact of a 100 mg/L Cs2[Mo6Br14]@SiO2 nanoparticle treatment (CS), we also treated Arabidopsis cells with clusters at 7,5 mg/L (C), SiO2 at 92,5 mg/L (S), and combined 7,5 mgCMB/L plus 92,5 mgSiO2/L (C+S).

2017-02-01 | GSE93182 | GEO

Expression data from human lung epithelial cells after amorphous silica nanoparticle exposure for 40 passages

Project description:Amorphous silica nanoparticles induce malignant transformation and tumorigenesis of human lung epithelial cells. We used microarrays to detail the global programme of gene expression underlying the cellular malignant transformation induced by amorphous silica nanoparticles and identified distinct classes of up-regulated and down-regulated genes during this process. The human lung epithelial cells, Beas-2B were continuously exposed to 5 Î¼g/mL amorphous silica nanoparticles for 40 passages, and named as BeasSiNPs-P40 (shortly as P40-5 during the further microarray detection). Meanwhile, the passage-matched control Beas-2B cells, named as Beas-P40 (shortly as NC during the further microarray detection).

2016-06-01 | E-GEOD-82062 | biostudies-arrayexpress

Transcriptional responses to engineered nanoplatforms for drug delivery in primary human aortic endothelial cells.

Project description:This study evaluated transcriptional effects of nanomaterials that have been proposed for use as platforms for drug delivery. We tested SiO2 that had been surface modified to have a positive zetapotential of different geometries as well PAMAM dendrimers with different surface charges. We tested these materials on human aortic endothelial cells (HAECs) since we were interested in determining if there was a toxicogenomic response in endothelial cells that may come into contact with drug delivery nanoplatforms. The most pronounced transcriptional response resulted from the SiO2 treatement - the most prevelant responses were cell cycle, lipid metabolism and pro-inflammatory responses - with fewer responses from the PAMAM dendrimers. The lipid metabolism responses may relate to teh positive surface character as this response was not observed in the G3.5-COOH dendrimers. Indeed, the G3.5-COOH dendrimers were non-toxic and did not demonstrate any consistent transcriptional response. Primary human aortic endothial cells (HAECs) were grown in 6 well plates (in 2 ml of medium) until they were >80% confluent by visual inspection. Daily media changes allowed continued growth for HAECs that demonstrate contact inhibition. The cells were then incubated with nanomaterials: surface modified SiO2 with worm and sphere goemetries (the spheres were 200 nm in diameter and the worm's cylindrical diameter 200 nm and the length was ~ 1000 nm); and PAMAM dendrimers with different surface charges (G3.5-COOH are negative and G4-NH2 are positive). RNA was collected after 4 and 24 hrs (one SiO2 worm sample was at 1.5 hrs due to space available on the 4-pack microarrays). Triplicate biological samples (indicated by the 'a', 'b', and 'c' designations in the sample names) were evaluated for gene expression changes by microarray analysis.

2013-12-20 | E-GEOD-35142 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

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