ArrayExpress Archive - Experiments (first 25 of 27536)

E-MTAB-933 - Transcriptional profiling by array to study the oxygen-sensitive genetic responses in rat vascular tissue after simulated diving

Fri, 10 Feb 2012 00:00:00 +0000

To identify genetic factors potentially involved in the etiology of DCS, using rats exposed to hyperoxic air in a pressure chamber to simulate diving

E-MTAB-800 - Transcription profiling by array of rat liver and kidney after exposure to approximately 130 chemicals collected from repeat dosing studies.

Fri, 10 Feb 2012 00:00:00 +0000

The Toxicogenomics Project was a 5-year collaborative project (2002-2007) by a consortium comprising the Japanese government and several pharmaceutical companies. The project produced the 'Toxicogenomics Project-Genomics Assisted Toxicity Evaluation system' (TG-GATEs), a large-scale database of transcriptomics and pathology data potentially useful for predicting the toxicity of new chemical entities. Conventional in vivo toxicology data was collected from single dose and repeat dosing studies on rats, and gene expression measured for the liver (and kidney in some cases). To provide information on species differences, gene expression was also measured in rat and human hepatocytes treated with the chemicals in vitro. Approximately 130 chemicals, primarily medicinal compounds, were tested at multipe doses. Gene expression was analysed using Affymetrix GeneChip arrays. The gene expression data has been submitted in four parts: in vivo single dose (E-MTAB-799), in vivo repeat dosing, in vitro rat (E-MTAB-797) and in vitro human (E-MTAB-798). This submission comprises the in vivo, repeat dosing studies. If publishing results based on this data, please cite the full project name 'Toxicogenomics Project and Toxicogenomics Informatics Project', the database name 'Open TG-GATEs' and the URL 'http://toxico.nibio.go.jp'. Please note that the European Bioinformatics Institute (EBI) was not involved in the Toxicogenomics Project in any way, acting only to submit the transcriptomics data to Array Express. Queries about the project can be addressed to the consortium directly via 'opentggates@nibio.go.jp'.

E-MTAB-799 - Transcription profiling by array of rat liver and kidney after exposure to approximately 130 chemicals collected from single dose studies.

Fri, 10 Feb 2012 00:00:00 +0000

The Toxicogenomics Project was a 5-year collaborative project (2002-2007) by a consortium comprising the Japanese government and several pharmaceutical companies. The project produced the 'ToxicoGenomics project-Genomics Assisted Toxicity Evaluation system' (TG-GATEs), a large-scale database of transcriptomics and pathology data potentially useful for predicting the toxicity of new chemical entities. Conventional in vivo toxicology data was collected from single dose and repeat dosing studies on rats, and gene expression measured for the liver (and kidney in some cases). To provide information on species differences, gene expression was also measured in rat and human hepatocytes treated with the chemicals in vitro. Approximately 130 chemicals, primarily medicinal compounds, were tested at multipe doses. Gene expression was analysed using Affymetrix GeneChip arrays. The gene expression data has been submitted in four parts: in vivo single dose, in vivo repeat dosing (E-MTAB-800), in vitro rat (E-MTAB-797) and in vitro human (E-MTAB-798). This submission comprises the in vivo, single dose studies. If publishing results based on this data, please cite the full project name 'Toxicogenomics Project and Toxicogenomics Informatics Project', the database name 'Open TG-GATEs' and the URL 'http://toxico.nibio.go.jp'. Please note that the European Bioinformatics Institute (EBI) was not involved in the Toxicogenomics Project in any way, acting only to submit the transcriptomics data to Array Express. Queries about the project can be addressed to the consortium directly via 'opentggates@nibio.go.jp'.

E-MTAB-798 - Transcription profiling by array of human hepatocytes treated with approximately 130 chemicals in vitro.

