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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Transcription profiling of mouse intestinal polyps from Apc Delta14 strain treated with parecoxib

ABSTRACT: A "Cartes d'Identite des Tumeurs" (CIT) project from the french Ligue Nationale Contre le Cancer (http://cit.ligue-cancer.net). Comparison of mouse intestinal polyps response to parecoxib with controls.

ORGANISM(S): Mus musculus

DISEASE(S): normal

SUBMITTER: Nadim Hamzaoui

PROVIDER: E-MEXP-2156 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Cyclooxygenase-2 inhibitors down-regulate osteopontin and Nr4A2-new therapeutic targets for colorectal cancers.

Zagani Rachid R Hamzaoui Nadim N Cacheux Wulfran W de Reyniès Aurélien A Terris Benoît B Chaussade Stanislas S Romagnolo Béatrice B Perret Christine C Lamarque Dominique D

Gastroenterology 20090621 4

<h4>Background & aims</h4>Cyclooxygenase-2 inhibitors reduce colon cancer risk by mechanisms that are not fully understood. We performed microarray analysis of adenomas from Apc(Delta14/+) mice to identify genes that respond to these drugs.<h4>Methods</h4>Apc(Delta14/+) mice were given a single daily injection of parecoxib for up to 9 weeks; intestinal tracts of these and control mice were analyzed by microarray analysis, immunohistochemistry, in situ hybridization, and quantitative real-time po ...[more]

PMID: 19549529

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Transcription profiling of mouse liver in conditional knockouts of the tumor suppressor gene Apc identifies Wnt/bet-catenin signaling activation in hepatocytes

Project description:A "Cartes d'Identite des Tumeurs" (CIT) project from the french Ligue Nationale Contre le Cancer (http://cit.ligue-cancer.net). Conditional Knockout mouse model for the tumor suppressor gene Ap, Apc 2lox. The disruption of the Apc gene is realized by injection of an adenovirus encoding the Cre recombinase (AdCre). Homozygous animals injected with a high dose of AdCre showed an activation of the Wnt/beta-catenin signaling in most of the hepatocytes and develop an hepatomegaly and die soon after. Analysis of gene up- and down regulation for liver-indicible APC disruption.

2006-03-13 | E-TABM-81 | biostudies-arrayexpress

Transcription profiling of liver from wild type and tumor suppressor Apc knock-out mice

Project description:A "Cartes d'Identite des Tumeurs" (CIT) project from the french Ligue Nationale Contre le Cancer (http://cit.ligue-cancer.net). This work aims to demonstrate a key role for the Wnt/beta-catenin pathway in liver embryonic growth and in controlling the fate of hepatoblasts, preventing them to differentiate towards the hepatocyte lineage, and guiding them to a duct morphogenesis. Through the inactivation of Apc (adenomatous Polyposis Coli) tumor suppressor gene in hepatoblasts by a Cre-loxP strategy, the ectopic activation of beta-catenin targeted in hepatoblasts after liver bud formation leads to a lethal embryonic phenotype, characterized by liver hypoplasia, a blockade of hepatocyte differentiation and commitment to a biliary fate. (this work was supported by INSERM and the B^SLigue Nationale

2007-08-07 | E-TABM-295 | biostudies-arrayexpress

Chromatin immunoprecipitation of the MSL-1 and MSL-3 vs a mock IP in Drosophila and transcription profiling of X linked genes in WT male or female III instar larvae to provide X chromosome wide profiling of MSL-1 distribution and dosage compensation in Drosophila

