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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Expression data from Mvt-1 clonal isolates over-expressing Ndn 50T or Ndn 50C

ABSTRACT: Ndn is a candidate metastasis suppressor gene that has been reported to regulate transcription. We examined the changes in gene expression caused by the stable over-expression of allelic variants of Ndn, 50T or 50C, using lentiviral transduction in the mouse mammary tumor cell line Mvt-1. A total of 9 samples were analyzed. In pairwise comparisons using Partek, genes with a Benjamini-Hochberg corrected p-value <0.05 and a fold-change â¥abs(2.5) were selected.

ORGANISM(S): Mus musculus

SUBMITTER: Nigel Crawford

PROVIDER: E-GEOD-65824 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Expression data from Mvt-1 clonal isolates over-expressing Ndn 50T or Ndn 50C

Project description:Ndn is a candidate metastasis suppressor gene that has been reported to regulate transcription. We examined the changes in gene expression caused by the stable over-expression of allelic variants of Ndn, 50T or 50C, using lentiviral transduction in the mouse mammary tumor cell line Mvt-1.

2016-02-08 | GSE65824 | GEO

Expression data from HEK wild-type cells treated with geneticin (16uM) or left untreated

Project description:In order to study the cellular response to aminoglycoside-induced mistranslation, we used a whole-genome microarray analysis of geneticin-treated versus untreated cells, which revealed a broad transcriptional response totaling 705 genes. comparison of four geneticin treated biological replicates with four untreated biological replicates (selected for a fold change > 1.2, Benjamini-Hochberg corrected p-value < 0.05)

2014-05-01 | E-GEOD-57198 | biostudies-arrayexpress

Expression data from Drd1a and Drd2 expressing neurons in striatum and cortex, at 6 weeks and 2 years of age

Project description:We performed a study of gene expression changes that occur during mouse aging in the striatum and cortex in specific neuronal populations. Using translating ribosome afifnity purificaiton, we captured cell type-specific mRNAs from Drd1a-expressing cortical neurons, Drd1a-expressing striatal neurons, Drd2-expressing cortical neurons, and Drd2-expressing striatal neurons. 31 total samples were anlayzed. We generated the followinf pairwise comparisons: Old (2 years) vs young (6 weeks) Drd1a expressing cortical cells; old (2 years) vs young (6 weeks) Drd2 expressing cortical cells; old (2 years) vs young (6 weeks) Drd1a expressing striatal cells; old (2 years) vs young (6 weeks) Drd2 expressing striatal cells. We used a restriction of Benjamini-Hochberg FDR <0.05, and a fold-change restriction of 1.2-fold.

2014-12-13 | E-GEOD-64140 | biostudies-arrayexpress

Expression data of IL-18 generated murine NK cells

2012-07-11 | GSE33627 | GEO

Transcription profiling of mouse dendritic cells compare the similarity of endogenous and exogenous antigens

Project description:Here we demonstrate by the use of extensive controls and stringent statistical analysis that dendritic cells differentially regulate hundreds of different genes based upon sequence similarity of endogenously- and exogenously-loaded antigens and in a T-cell independent fashion. When endogenously and exogenously-derived antigens are identical, dendritic cells upregulate many different components of the Th-1 response, favoring the priming of CD8+ effectors and promulgating cellular immunity. Experiment Overall Design: Dendritic cells were loaded by 1 of 5 different methods, then matured for 48 hours. Total cellular RNA was then extracted from 9 unloaded DC populations, 10 mRNA-loaded populations, 11 lysate-loaded populations, 7 doubly-loaded (matched) populations, and 7 doubly-loaded (mismatched) populations, a total of 44 different experiments. Each population was derived from a different normal human donor. Matched/mismatched refers to the source of the mRNA and lysate used to load the DCs. Matched signifies that the mRNA and lysate came from the same source. Mismatched signifies that the mRNA and lysate came from disparate sources. Gene expression profiles were then determined according to the method by which the DCs had been loaded. Genes were identified as differentially expressed by DCs doubly-loaded with matched antigens, only if they were significantly different from all of the other four controls. Significance was defined as Cohenâ??s |d| > 1.0 (large effect) and q-value (Benjamini-Hochberg false discovery) < 0.01.

