Transcription profiling of rat cell lines using Illumina arrays to verify a previous experiment (E-TABM-202)
Ontology highlight
ABSTRACT:
ORGANISM(S): Rattus norvegicus
SUBMITTER: Vidar Beisvag
PROVIDER: E-TABM-307 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:We performed a dye-swap microarray experiment using a total of 24 Rat 15k cDNA duplicates microarrays. The study included RNA from samples with high expected differential gene expression termed high contrasts compared to self-self hybridization (rat cell lines AR42J and NRK52E). We than optimized a pipeline to maximize the number of genes found differentially expressed between the two different RNA samples while at the same time making sure that the methodology finds no differentially expressed genes in selfself experiments with the same cell lines. In this high-contrast vs. self-self method (HCSSM) significantly expressed genes is determined by estimating the false discovery rate (FDR) using a null distribution obtained from self-self experiment. The optimization criterion requires only 4 microarrays per evaluation, and the effects of blocking reagent dose, filtering, and background corrections methodologies were investigated. In our experiments a dose of 250 ng LNA dT blocker gave the highest number of differentially expressed genes. When the criterion was used to evaluate steps in the computational analysis of microarray data we found that no background correction and weight based filtering gave the largest number of differentially expressed genes. Background correction method, however, has a greater influence on the number of differentially expressed genes found than filtering.
2007-01-19 | E-TABM-202 | biostudies-arrayexpress
Project description:By use of time series microarray experiment we identified the characteristic temporal behaviour of ~2000 new gastrin-regulated genes (accession numbers: GSE32869). To inform gastrin regulatory networks with an additional experimental dimension, we determined the temporal transcriptome in the presence of the protein synthesis inhibitor cycloheximide (CHX). For those genes where the gastrin response in the presence of CHX was higher than the response with CHX alone the gene was classified as a primary gene not dependent on de novo protein synthesis for gastrin-induced expression.Gastrin induced genes that were not upregulated in the presence of CHX were classified as secondary genes, i.e., genes whose transcriptional activation dependends on de novo protein synthesis of one or several factors that must be induced by gastrin previous to these secondary genes.
2012-10-01 | E-MTAB-1268 | biostudies-arrayexpress
Project description:Hypoxia is a low oxygen condition that occurs in the developing tumor mass and that is associated with poor prognosis and resistance to chemo- and radio-therapy. The definition of the hypoxia gene signature is fundamental for the understanding of tumor biology, as in the case of neuroblastoma, the most common pediatric solid tumor. The issue of identifying a significant group of variables in microarray gene expression experiments is particularly difficult due to the typical high dimensional nature of the data and great effort has been spent in the development of feature selection techniques. Our main goal is to define a robust hypoxia gene signature in neuroblastoma cell lines. A set of 11 neuroblastoma cell lines were cultured under normoxic and hypoxic conditions for 18 hours, and their gene expression profiles were measured with Affymetrix GeneChip HG-U133 Plus 2.0. We used the l1-l2 regularization framework in order to select the significant probesets defining hypoxic versus normoxic cell lines. Experiment Overall Design: The expression profiles of 11 neuroblastoma cell lines under normoxia vs hypoxia were studied.
2009-10-10 | E-GEOD-17714 | biostudies-arrayexpress
Project description:We integrated metabolome and proteome profiles of the parental cell line 143B.TK- versus ρ0, including PTM analyses such as phosphorylation and ubiquitination to characterize the impact of the absence of mtDNA for the entire cell. For quantitative proteome profiling, we used a shotgun LC-MS/MS approach including the classical SILAC labeling. For comprehensive metabolome profiling, we applied a targeted LC-MS approach, based on multiple reaction monitoring (MRM).</br></br>Our study revealed that mtDNA depletion leads to a non-uniform down-regulation of the mitochondrial energy metabolism in ρ0 cells on the proteome level. Metabolites of the TCA cycle were highly dysregulated which in turn had an impact on the amino acid levels, which were up regulated. Perturbation of the mitochondrial energy metabolism could lead to an activation of the retrograde response, indicated by sets of up-regulated signaling pathways in ρ0 cells, further supported by altered phosphorylation in signaling pathways and the cytoskeleton as well as de-ubiquitination of SLC transporters.
