Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Gene expression analysis of TNF-alpha stimulated THP-1 cells

ABSTRACT: The series was designed to obtain gene expression patterns of TNF-alpha stimulated THP-1 cells. Keywords: TNF-alpha stimulation This series represents a group of 15 samples in two groups: 7 samples derived from not stimulated THP-1 cells, 8 from THP-1 cells stimulated with TNF-alpha in a final concentration of 5 ng/ml for 60 min.

ORGANISM(S): Homo sapiens

SUBMITTER: Susanna Nikolaus

PROVIDER: E-GEOD-10106 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

From model cell line to in vivo gene expression: disease-related intestinal gene expression in IBD.

Schulze H A HA Häsler R R Mah N N Lu T T Nikolaus S S Costello C M CM Schreiber S S

Genes and immunity 20080313 3

Crohn's disease (CD) and ulcerative colitis (UC) are subforms of inflammatory bowel diseases (IBD). Genetic and environmental factors influencing the onset and course of the diseases have been recently identified. This study uses a two-step approach to detect genes involved in the pathogenesis of IBD by microarray analysis and real-time PCR (RT-PCR). In a first step, microarray expression screening was used to obtain tumour necrosis factor-alpha (TNF-alpha) induction profiles of two human cell l ...[more]

PMID: 18340362

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Project description:Data presented here show that gene expression in the mouse brain changes during systemic infection relative to a steady state (uninfected control) mouse during systemic Listeria monocytogenes infection. Microarray analysis of gene expression in the brain following i.v. inoculation of 1-2 LD 50 L. monocytogenes showed changes in brain transcriptional activity occurred prior to brain infection. Keywords: infectious diseases model, gene expression profiling for cell signaling/trafficking Mice were injected with 1-2 LD50 wild type L. monocytogenes or with sterile PBS (control) then seven animals from each group were harvested daily for 4 days. From each day, groups of five infected animals were selected for microarray analysis based upon similarities in CFU bacteria in the spleen (day 1), blood (day 2), and brain (days 3 and 4) and were randomly paired with brains harvested from control animals. RNA was extracted from the brain halves using the Atlasâ¢ Pure Total RNA Labeling System and hybridized to plastic slides with 32P-labeled probes using Atlasâ¢ Plastic Mouse 5K Microarray (Clontech, Mountain View, CA) according to the manufacturerâs directions. Hybridization to the arrays and phosphorimaging analysis were performed in the OUHSC microarray facility. Phosphorimaging analysis was performed using a Stormâ¢ optical scanner (Molecular Dynamics Inc., Sunnyvale, CA), and initial background corrections were performed using the Array Vision Software (Imaging Research Inc., St. Catharines, Ontario). Data analyses were performed using Genespring GX v. 7.3 (Agilent Technologies, Palo Alto, CA). Raw signal data were normalized to the median of the entire chip for each sample, and all samples were further normalized per gene to the medians of data from the uninfected samples. Data for each day were analyzed by Mann Whitney Wilcoxen nonparametric test with a p-value cutoff of 0.05. Lists of genes were generated to reflect 2, 3, or 5-fold upregulation and downregulation based on significance. Expression data were incorporated into Ingenuity software (Ingenuity Systems, Inc., Redwood City, CA) to enable further understanding of complex relationships as well as provide further information about key canonical pathways in which the genes of interest functions.

Project description:Background: Gene expression profiling of breast carcinomas has increased our understanding of the heterogeneous biology of this disease and promises to impact clinical care. The aim of this study was to evaluate the prognostic value of gene expression-based classification along with established prognostic markers and mutation status of the TP53 gene, in a group of breast cancer patients with long-term (12-16 years) follow-up. Methods: The clinical and histopathological parameters of 200 breast cancer patients were studied for their effects on clinical outcome using univariate/multivariate Cox regression. The prognostic impact of mutations in the TP53 gene, identified using TTGE and sequencing, was also evaluated. Eighty of the samples were analyzed for gene expression using 42K cDNA microarrays and the patients were assigned to five previously defined molecular expression groups. The strength of the gene expression based classification versus standard markers was evaluated by adding this variable to the Cox regression model used to analyze all samples. Results: Both univariate and multivariate analysis showed that TP53 mutation status, tumor size and lymph node status were the strongest predictors of breast cancer survival for the whole group of patients. Analyses of the patients with gene expression data showed that TP53 mutation status, gene expression based classification, tumor size and lymph node status were significant predictors of survival. The TP53 mutation status showed strong association with the ?basal-like? and ?ERBB2+? gene expression subgroups, and tumors with mutation had a characteristic gene expression pattern. Conclusions: TP53 mutation status and gene-expression based groups are important survival markers of breast cancer, and these molecular markers may provide prognostic information that complements clinical variables. The study adds experience and knowledge to an ongoing characterization and classification of the disease. Experiment set consisting of 80 primary breast carcinomas collected at Ulleval University Hospital (ULL-samples), Oslo, Norway from 1990-94, and one normal sample from breast reduction surgery.

Project description:The subcellular localization of specific mRNAs is an evolutionary conserved mechanism that underlies the establishment of cellular polarity and specialized cell functions. In neurons, mRNA trafficking and local protein translation in dendrites provides an important mechanism that mediates synaptic development and plasticity. The significance of mRNA targeting and protein synthesis in axons, however, is still unclear. Only a small number of transcripts have been identified in axons to date, and their contribution to axon growth and neuronal survival remains largely unknown. Here, we report the results of a novel screen that allowed the separate identification of mRNAs localized in cell bodies and in axons of developing neurons. Using compartmentalized cultures of sympathetic neurons and Sequential Analysis of Gene Expression (SAGE), the screen identified more than 200 axonal mRNAs, including ones that encode cytoskeletal proteins and proteins that function in neural development and signal transduction. Importantly, several classes of transcripts were selectively enriched in axons, indicating that an active process drives the targeting of specific mRNAs from the cell bodies to the axons. This study is the first comprehensive and unbiased analysis of mRNA localization in subcellular domains of any neuronal cell type. We used compartmentalized chambers to culture neonatal rat sympathetic neurons (Campenot, 1977). In these cultures, the cell bodies are separated from the distal axons by a 1 mm wide Teflon divider, which maintains the cell bodies and axon terminals in separate fluid compartments. Primary rat sympathetic neurons are especially suitable for compartmentalized culture because they can be grown as a highly homogeneous population without glial cells. Neurons were seeded in the central compartment with nerve growth factor (NGF), and after a few days, the NGF was lowered in this compartment and supplied only to the peripheral compartment to stimulate axon growth. The anti-mitotic agent cytosine arabinoside C (Ara-C) was added to both compartments to remove non-neuronal cells. mRNA was then isolated after 12 days in culture (DIV) from cell body or axon compartments. As the initial mRNA content in axons was not sufficient to perform the SAGE analysis, both axon and cell body mRNAs were subjected to two rounds of linear amplification to obtain antisense RNA (aRNA). The amplified aRNA was then reverse transcribed and second strand synthesis was performed to proceed with the SAGE assay using the LongSAGE kit (Invitrogen) according to the manufacturer’s protocol.

Dataset Information

Gene expression analysis of TNF-alpha stimulated THP-1 cells

Publications

From model cell line to in vivo gene expression: disease-related intestinal gene expression in IBD.

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