Fri, 10 Feb 2012 00:00:00 +0000

The Toxicogenomics Project was a 5-year collaborative project (2002-2007) by a consortium comprising the Japanese government and several pharmaceutical companies. The project produced the 'Toxicogenomics Project-Genomics Assisted Toxicity Evaluation system' (TG-GATEs), a large-scale database of transcriptomics and pathology data potentially useful for predicting the toxicity of new chemical entities. Conventional in vivo toxicology data was collected from single dose and repeat dosing studies on rats, and gene expression measured for the liver (and kidney in some cases). To provide information on species differences, gene expression was also measured in rat and human hepatocytes treated with the chemicals in vitro. Approximately 130 chemicals, primarily medicinal compounds, were tested at multipe doses. Gene expression was analysed using Affymetrix GeneChip arrays. The gene expression data has been submitted in four parts: in vivo single dose (E-MTAB-799), in vivo repeat dosing (E-MTAB-800), in vitro rat (E-MTAB-797) and in vitro human. This submission comprises the in vitro human studies. If publishing results based on this data, please cite the full project name 'Toxicogenomics Project and Toxicogenomics Informatics Project', the database name 'Open TG-GATEs' and the URL 'http://toxico.nibio.go.jp'. Please note that the European Bioinformatics Institute (EBI) was not involved in the Toxicogenomics Project in any way, acting only to submit the transcriptomics data to Array Express. Queries about the project can be addressed to the consortium directly via 'opentggates@nibio.go.jp'.

E-MTAB-797 - Transcription profiling by array of rat hepatocytes treated with approximately 130 chemicals in vitro.

Fri, 10 Feb 2012 00:00:00 +0000

The Toxicogenomics Project was a 5-year collaborative project (2002-2007) by a consortium comprising the Japanese government and several pharmaceutical companies. The project produced the Toxicogenomics Project-Genomics Assisted Toxicity Evaluation system (TG-GATEs), a large-scale database of transcriptomics and pathology data potentially useful for predicting the toxicity of new chemical entities. Conventional in vivo toxicology data was collected from single dose and repeat dosing studies on rats, and gene expression measured for the liver (and kidney in some cases). To provide information on species differences, gene expression was also measured in rat and human hepatocytes treated with the chemicals in vitro. Approximately 130 chemicals, primarily medicinal compounds, were tested at multipe doses. Gene expression was analysed using Affymetrix GeneChip arrays. The gene expression data has been submitted in four parts: in vivo single dose (E-MTAB-799), in vivo repeat dosing (E-MTAB-800), in vitro rat and in vitro human (E-MTAB-798). This submission comprises the in vitro rat studies. If publishing results based on this data, please cite the full project name Toxicogenomics Project and Toxicogenomics Informatics Project, the database name Open TG-GATEs and the URL http://toxico.nibio.go.jp. Please note that the European Bioinformatics Institute (EBI) was not involved in the Toxicogenomics Project in any way, acting only to submit the transcriptomics data to Array Express. Queries about the project can be addressed to the consortium directly via 'opentggates@nibio.go.jp'.

E-MTAB-708 - RNA-Seq of yeast FBY107, FBY106 strains to investigate pre-mRNA degradation pathway

Fri, 10 Feb 2012 00:00:00 +0000

General discard pathways eliminate unprocessed and irregular pre-mRNAs to control the quality of gene expression. In contrast to such general pre-mRNA decay, we describe here a nuclear pre-mRNA degradation pathway that controls the expression of select intron-containing genes. We show that the fission yeast nuclear poly(A)-binding protein, Pab2, and the nuclear exosome subunit, Rrp6, are the main factors involved in this polyadenylation-dependent pre-mRNA degradation pathway. Transcriptome analysis and intron swapping experiments revealed that inefficient splicing is important to dictate susceptibility to Pab2-dependent pre-mRNA decay. We also show that negative splicing regulation can promote the poor splicing efficiency required for this pre-mRNA decay pathway, and in doing so identify a mechanism of cross-regulation between paralogous ribosomal proteins through nuclear pre-mRNA decay. Our findings unveil a layer of regulation in the nucleus in which the turnover of specific pre-mRNAs, besides the turnover of mature mRNAs, is used to control gene expression.