2016-02-08 | PXD002425 | Pride
Project description:Cycloheximide has been used for inhibiting protein synthesis in order to identify IL-2 direct targeted genes in T cells, but the effects of cycloheximide itself on genomewide genes are not well defined; We conducted a global analysis of cycloheximide regulated genes in mouse T cell line CTLL-2 using Affymetrix mouse genome array, and identified 213 genes differentially expressed (?1.5-fold change) in response to cycloheximide 30min after adding cylcoheximide to T cells cultured without IL-2 for 14 hours. These genes involve in a number biological processes. Experiment Overall Design: Murine cytotoxic T lymphocyte cell line CTLL-2, derived from a C57BL/6 mouse, is an IL-2 dependent cell line. Cells were cultured in D10 medium in an incubator with 5% CO2 at 37oC to mid-log phase (~2 X 105 cells/mL), and collected by centrifugation, washed with phosphate buffered saline (PBS) (Invitrogen), resuspended at 1 X 106 cells/mL in the medium without IL-2 (IL-2 starvation) and cultured for 14 hours (No IL-2 stimulation, T0, 5 reps), followed by adding cycloheximide (20 ?g/mL) for 30min (T4-CHX, 4 reps). Total RNA were extracted from the cells and was hybridized on Affymetrix GeneChip Mouse Genome 430 2.0 Array.
2009-01-17 | E-GEOD-6084 | biostudies-arrayexpress
Project description:Hypoxia is a low oxygen condition that occurs in the developing tumor mass and that is associated with poor prognosis and resistance to chemo- and radio-therapy. The definition of the hypoxia gene signature is fundamental for the understanding of tumor biology, as in the case of neuroblastoma, the most common pediatric solid tumor. The issue of identifying a significant group of variables in microarray gene expression experiments is particularly difficult due to the typical high dimensional nature of the data and great effort has been spent in the development of feature selection techniques. Our main goal is to define a robust hypoxia gene signature in neuroblastoma cell lines. A set of 9 neuroblastoma cell lines were cultured under normoxic and hypoxic conditions for 18 hours, and their gene expression profiles were measured with Affymetrix GeneChip HG-U133 Plus 2.0. The clustering analysis of the expression profiles based on different clustering methods consistently revealed that hypoxia was not the major factor characterizing the data set. T-test analysis with multiple testing correction fails to identify significantly differentially expressed genes. Conversely the l1-l2 regularization selects 11 significant probesets while building an effective classification rule. The algorithm is cast within a cross-validation framework in order to achieve an unbiased analysis. The estimated cross-validation error is 17% (3 out of 18). We show that the use of l1-l2 regularization allowed us to model the effect of hypoxia, which was not detected by conventional t-test based approaches and we find a panel of genes able to properly discriminate the normoxic versus the hypoxic status of neuroblastoma cell lines. Experiment Overall Design: The expression profile of 9 neuroblastoma cell lines under normoxia vs hypoxia was studied
2009-04-24 | E-GEOD-15583 | biostudies-arrayexpress
Project description:The RNA-binding protein AU-rich-element factor-1 (AUF-1) regulates mRNA decay and translation of genes during inflammation and cellular senescence, two pathogenic mechanisms of chronic obstructive pulmonary disease (COPD). Decreased AUF-1 expression was described in bronchiolar epithelium of COPD patients versus controls and in vitro cytokine-challenged airway epithelial cells, prompting the identification of epithelial AUF-1-targeted transcripts and function. RNA immunoprecipitation-sequencing (RIP-Seq) identified, in the human BEAS-2B cell line, 494 AUF-1-bound mRNAs enriched in their 3’-untranslated regions for a Guanine-Cytosine (GC)-rich binding motif, selectively confirmed by biotin pulldown. AUF-1-targets’ steady-state levels were equally affected by partial or near-total AUF-1 loss induced by cytomix (TNF/IL1/IFN/10 nM each) and siRNA, respectively, with differential transcript decay rates. Cytomix-decreased AUF-1 levels in BEAS-2B and primary human small-airways epithelium (HSAEC) associated with cell-cycle arrest, increased lysosomal damage and senescence-associated secretory phenotype (SASP) factors and with increased AUF-1 in extracellular vesicles. In-silico analysis found enriched AUF-1-targets in COPD-related pathways, SASP proteome atlas, transcriptomic COPD databases of HSAEC, lung tissue and single-cell RNA-sequencing. Intracellular and exosomal-associated AUF-1 may mediate airway epithelial inflammatory responses.
