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Genome wide analysis of pancreatic gene expression by Interleukin 1? in human epithelial pancreatic Mia Paca-2 cells

ABSTRACT: Analysis of the pancreatic gene expression with IL-1β stimulation. Components of the integrin pathway were significantly altered with IL-1β which play critical role in the execution of apoptosis.The results revealed several important cellular pathways and the biological processes of the genes (Up and Downregulated) altered by IL-1β induction. Total RNA was isolated from cells incubated in the absence (Control) and presence of IL-1β (2ng/ml) for 36 hours. These were then subjected to microarray hybridisation in a WG_6_V3 bead chip, Illumina. Differentially expressed genes were functionally categorised into biological processess and cellular pathways using the PANTHER Classification system. The significantly emerging cellualr pathway was validated by Western Blot analyses.

ORGANISM(S): Homo sapiens

SUBMITTER: Verma G

PROVIDER: S-ECPF-GEOD-26702 | biostudies-other | 2012 Jul

REPOSITORIES: biostudies-other

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Genome wide analysis of pancreatic gene expression by Interleukin 1β in human epithelial pancreatic Mia Paca-2 cells.

Project description:Analysis of the pancreatic gene expression with IL-1β stimulation. Components of the integrin pathway were significantly altered with IL-1β which play critical role in the execution of apoptosis.The results revealed several important cellular pathways and the biological processes of the genes (Up and Downregulated) altered by IL-1β induction.

2012-06-21 | GSE26702 | GEO

Genome wide analysis of pancreatic gene expression by Interleukin 1M-NM-2 in human epithelial pancreatic Mia Paca-2 cells.

Project description:Analysis of the pancreatic gene expression with IL-1M-NM-2 stimulation. Components of the integrin pathway were significantly altered with IL-1M-NM-2 which play critical role in the execution of apoptosis.The results revealed several important cellular pathways and the biological processes of the genes (Up and Downregulated) altered by IL-1M-NM-2 induction. Total RNA was isolated from cells incubated in the absence (Control) and presence of IL-1M-NM-2 (2ng/ml) for 36 hours. These were then subjected to microarray hybridisation in a WG_6_V3 bead chip, Illumina. Differentially expressed genes were functionally categorised into biological processess and cellular pathways using the PANTHER Classification system. The significantly emerging cellualr pathway was validated by Western Blot analyses.

2012-06-20 | E-GEOD-26702 | biostudies-arrayexpress

Genome-wide analysis gene expression in SUM-149 cells expressing AREG shRNA

Project description:Results of knocking-down AREG expression in SUM-149 cells by lenitviral infection of shRNA vectors and measuring gene expression provides information as to what genes are regulated by AERG in inflammatory breast cancer cells. SUM-149 cells were infected with a single AREG shRNA virus (sh4) or three AREG shRNA viruses (shPld) and the non-silencing vector (shNS). Total RNA was collected and genome-wide analysis of expression was performed on RNA from each cell line.

| S-ECPF-GEOD-26079 | biostudies-other

Genome-wide analysis of promoter methylation associated with gene expression profile in pancreatic adenocarcinoma.

Project description:The goal of this study was to comprehensively identify CpG island methylation alterations between pancreatic cancers and normal pancreata and their associated gene expression alterations.We employed methylated CpG island amplification followed by CpG island microarray, a method previously validated for its accuracy and reproducibility, to analyze the methylation profile of 27,800 CpG islands covering 21 MB of the human genome in nine pairs of pancreatic cancer versus normal pancreatic epithelial tissues and in three matched pairs of pancreatic cancer versus lymphoid tissues from the same individual.This analysis identified 1,658 known loci that were commonly differentially methylated in pancreatic cancer compared with normal pancreas. By integrating the pancreatic DNA methylation status with the gene expression profiles of the same samples before and after treatment with the DNA methyltransferase inhibitor 5-aza-2'-deoxycytidine, and the histone deacetylase inhibitor, trichostatin A, we identified dozens of aberrantly methylated and differentially expressed genes in pancreatic cancers including a more comprehensive list of hypermethylated and silenced genes that have not been previously described as targets for aberrant methylation in cancer.We expected that the identification of aberrantly hypermethylated and silenced genes will have diagnostic, prognostic, and therapeutic applications.

| S-EPMC3131423 | biostudies-literature

Genome wide analysis of pancreatic cancer cell gene expresison exposed to stromal pancreatic stellate cells in 3D gel matrix

Project description:Capan1 (well differentiated pancreatic cancer cell line) was co-cultured with pancreatic stellate cell line (PS1) embedded in a 3D organotypic model and gene expression was analysed in comparison to cancer cells cultured alone without stellate cells. Pancreatic stellate cells were embedded within a gel matrix composing collagen type I and Matrigel, and cancer cells were seeded on top. The gel was lifted on to metal grid after 24 hour and fed from below. Gels were harvested on day 10 and frozen sections obtained. The cancer cell layer on top of the gel was captured by laser microdissection for RNA extraction.