2008-06-15 | E-GEOD-7247 | biostudies-arrayexpress

Gene expression profiles in HepG2 cells exposed to atorvastatin

Project description:In the exon array data set, gene level analysis was performed on HepG2 cells exposed to atorvastatin. No genes were found to be statistically significantly differentially expressed upon atorvastatin treatment. 3 control and 3 atorvastatin treated HepG2 samples were analysed. Genes with an FDRM-bM-^IM-$5% after Benjamini-Hochberg correction was considered as differentially expressed.

2014-04-26 | E-GEOD-57071 | biostudies-arrayexpress

Expression data of IL-18 generated murine NK cells

Project description:We analyzed gene expression profiles of IL-18 generated murine NK cells in comparison to unstimulated, freshly isolated splenic NK cells. We identified a set of 1414 Affymetrix probe sets showing significant misregulation (Welch's T-test, p<0.05; Benjamini-Hochberg FDR corrected). IL-18 generated as well as unstimulated NK cells were isolated in three independent preparations and used for RNA extraction and hybridization on Affymetrix microarrays.

2012-07-10 | E-GEOD-33627 | biostudies-arrayexpress

Microarray profiling of PFC, HPC and STR from subjects with schizophrenia, bipolar, MDD or control

Project description:Schizophrenia is a complex psychiatric disorder encompassing a range of symptoms and etiology dependent upon the interaction of genetic and environmental factors. Several risk genes, such as DISC1, have been associated with schizophrenia as well as bipolar disorder (BPD) and major depressive disorder (MDD), consistent with the hypothesis that a shared genetic architecture could contribute to divergent clinical syndromes. The present study compared gene expression profiles across three brain regions in post-mortem tissue from matched subjects with schizophrenia, BPD or MDD and unaffected controls. Post-mortem brain tissue was collected from control subjects and well-matched subjects with schizophrenia, BPD, and MDD (n=19 from each group). RNA was isolated from hippocampus, Brodmann Area 46, and associative striatum and hybridized to U133_Plus2 Affymetrix chips. Data were normalized by RMA, subjected to pairwise comparison followed by Benjamini and Hochberg False Discovery Rate correction (FDR). Samples derived from patients with schizophrenia exhibited many more changes in gene expression across all brain regions than observed in BPD or MDD. Several genes showed changes in both schizophrenia and BPD, though the magnitude of change was usually larger in schizophrenia. Several genes that have variants associated with schizophrenia were found to have altered expression in multiple regions of brains from subjects with schizophrenia. Continued evaluation of circuit-level alterations in gene expression and gene-network relationships may further our understanding of how genetic variants may be influencing biological processes to contribute to psychiatric disease. Pre-frontal cortex, striatum and hippocampus were obtained from subjects with schizophrenia, bipolar disorder, major depressive disorder and matched controls.

2014-01-11 | E-GEOD-53987 | biostudies-arrayexpress

Expression data from peripheral blood - blood draws at Pre and Post time points of Allergen inhalation challenge (PAX.NGR)

Project description:Detecting differential changes in the peripheral whole-blood transcriptome, post-challenge compared to pre-challenge; using non-globin reduced PAXgene (PAX.NGR) tubes Blood was collected immediately prior to, and two hours after challenge Preprocessing and filtering were applied to the PAX.NGR dataset using the Factor Analysis for Robust MicroArray Summarization (farms) package in R The Linear Models for MicroArrays (limma) package in R was used to determine differential gene expression using a Benjamini Hochberg FDR of 5%.

2012-01-26 | E-GEOD-34159 | biostudies-arrayexpress

AIP inactivation exerts its tumor-promoting action through defected GÎ±i signaling and elevated cyclic-AMP levels

Project description:Gene-level expression profiles of 7 Aip knock-out (triplicates from each) and 9 Aip wild-type mouse embryonic fibroblast cell lines were studied using Affymetrix GeneChip Mouse Exon 1.0 ST Arrays All samples were quantile-normalized by the RMA method (Robust Multichip Average) using re-mapped gene annotations from Brainarray Custom CDF files (MoEx10stv1, Version 14.1.0, http://brainarray.mbni.med.umich.edu/Brainarray/default.asp). A 2-way ANOVA was constructed to identify genes that differentially expressed between KO and WT samples. False discovery rate control (FDR) with Benjamini and Hochberg method was used to correct for multiple testing

2014-03-05 | E-GEOD-37927 | biostudies-arrayexpress

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