Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

84 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Gene Expression Analysis for HBx-induced HCC Mouse Model

ABSTRACT: Hepatoarcinogenesis is a slow and multistep process. We used Hepatitis B virus X antigen (HBx) induced Hepatocellular carcinoma (HCC) as model. We also identify the biomarkers, the pathways and networks underlying HCC formation in this animal model. We analyzed the events from the early, middle, and late stages, in order to predict and prevent the development of cancer. At each specific stage, we analyzed the expression level that differed at least two-fold between HBx transgenic and wild-type mouse liver. Statistical approaches were used to identify genes displaying an increasing or decreasing trend throughout hepatocarcinogenesis. The liver was excised from 6-week-, 8-month-, 12-month-, 14-month-, and 16-month-old HBx transgenic mice (A106 strain) and RNA samples were isolated. In both 14-month- and 16-month-old mice, samples were obtained from both the tumor tissue and the normal.

ORGANISM(S): Mus musculus

SUBMITTER: Chiou-Hwa Yuh

PROVIDER: E-GEOD-15251 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Shared Molecules

Only show the datasets with similarity scores above: 0.5

Threshold

0.5

Similar Datasets

Long non-coding RNAs and mRNAs expression analysis of HCC

Project description:Although many protein-coding genes have been identified to be aberrantly expressed in hepatocellular carcinoma (HCC), the mechanisms that account for development and progression of HCC remain unclear. In recent years, long noncoding RNAs (lncRNAs) have been shown to have critical regulatory roles in mammalian cell biology. Many lncRNAs can result in aberrant expression of gene products that may contribute to cancer biology. In this study, we first identified non-overlapping signatures of a small number of lncRNAs that are aberrantly expressed in human HCC compared with paired peritumoral tissues. Then we used real-time PCR to validate five lncRNAs whose expression was altered in HCC compared with paired peritumoral tissues. Using loss-of-function and gain-of-function approaches, we found that an lncRNA (termed lncRNA-HEIH) plays a key role in cell cycle regulation. We further demonstrated that lncRNA-HEIH bound to enhancer of zeste homolog 2 (EZH2) and that this interaction was required for the repression of EZH2 target genes. Together, these results reveal insights into the molecular regulation mechanisms of HCC cell cycle regulation and lead us to propose that lncRNAs may serve as key regulatory hubs in cancer biology. A ten chip study using total RNA recovered from five separate HCC tissues and five corresponding paired non-tumor samples.

2011-09-04 | E-GEOD-27462 | biostudies-arrayexpress

Wild-type versus HBx-transfected mive

Project description:Hepatitis B virus (HBV) has been clearly recognized as an etiological factor for hepatocellular carcinoma (HCC). HBV encodes the potentially oncogenic HBx protein. We aimed to elucidate the molecular mechanism of HCC caused by HBx and to discover the biomarker related to HCC by HBx. Three experimental groups, 3, 9 and 13 month aged HBx Tg mice and age matched normal wild type B6 mouse which have same background of HBx Tg mice were used to find differentially expressed genes during HCC. Keywords: Genetic modification 3-month-old, 9-month-old, 13-month-old wild type B6 mice vs 3-month-old, 9-month-old, 13-month-old HBx transfected mice; Biological replicates at each timepoint; 9 controls vs 9 HBx-mice

2010-06-19 | E-GEOD-12723 | biostudies-arrayexpress

Expression analysis of zebrafish liver after exposure in naphthalene

Project description:Investigation of whole genome gene expression level changes in zebrafish liver under naphthalene treatedï¼?high-concentration group and low-concentration groupï¼?, compared to the solvent control group revealed that 76 genes and 88 genes were differentially expressed respectively in the fish caged at the low-concentration and high-concentration. KEGG pathway and GO analysis of the differentially expressed genes, showed significant enrichment in several meaningful categories. Healthy 5-month-old adult zebrafish (AB strain) maintenance and chemical exposure to 84Î¼g/L and 840Î¼g/L naphthalene and 0.005% Dimethyl sulfoxide as the solvent control were performed according to published research protocols. Prior to exposure, the fish were acclimatized in 50L aerated fresh water in glass tanks for 2 weeks, under controlled environmental conditions with the water temperature maintained at 26Â±0.5â?? for 16-h light and 8-h dark photoperiod. After 21 d of treatment, adult zebrafish livers were removed by dissection, and immediately transferred to RNA-later Stabilization Reagent(Qiagen,76106) , prior to storage at 4â?? for histopathological and microarray analysis. NimbleGen Gene Expression 12X135K zebrafish microarrays and One-Color DNA labeling Kit (NimbleGen, WI) were used for genome-wide expression analysis of naphthalene-treated zebrafish.

