Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

40 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

MiRNA profile of SEB-activated in vitro female C57BL/6 mouse splenocytes treated with Indole-3-carbinol (I3C) or 3,3'-diindolylmethane (DIM)

ABSTRACT: Splenocytes from female C57BL/6 mice were activated with SEB (1ug/ml) for 24 hours in 96-well plates. Control group was treated with vehicle (0.5% DMSO in media), and experimental groups were given either I3C or DIM (100uM). After 12 hours, cells were harvested and total RNA was isolated. Total RNA extraction was performed using Qiagen miRNeasy kit and RNA quality was assessed specrophotometrically. Affymetric Gene Chip miRNA 3.0 array was used for miRNA profiling using FlashTag Biotin HSR RNA labeling kit.

ORGANISM(S): Mus musculus

SUBMITTER: Philip Brandon Busbee

PROVIDER: E-MTAB-3185 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Publications

Natural indoles, indole-3-carbinol (I3C) and 3,3'-diindolylmethane (DIM), attenuate staphylococcal enterotoxin B-mediated liver injury by downregulating miR-31 expression and promoting caspase-2-mediated apoptosis.

Busbee Philip B PB Nagarkatti Mitzi M Nagarkatti Prakash S PS

PloS one 20150223 2

Staphylococcal enterotoxin B (SEB) is a potent superantigen capable of inducing inflammation characterized by robust immune cell activation and proinflammatory cytokine release. Exposure to SEB can result in food poisoning as well as fatal conditions such as toxic shock syndrome. In the current study, we investigated the effect of natural indoles including indole-3-carbinol (I3C) and 3,3'-diindolylmethane (DIM) on SEB-mediated liver injury. Injection of SEB into D-galactosamine-sensitized female ...[more]

PMID: 25706292

Similar Datasets

miRNA expression in lung infiltrating mononuclear cells after exposure to Staphylococcal enterotoxin B

Project description:C57BL/6 mice were either given Staphyloccocal entertoxin B (SEB) or PBS as a control for 48 hours. Mice were sacrificed and lung infiltrating mononuclear cells were isolated. Total RNA extraction was performed using Qiagen miRNeasy kit and RNA quality was assessed specrophotometrically. Affymetric Gene Chip miRNA 1.0 array was used for miRNA profiling using FlashTag Biotin HSR RNA labeling kit.

2014-04-01 | E-MTAB-2379 | biostudies-arrayexpress

miRNA expression profile following Staphylococcal Enterotoxin B exposure in C3h/HeJ mice

Project description:C3H/HeJ mice were either given a Dual Dose (5 ug intranasal and 2 ug intraperitoneal two hours apart) of Staphyloccocal entertoxin B (SEB) or PBS as a control for 72 hours in a Mice were sacrificed and lung infiltrating mononuclear cells were isolated. Total RNA extraction was performed using Qiagen miRNeasy kit and RNA quality was assessed specrophotometrically. Affymetric Gene Chip miRNA 3.0 array was used for miRNA profiling using FlashTag Biotin HSR RNA labeling kit.

2014-06-30 | E-MTAB-2641 | biostudies-arrayexpress

Toxicogenomic profiling of trout tumor promoters

Project description:Indole-3-carbinol (I3C), from cruciferous vegetables, has been found to suppress or enhance tumors in several animal models. We previously reported that dietary I3C promotes hepatocarcinogenesis in rainbow trout (Oncorhynchus mykiss) at concentrations that differentially activated estrogen receptor (ER) or aryl hydrocarbon receptor (AhR)-mediated responses based on individual protein biomarkers. In this study, we evaluated the relative importance of these pathways as potential mechanisms for I3C on a global scale. Hepatic gene expression profiles were examined in trout after dietary exposure to 500 and 1500 ppm I3C and 3,3,-diindolylmethane (DIM), a major in vivo component of I3C, and were compared to the transcriptional signatures of two model hepatic tumor promoters; 17beta-estradiol (E2), an ER agonist, and beta-naphthoflavone, an AhR agonist. We demonstrate that I3C and DIM acted similar to E2 at the transcriptional level based on correlation analysis of expression profiles and clustering of gene responses. Of the genes regulated by E2 (fold change >2.0 or <0.50), most genes were regulated similarly by DIM (87-92%) and I3C (71%) suggesting a common mechanism of action. Of interest were upregulated genes associated with signaling pathways for cell growth and proliferation, vitellogenesis, and protein folding, stability and transport. Other genes down-regulated by E2, including those involved in acute-phase immune response, were also down-regulated by DIM and I3C. Gene regulation was confirmed by qRT-PCR and western blot. These data indicate I3C promotes hepatocarcinogenesis through estrogenic mechanisms in trout liver and suggest DIM may be an even more potent hepatic tumor promoter in this model. Keywords: dose response

2005-09-28 | GSE3324 | GEO

Aspergillus niger : Control (fructose) vs. steam-exploded sugarcane induction (SEB)

Project description:Transcriptional profiling of A. niger comparing mutant strains with the disrupted xylanolytic transcriptional activator gene, XlnR, the arabinolytic transcriptional activator gene, AraR, and the double mutant (ΔXlnR, ΔaraR and ΔaraRΔXlnR, repsectively) treated with steam-exploded sugarcane bagasse (SEB) for 12 and 24 h. The main objective was to identify genes related to cellulases and hemicellulases in mutant strains grown on SEB, with indirect comparisons with the WT strain grown on SEB [the (WT/SEB) data deposited in GSE24798]. The experiment was further validated by real-time PCR and enzymatic assay.