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CDX2 regulates interleukin-33 gene expression in intestinal epithelial cells (LS174T).

Project description:Dysregulation of interleukin-33 (IL-33) has been implicated in the pathogenesis of several autoimmune and inflammatory diseases, but few studies have examined transcriptional regulation of the IL33 gene. In the intestines, gene regulation is controlled by a transcription factor network of which the intestinal-specific transcription factor CDX2 is a key component. In this study, we investigated whether CDX2 regulates IL33 mRNA expression. We examined IL33 mRNA expression in primary colonic epithelial cells from healthy humans and epithelial cell lines, revealing high expression levels in primary colonic and LS174T cells. Combining genomics data (ChIP-seq, RNA-seq) and IL33 promoter analyses in LS174T cells revealed intronic enhancer activity in the IL33 gene that is dependent on CDX2 expression. Western blotting and qRT-PCR confirmed that IL33 expression is upregulated in a CDX2 concentration-dependent manner, thereby providing the first evidence that CDX2 regulates the expression of IL33.

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Genome-wide analysis of gene and protein expression of dysplastic naevus cells.

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Genome-wide gene expression profiling of homeodomain-interacting protein kinase 2 deficient medullary thymic epithelial cells.

Project description:The establishment of central tolerance essentially depends on the promiscuous gene expression (pGE) of a plethora of tissue restricted antigens by the medullary thymic epithelial cells. The antigens are presented to developing thymocytes in the thymus to select for non-self reactive T-cell receptors in order to prevent autoimmune reactions in the periphery. However the molecular regulation of tissue-restricted antigen expression is still poorly understood. The only regulator known to play a role in the transcriptional regulation so far is the autoimmune regulator (AIRE). AIRE is thought to act in a multi-protein complex, promoting transcription, elongation and splicing of target genes. Yet the full composition of this Aire-associated multi-protein complex and its mode of action remain to be elucidated. Here we describe the experimental details and controls of the gene array analysis on the impact of the homeodomain-interacting protein kinase 2 (Hipk2) on promiscuous gene expression in medullary thymic epithelial cells based on the analysis of newly generated TEC-specific Hipk2 conditional knockout mice. The changes in gene expression are presumably mediated through a regulatory effect of Hipk2 on AIRE as published in the study by Rattay and colleagues in the Journal of Immunology [1]. The gene array data reported in this paper have been deposited in the Gene Expression Omnibus (GEO) database, www.ncbi.nlm.nih.gov/geo (accession no. GSE63432).

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Genome-wide DNA methylation analysis of lung carcinoma : Gene expression data

Project description:Lung cancer is the worldwide leading cause of death from cancer. DNA methylation in gene promoter regions is a major mechanism of gene expression regulation that may promote tumorigenesis. Experimental Design Whole-genome DNA methylation analysis using 450K Illumina BeadArrays was performed on 12 normal lung tissues and 124 tumors including 83 adenocarcinomas, 23 squamous cell carcinomas (SqCC), one adenosquamous cancer, five large cell carcinomas, nine large cell neuroendocrine carcinomas (LCNEC), and three small cell carcinomas (SCLC). Complimentary gene expression analyses was performed on 117 of the 124 tumors using Illumina HT12 V4 arrays (reported here). Gene expression profiling of 117 lung carcinomas using Illumina HT-12 V4 microarrays.

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Genome-wide analysis of cancer/testis gene expression.

Project description:Cancer/Testis (CT) genes, normally expressed in germ line cells but also activated in a wide range of cancer types, often encode antigens that are immunogenic in cancer patients, and present potential for use as biomarkers and targets for immunotherapy. Using multiple in silico gene expression analysis technologies, including twice the number of expressed sequence tags used in previous studies, we have performed a comprehensive genome-wide survey of expression for a set of 153 previously described CT genes in normal and cancer expression libraries. We find that although they are generally highly expressed in testis, these genes exhibit heterogeneous gene expression profiles, allowing their classification into testis-restricted (39), testis/brain-restricted (14), and a testis-selective (85) group of genes that show additional expression in somatic tissues. The chromosomal distribution of these genes confirmed the previously observed dominance of X chromosome location, with CT-X genes being significantly more testis-restricted than non-X CT. Applying this core classification in a genome-wide survey we identified >30 CT candidate genes; 3 of them, PEPP-2, OTOA, and AKAP4, were confirmed as testis-restricted or testis-selective using RT-PCR, with variable expression frequencies observed in a panel of cancer cell lines. Our classification provides an objective ranking for potential CT genes, which is useful in guiding further identification and characterization of these potentially important diagnostic and therapeutic targets.

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