2015-11-07 | E-GEOD-74776 | biostudies-arrayexpress

The gene expression profiling array of LncRNA between tumor tissues and paired non-tumor tissues in HBV-positive hapatocellular carcinoma

Project description:Investigation of whole genome gene expression level changes of LncRNAs in tumor tissues and paired non-tumor tissues in HBV-positive hapatocellular carcinoma. The different expression genes were further analysised. The human LncRNA microarray analysis of the 10 samples (5 non-tumor tissues and 5 paired tumor tissues) were completed. Total RNA from each sample was quantified using the NanoDrop ND-1000 and RNA integrity was assessed using standard denaturing agarose gel electrophoresis. Total RNA of each sample was used for labeling and array hybridization as the following steps: 1) Reverse transcription with by Invitrogen Superscript ds-cDNA synthesis kit; 2) ds-cDNA labeling with NimbleGen one-color DNA labeling kit; 3) Array hybridization using the NimbleGen Hybridization System and followed by washing with the NimbleGen wash buffer kit; 4) Array scanning using the Agilent Scanner G2505C. Scanned images (TIFF format) were then imported into NimbleScan software (version 2.5) for grid alignment and expression data analysis. Expression data were normalized through quantile normalization and the Robust Multichip Average (RMA) algorithm included in the NimbleScan software. The Probe level (*_norm_RMA.pair) files and mRNA level (*_RMA.calls) files were generated after normalization. All mRNAs level files were imported into Agilent GeneSpring GX software (version 11.5.1) for further analysis.mRNAs that at least 3 out of 6 samples have values greater than or equal to lower cut-off: 50.0 (“All Targets Value”) were chosen for further data analysis. Differentially expressed mRNAs were identified through Volcano Plot filtering. Pathway analysis and GO analysis were applied to determine the roles of these differentially expressed mRNAs played in these biological pathways or GO terms. Finally, Hierarchical Clustering was performed to show the distinguishable mRNAs expression pattern among samples.

2013-08-10 | E-GEOD-49713 | biostudies-arrayexpress

Wild-type versus HBx-transfected mive

2008-09-11 | GSE12723 | GEO

Genome conformation capture reveals that the Escherichia coli chromosome is organized by replication and transcription

Project description:To fit within the confines of the cell, bacterial chromosomes are highly condensed into a structure called the nucleoid. Despite the high degree of compaction in the nucleoid, the genome remains accessible to essential biological processes, such as replication and transcription. Here, we present the first high-resolution chromosome conformation capture-based molecular analysis of the spatial organization of the Escherichia coli nucleoid during rapid growth in rich medium and following an induced amino acid starvation that promotes the stringent response. Our analyses identify the presence of origin and terminus domains in exponentially growing cells. Moreover, we observe an increased number of interactions within the origin domain and significant clustering of SeqA-binding sequences, suggesting a role for SeqA in clustering of newly replicated chromosomes. By contrast, ‘histone-like’ protein (i.e. Fis, IHF and H-NS) binding sites did not cluster, and their role in global nucleoid organization does not manifest through the mediation of chromosomal contacts. Finally, genes that were downregulated after induction of the stringent response were spatially clustered, indicating that transcription in E. coli occurs at transcription foci. A 4 chips study of exponentially growing wild type E. coli strain MG1655 grown in LB rich media or after induction of the stringent response by serine hydroxamate for 30 min. Two technical replicates, Three biological replicates mixed prior hybridization on the chip.

2013-05-01 | E-GEOD-40304 | biostudies-arrayexpress

Comparative analysis of chrysanthemum transcriptome in response to infection of three viruses: Cucumber mosaic virus, Tomato spotted wilt virus, and Potato virus X

Project description:Gene expression analysis of chrysanthemum infected with three different viruses including Cucumber mosaic virus, Tomato spotted wilt virus, and Potato virus X have been performed using the chrysanthemum 135K microarray. Mock and each virus infected chrysanthemum plants were subjected for microarray analysis.

2015-01-01 | E-GEOD-55985 | biostudies-arrayexpress

Comprehensive transcriptional profiling analysis reveals candidate regulators in cold-stressed seedlings of Petunia hybrida

Project description:Investigation of gene expression level changes in Petunia hybrida seedlings subjected to cold at 2°C for 0.5 h, 2 h, 24 h and 5 d, compared to the CK. The custom-designed four-plex microarray with 72000 features was constructed based on the EST sequences generated in Breuillin's study together with all sequences of P.hybrida and P.axillaris available at Genbank, TIGR, and the Solanaceae genomics network SGN, which was ultimately composed by a set of 24816 non-redundant unique sequences (unigenes).The probe intensity files resulting from RNA hybridization were first read into R. Background Correction, quantile normalization and summarization were then performed using the Robust Multi-array Average (RMA) method included in Bioconductor Affy package based on the home made chip description library.

2015-01-15 | E-GEOD-64963 | biostudies-arrayexpress

Expression analysis of Lactococcus lactis NIAI712 and its plasmid cured variant

Project description:L. lactis NIAI712 carries five different plasmids, including an 8.7-kb plasmid designated pAG6. In this study, genome-wide expression profiles of the pAG6-cured variant was compared to the wild-type strain. Two samples of total RNA recovered from a wild-type culture of L. lactis NIAI712 and a pAG6-cured variant were examined

2013-08-31 | E-GEOD-48143 | biostudies-arrayexpress

Expresion analyses of red2 deletion cells

Project description:Investigation of whole genome gene expression level changes in red2?, compared to the parental wild-type strain. The red2 deletion cells analyzed in this study will be described in Sugiyama and Sugioka-Sugiyama. An mRNA profiling study using total RNA recovered from vegetatively growing wild-type culture of fission yeast and red2 deletion cultures of fission yeast. Each chip measures the expression level of 4.997 genes from S.pombe with fourteen 60-mer probe pairs (PM/MM) per gene, with seven-fold technical redundancy.

2013-12-01 | E-GEOD-49006 | 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