E-MEXP-3454 - Global gene analysis of oocytes from early stages in human folliculogenesis

Fri, 10 Feb 2012 00:00:00 +0000

Global gene analysis of oocytes from early stages in human folliculogenesis

E-MEXP-3445 - Transcriptional profiling by array of human T84 colonic adenocarcinoma cells co-incubated with L. fermentum or L. gasseri to study the beneficial effects of probiotic bacteria in enhancing epithelial barrier integrity

Fri, 10 Feb 2012 00:00:00 +0000

The intestinal ecosystem is balanced by dynamic interactions between resident and incoming microbes, the gastrointestinal barrier, and the mucosal immune system. However, in the context of inflammatory bowel diseases (IBD) where the integrity of the gastrointestinal barrier is compromised, resident microbes contribute to the development and perpetuation of inflammation and disease. In this context, probiotic bacteria exert beneficial effects enhancing epithelial barrier integrity. However, the mechanisms underlying these beneficial effects are only poorly understood. Here, we comparatively investigated the effects of four probiotic lactobacilli, namely L. acidophilus, L. fermentum, L. gasseri, and L. rhamnosus in a T84 cell epithelial barrier model. Results of DNA-microarray experiments indicating that lactobacilli modulate the regulation of genes encoding in particular adherence junction proteins such as E-cadherin and b-catenin were confirmed by qRT-PCR. Furthermore, we show that epithelial barrier function is modulated by Gram-positive probiotic lactobacilli via their effect on adherence junction protein expression and complex formation. In addition, incubation with lactobacilli differentially influences the phosphorylation of adherence junction proteins and of PKC isoforms such as PKCd which thereby positively modulates epithelial barrier function. Further insight into the underlying molecular mechanisms triggered by these probiotics might also foster the development of novel strategies for the treatment of gastrointestinal diseases (e.g. IBD).

E-MEXP-3415 - Comparative analysis of algorithms for integration of copy number and expression data

Fri, 10 Feb 2012 00:00:00 +0000

Chromosomal instability is a hallmark of cancer and genes that display abnormal expression in chromosomally aberrant regions are likely to be key players in tumor progression. Identifying such driver genes from high-throughput data requires computational methods that are capable of integrating data from several sources and thereby enhance the reliability of driver gene identification. Hence, several algorithms that integrate copy number and expression data have been developed but their relative performance has not been assessed so far. We have compared 10 algorithms that integrate high-throughput copy number and transcriptomics data using simulated, cancer cell line and primary tumor data. Our results show that there are significant differences between the methods and their performance decreases significantly with small sample sets. Head and neck squamous cell carcinoma (HNSCC) cell lines from the tongue (UT-SCC-21,UT-SCC-24B, UT-SCC-30, UT-SCC-67, UT-SCC-73, UT-SCC-76A, UT-SCC-81, UT-SCC-87,UT-SCC-95) and larynx (UT-SCC-8, UT-SCC-11, UT-SCC-75) were provided by the Department of Otorhinolaryngology-Head and Neck Surgery at the Turku University Central Hospital (Turku, Finland). HNSCC cell lines SCC-4, SCC-9, SCC-25 and human skin keratinocyte HPV-16 E6/E7 transformed cell line CCD1106 KERTr was ordered from American Type Culture Collection (ATCC; Manassas, VA) and cultured according to the ATCC recommendations.

E-MEXP-3130 - Gene expression analysis of ZNF469 mutations

Fri, 10 Feb 2012 00:00:00 +0000

Gene expression analysis with microarrays to compare mutant human fibroblast with mutations in ZNF469 versus aged-matched controls.

E-MEXP-3110 - Transcription profiling of Arabidopis leaves treated with organic acids

Fri, 10 Feb 2012 00:00:00 +0000

Exogenous supply of citrate and malate to Arabidopsis leaves to monitor transcriptional changes resulting from these treatments.

E-MEXP-2578 - Transcription profiling of human CD4 positive T cell subsets

Fri, 10 Feb 2012 00:00:00 +0000

Peripheral Blood Mononuclear Cells (PBMCs) were isolated from a buffy coat (Australian Blood Bank) using Ficoll methodology. CD4+ T cells were isolated using Dynal Beads kit. Pure CD4+ T cells were then stained using a cocktail of monoclonal antobodies (mAbs), including: anti-CD4PE, CD45RO ECD, CD62L APC-Cy7, CD25 APC, CD127 Pacific Blue. After incubation, cells were washed twice in PBS/FCS (0.2%), and sorted into five different cell subsets: CD4+CD25+CD127low CD62L+CD45RO- (naive regulatory T cells), CD4+CD25+CD127low CD62L+/- CD45RO+ (activated regulatory T cells), CD4+CD25+CD127hi CD62L+/- CD45RO+ (memory T cells), CD4+CD25-CD127low CD62L+/- CD45RO+ (effector T cells) and CD4+CD25-CD127hi CD62L+ CD45RO- (naive T cells).