2012-05-07 | GSE37758 | GEO

Indoles (I3C and DIM)-mediated regulation of microRNAs in DTH model

Project description:Our laboratory observed that indoles (I3C and DIM) suppressed the development of delayed type hypersensitivity (DTH) in mice. Also, we observed differential regulation of regulatory T cells (Tregs) and Th17 cells in mice treated with I3C or DIM. The aim of this experiment was, therefore, to understand the role of I3C or DIM in the regulation of microRNAs (miRs) in immune cells and generation of Tregs and Th17 cells. We also used FICZ, an aryl hydrocarbon receptor (AhR) ligand to understand the role of various ligands in the regulation of Tregs and Th17 cells. To this end, we used draining (inguinal) lymph nodes (LNs) of mice (C57BL/6) with DTH and treated with Vehicle (corn oil, VEH) or I3C or DIM or FICZ. In brief, total RNA including miRs from inguinal LNs were isolated using miRNeasy kit and the protocol of the company was followed (QIAGEN, Valencia, CA). Next, miR arrays were performed at Johns Hopkins University Microarray and Sequencing Core facility using platform.

2019-01-02 | E-MTAB-4076 | biostudies-arrayexpress

Aspergillus niger : Control (fructose) vs. steam-exploded sugarcane induction (SEB)

Project description:Transcriptional profiling of A. niger comparing mutant strains with the disrupted xylanolytic transcriptional activator gene, XlnR, the arabinolytic transcriptional activator gene, AraR, and the double mutant (M-NM-^TXlnR, M-NM-^TaraR and M-NM-^TaraRM-NM-^TXlnR, repsectively) treated with steam-exploded sugarcane bagasse (SEB) for 12 and 24 h. The main objective was to identify genes related to cellulases and hemicellulases in mutant strains grown on SEB, with indirect comparisons with the WT strain grown on SEB [the (WT/SEB) data deposited in GSE24798]. The experiment was further validated by real-time PCR and enzymatic assay. Two-condition experiment : A. niger mutant strains on SEB for 12 and 24 h at 30 oC in batch culture. Firstly, the strains were pre-grown in minimal medium with fructose as carbon source (control), and then transferred to SEB as carbon source.

2012-05-06 | E-GEOD-37758 | biostudies-arrayexpress

Gene expression during tumor enhancement by 3,3’-diindolylmethane in rainbow trout: Timecourse

Project description:Indole-3-carbinol (I3C) and 3,3’-diindolylmethane (DIM), a primary I3C derivative in vivo, are known dietary chemopreventive agents also available as dietary supplements. However, I3C has been found to act as a tumor promoter in rat (multi-organ) and trout (liver) models. I3C and DIM were previously found to be estrogenic in trout liver based on toxicogenomic profiles. In this study, we compare the post-initiation effects of DIM and 17β-estradiol (E2) on aflatoxin B1 (AFB1)-induced hepatocarcinogenesis in trout. Trout were initiated as embryos with 50 ppb AFB1, fed control diet for three months followed by diets containing 0, 120 or 400 ppm DIM or 5 ppm E2 for 18 weeks before returning all groups to control diet. Tumor incidence was determined 13 months later and found to be significantly elevated in AFB1-initiated trout fed either 400 ppm DIM or 5 ppm E2 compared to control animals. To evaluate the mechanism of tumor enhancement, hepatic gene expression profiles were examined in animals fed promotional diets during the course of tumorigenesis and in hepatocellular carcinomas (HCCs) of initiated animals using a rainbow trout 70-mer custom oligonucleotide array. We demonstrate that DIM alters gene expression profiles similar to E2 in liver samples during tumorigenesis and in HCC tumors. Further, HCCs from animals on DIM and E2 promotional diets had a transcriptional signature indicating decreased invasive or metastatic potential compared to HCCs from control animals. Overall, these findings are the first to demonstrate tumor promotion by DIM. They confirm the importance of estrogenic signaling in the mechanism of promotion by dietary indoles in trout liver and indicate a possible dual effect that enhances tumor incidence and decreases potential for metastasis. Keywords: time course

2006-12-31 | GSE5644 | GEO

Gene expression during tumor enhancement by 3,3’-diindolylmethane in rainbow trout: HCC tumor samples

2006-12-31 | GSE5643 | GEO

Feasibility of global microRNA analysis from fine-needle biopsy FFPE material in patients with hepatocellular carcinoma treated with sorafenib

Project description:Tumor cells were microdissected from FFPE sections of hepatocellular carcinoma (HCC) samples. micro RNA expression were correlated to clinical outcome and sorafenib-therapy. miRNA was labeled with the Affymetrix FlashTag Biotin HSR RNA Labeling Kit

2014-07-29 | GSE56059 | GEO

MicroRNA Profiling of Laser-Microdissected Hepatocellular Carcinoma Reveals an Oncogenic Phenotype of the Tumor Capsule

Project description:Tumor cells were microdissected from FFPE sections of hepatocellular carcinoma (HCC) samples. Samples were compared between different localisations either within or around the tumor. miRNA was labeled with the Affymetrix FlashTag Biotin HSR RNA Labeling Kit

2015-01-14 | GSE54537 | GEO

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