2023-04-14 | E-MTAB-12583 | biostudies-arrayexpress
Project description:Follicular lymphoma (FL) is an indolent lymphoma associated with follicular center B cells, and typically contains the Bcl-2 chromosomal translocation t(14;18), which leads to overexpression of the anti-apoptotic intracellular protein Bcl-2. FLs are sensitive to chemotherapy; however, patient relapses occur and response duration becomes progressively shorter, with the majority of patients eventually dying from the disease. Enzastaurin (LY317615), an acyclic bisindolylmaleimide, was initially developed as an ATP-competitive selective inhibitor of PKC. We found, in agreement with recent reports, that enzastaurin inhibits cell proliferation and induces apoptosis. These results are consistent with decreased phosphorylation of the Akt pathway and its downstream targets. To provide new insights into the anti-tumor action of enzastaurin on non-Hodgkin lymphoma, we investigated its effects on gene expression profiles of the B cell lymphoma RL cell line by oligonucleotide microarray analysis. We identified a set of 41 differentially expressed genes, mainly involved in cellular adhesion, apoptosis, inflammation, and immune and defense responses. These observations provide new insights into the mechanisms involved in the induction of apoptosis by enzastaurin in B cell lymphoma cell lines, and identify possible pathways that may contribute to the induction of apoptosis. This series of microarray experiments contains the gene expression profiles of independent replicates of the B lymphoma RL cell line carrying t(14;18) before and after LY317615 treatment. 100 nanograms of total RNA were processed and fragmented. Biotin-labelled single-stranded DNA target was hybridized to the GeneChip® Gene 1.0 ST array following the Affymetrix manufacturer's instructions.
2011-09-14 | E-GEOD-24183 | biostudies-arrayexpress
Project description:We report microcystin-LR, a cyclic heptapeptide that acts as a potent hepatotoxin and carcinogen, was used to induce the malignant transformation of the WRL-68 cell line and alterations in microRNA (miRNA) expression in the transformed cells. In this work, MC-LR was used to induce the malignant transformation of the WRL-68 cell line and alterations in microRNA (miRNA) expression in the transformed cells.
2012-07-30 | E-GEOD-30560 | biostudies-arrayexpress
Project description:Pentavalent vanadium compounds induce intracellular changes in vitro that are consistent with those of other carcinogenic substances, including alteration of transcription factor levels, promotion of oxidative stress, inflammation, DNA damage, stimulation of mitogenic signals, and suppression of apoptosis. While there is no clear evidence that vanadium compounds cause cancer in humans, vanadium pentoxide causes lung cancer in rodents after long-term inhalation exposures and in turn IARC has categorized it as a group 2B possible human carcinogen. The goal of this study was to investigate the carcinogenicity of NaVO3 in the human immortalized bronchial epithelial cell line, Beas-2B. Cells were treated with 10 µM NaVO3 for 5 weeks, with or without recovery time, followed by gene expression microarray analysis. In a separate experiment, cells were exposed to 1-10 µM NaVO3 for 4 weeks and then grown in soft agar to test for anchorage-independent growth. A dose-dependent increase in the number of colonies was observed. NaVO3-transformed clones could repair a wound faster than controls during the scratch test. In a gene expression microarray analysis of soft agar clones there were 2010 differentially expressed genes (DEG) (adjusted p-value ⤠0.05) in NaVO3-transformed clones relative to control clones. DEG from this experiment were compared with the DEG of 5 week NaVO3 exposure with or without recovery, all with adjusted p-values <0.05, and 469 genes were altered in the same direction for transformed clones, 5 week NaVO3-treated cells, and the recovered cells; a subset of these changes were validated by QRT-PCR. The data from this study imply that chronic exposure to NaVO3 causes changes that are consistent with cellular transformation including anchorage- independent growth, enhanced migration ability, and gene expression changes that were epigenetically inherited through cell division. Beas-2B cells were chronically exposed to sodium metavanadate in growth media for 4 weeks. Then exposed cells and unexposed control cells were grown in soft agar for 3 weeks in the absence of vanadate. Transformed colonies (arising from vanadate-exposed cells) and control colonies (spontaneously grew from unexposed cells) were extracted from soft agar and expanded in the absence of vanadate, then processed for gene expression analysis on Affymetrix GeneChip Human Exon 1.0 ST array. 5 transformed clones, 3 control clones, 1 parental Beas-2B cell sample, and acute 24 hour vanadate exposed cell samples were analyzed.
2013-01-19 | E-GEOD-43386 | biostudies-arrayexpress