E-MTAB-745 - Identification of candidate susceptibility and resistance genes of mice infected with Streptococcus suis type 2

Thu, 09 Feb 2012 00:00:00 +0000

There were four groups:control A/J mice;control B6 mice;SS2-infected A/J mice;SS2-infected B6 mice.The RNA samples of four groups were sent to Biostar Genechip Inc. (Shanghai, China) for microarray hybridization. The pooled RNA sample from each group was hybridized to one Illumina mouse Genome Beadchip Array (catalog number 5022612022, Mouse WG-6_V2, Illumina). Therefore, four BeadChips were used in total, one for each of the A/J and B6 infected and control mice groups. Biotin-labeled cRNA preparation and hybridization were performed as described previously. The arrays were scanned on an Illumina BeadStation 500 System and the hybridization data analyzed using Illumina BeadStudio software. The following filtering criteria were used for selection of differentially expressed genes: positive gene in either test or control, and test DiffScore e +20 or dc20. The differentially expressed genes were selected by comparing the following groups: SS2-infected A/J vs. SS2-infected B6; control A/J vs. control B6; SS2-infected A/J vs. control A/J; SS2-infected B6 vs. control B6. Four RNA samples were hybridized with four BeadChips of Illumina. They were respectively control A/J mice, control B6 mice, SS2-infected A/J mice, and SS2-infected B6 mice.The differentially expressed genes were selected by comparing the following groups: SS2-infected A/J vs. SS2-infected B6; control A/J vs. control B6; SS2-infected A/J vs. control A/J; SS2-infected B6 vs. control B6.In the raw and normalized date, A/J1 represents control A/J, A/J2 represents SS2-infected A/J, B61 represents control B6, B62 represents SS2-infected B62.

E-MTAB-516 - Transcription profiling by array of human breast cancer stem cells treated with TGF-beta or a TGF-beta receptor I inhibitor

Thu, 09 Feb 2012 00:00:00 +0000

Analyze TGF-beta pathway transcriptional regulation in breast cancer stem cells with different responses upon TGF-beta pathway activation. Total RNA from four breast cell lines grown as mammospheres treated with recombinant TGF-beta or a TGF-beta receptor I inhibitor was used in the analysis.

E-MEXP-3503 - Methylation profiling by array in the CA3 region of the mouse hippocampus in epileptic tolerance and status epilepticus.

Thu, 09 Feb 2012 00:00:00 +0000

Comparison of methylation profiles in the CA3 region of the mouse hippocampus in epileptic tolerance and status epilepticus.

E-MTAB-974 - De novo sequencing and analysis of the Panax ginseng transcriptome in the leaf-expansion period

Wed, 08 Feb 2012 00:00:00 +0000

In order to analyze the transcriptome of ginseng root during leaf-expansion period and discover the genes during development, a cDNA sample was prepared from the leaf-expansion period of ginseng root and sequenced using the Illumina sequencing platform.The transcriptomic sequencing technology was set up the first time for five years the transcription of the ginseng root in the leaf-expansion period.

E-MTAB-911 - MOF, H4 and H4K16ac ChIP-seq experiments in D.melanogaster

Wed, 08 Feb 2012 00:00:00 +0000

We generated MOF, H4 and H4K16ac ChIP-seq experiments in D.melanogaster male and female wt. All experiments were performed with 3rd instard salivary glands biological material. Raw and processed data are provided here.

E-MTAB-673 - The Variantome of the malaria parasite Plasmodium falciparum.

Tue, 07 Feb 2012 00:00:00 +0000

We compared transcript levels at several points along the asexual blood cycle between 21 P. falciparum lines. These 21 parasite lines are organized in 4 sets of parasite lines, with all parasite lines within a set sharing a clonal origin. We compared transcript levels within each set. We also performed comparative genome hybridization (CGH) for all 21 parasite lines.

E-MEXP-3541 - Genotyping by array of microbiota in anaerobic digestion process

Mon, 06 Feb 2012 00:00:00 +0000

The aim of the study was to use microarray for profiling the microbiota in anaerobic digestion process. The probes are ssDNA molecules that are ligated into circular molecules if a complementary target sequence is present in the sample DNA. Ligated probes are PCR amplified with a labeled primer, and the amplicons are hybridized on DNA microarray by tag sequences.

E-MEXP-3539 - BIGenomics_bioreactor_sensitivity

Mon, 06 Feb 2012 00:00:00 +0000

Ligation probe pool was tested with different concentrations of synthetic dsDNA template molecules to determine analytical sensitivity of the method. Probes are ligated into circular molecules if their target sequence is present in the reaction. Ligated probes are then PCR amplified and the PCR products are hybridized to a microarray by tag sequences.

E-MEXP-3500 - Transcriptional profiling by array of mouse to identify RNA bound to the TDP-43 ribonucleoprotein complex

Mon, 06 Feb 2012 00:00:00 +0000

In total 3 mice brain tissues were used for this experiment. Tissue from each mouse brain was divided for immunoprecipitation with 5ug of either rabbit anti-TDP-43 antibody (Abcam) or normal rabbit IgG (Sigma) .The antibodies were first incubated with the lysate overnight at 4 degrees C, after which 50 uL of protein G Dynabeads(tm) (Invitrogen(tm)) added and the solution incubated for 1 hour at 4 degrees C with rotation. Following several washing with washing buffer (Invitrogen(tm)), the protein-RNA complex was eluted from 20 uL of bead-protein complex using 10 uL of elution buffer (Invitrogen(tm)) and seperated on a 10% NuPage(tm) Bis-Tris gel (Invitrogen(tm)). RNA was isolated from the remaining 30 uL of protein-bead complex using TRIzol reagent (Invitrogen) followed by DNaseI treatment (Ambion). The TDP-43 immunoprecipitated RNA was converted to cDNA, fragmented and biotin labelled using WT cDNA synthesis & amplification kit and Terminal Labeling Kit (Affymetrix(tm)) for Affymetrix(tm) GeneChip(tm) Mouse Gene 1.0 ST and 3'-IVT expression analysis kit (Affymetrix(tm)) for GeneChip(tm) Mouse 430_2 arrays according to the standard protocol. Labelled RNA was hybridised to arrays in a hybridization oven (Affymetrix(tm)) at 45 degrees C rotating at 60 rpm for 17 hours and scanned using the Affymetrix(tm) GeneChip Scanner. Successful hybridisation to the microarray was checked using Expression Console software (Affymetrix(tm)) and the data (.CEL files) transferred to Partek Genomics Suite for statistical analysis. TDP-43 and IgG immunoprecipitated RNA samples were each hybridised to 3 GeneChip Mouse Gene 1.0 ST and 3 GeneChip Mouse 430 (n = 6 for each group).

E-MEXP-3098 - Gene expression profiling of mouse chronic intestinal inflammation

Sun, 05 Feb 2012 00:00:00 +0000

Trichuris muris (T. muris) induces chronic colitis in susceptible mouse strains with clinical, histological, and immunological homology to human Crohn’s disease. Gene expression profiling was performed on colon tissue of resistant (BALB/c) and susceptible (AKR) mice following T. muris infection.

E-MEXP-3095 - PAX5TEL GENE EXPRESSION IN PREBI CELLS - FAZIO G.

Sat, 04 Feb 2012 00:00:00 +0000

In the present study, we investigated PAX5TEL function in transcription processes by transduction of PAX5TEL construct in wild type preBI cells, a primary culture of immature B cells expressing endogenous wild type PAX5 protein.

E-TABM-1184 - Chromatin immunoprecipitation of Drosophila to identify pMad, dTcf, Doc, Pnr and Slp1 proteins binding during embryonic development

Fri, 03 Feb 2012 00:00:00 +0000

Genomewide mapping of Drosophila melanogaster pMad, dTcf, Doc, Pnr and Slp1 protein binding during embryonic development. Two consecutive timepoints (4-6 and 6-8 hrs after egg-laying) were assayed in two independent repeats each. Additionally the respective preimmune-serum was used as a control for every precipitation. The enriched DNA was hybridized to high density Affymetrix GeneChip Drosophila Tiling 1.0R array.

E-MTAB-525 - Kalluri-microarray

Fri, 03 Feb 2012 00:00:00 +0000