Project description:Dosage compensation ensures that males and females, despite unequal number of X chromosomes, equalize for X linked gene expression. In Drosophila, it is achieved by a two-fold up-regulation of most of the genes present on the male X chromosome, and requires the association of the Dosage Compensation Complex (DCC) on the X chromosome. One of the main intriguing aspects of dosage compensation is how this complex is able to target specifically hundreds of sites only on the X chromosome in order to ensure dosage compensation. In order to better understand the targeting of the DCC and the dosage compensation mechanism, we have then decided to analyze the distribution of the DCC as well as the expression levels in male and female in a more complete and precise manner, using microarrays. In this experiment, we present the data used to analyse the distribution of the MSL-1 and MSL-3 protein (part of the DCC complex) on the X chromosome in WT embryos aged from 0H-14H, as well as the distribution of MSL-1 in embryos aged from 4-6H and in male III instar salivary glands. The DNA amplified from the specific immunoprecipitation (MSL-1 or MSL-3 IP) were labelled using Cy5-dCTP and hybridized against DNA amplified from a non specific immunoprecipitation (mock IP), labeled with Cy3 dye. In parralel we present the data used to analyse the expression profile of X-linked genes in WT male or female III instar larvae salivary glands. The cDNA amplified from the RNA extracted from the male or female salivary glands were labelled using Cy5-dUTP and hybridized against the reference sample, labelled with Cy3-dUTP (pool RNA from ON embryos, adultes, and salivary glands mixed at a ratio 1:1:1.and amplified as the RNA from salivary glands). We used for this study a cDNA array developed by the Genecore facility in EMBL, covering the DGC1 and DGC2 cDNA libraries from the Berkeley Drosophila Genome Project, which represents more than 70% of the coding Drosophila genome.

2006-04-01 | E-MEXP-554 | biostudies-arrayexpress

Transcription profiling of fusiform cambial and ray cambial cells from poplar trees

Project description:(paper abstract) Wood is a renewable resource that serves as a sustainable raw material for energy, fuels and materials. A basic understanding of the cambial meristem and the origin of wood cells is critical for forest tree molecular breeding to increase the availability of woody raw materials. Gene expression per cell type in the cambium of poplar (Populus trichocarpa x P. deltoïdes cultivar Boelare) was investigated using poplar microarray. Cells were hand microdissected from lyophilized sections of vascular cambial zone sampled in growing poplar. Two cell types were isolated, fusiform cambial cells (FCCs) and ray cambial cells (RCCs). Results showed about one thousand genes differentially expressed per cell type. Microarray expression results were validated by a second cell sampling used for reverse northern dot blot and RT-PCR analysis. RCCs revealed specific photosynthetic competences involving at least 35 genes of the photosystems. RCCs revealed also a marked difference for intercellular transport involving notably aquaporin genes. Distinct classes of cell-wall related genes were detected in RCCs and FCCs. A candidate xyloglucan endotransglycosylase showed to be upregulated and highly expressed in FCCs and an extensin family gene was also very highly expressed in these cells. A candidate polygalacturonase was strikingly expressed specifically in RCCs. A marked expression of cytoskeleton genes was also reported for FCCs where profilin family genes were very highly expressed. Related to cell signaling and regulation, one of the most intriguing result was the observation of LAX1 gene specificity in FCCs whereas PIN genes were expressed in both cell types.

2008-06-30 | E-MEXP-794 | biostudies-arrayexpress

Transcription profiling by array of human HT29 colorectal cells treated with eicosapentaenoic acid

Project description:Effects of eicosapentaenoic acid on gene expression profiles in HT29 human colorectal cells

2011-04-12 | E-MEXP-2673 | biostudies-arrayexpress

Transcription profiling of Baseline gene expression in circulating peripheral blood mononuclear cells isolated from 18 apparently healthy volunteers (10 females and 8 males)

Project description:Baseline gene expression in circulating peripheral blood mononuclear cells isolated from 18 apparently healthy volunteers (10 females and 8 males). The volunteers fasted overnight for 10 hours prior to collection of blood samples (but they were allowed water). 5 blood samples were collected from each volunteer at consecutive 8-day intervals. Volunteers were included in this study provided they met the following selection criteria, that they should be <br>?Aged between 20 and 45 years of age; <br>?A non-smoker (or an ex-smoker);<br>?Not pregnant or been pregnant in the last 12 months <br>?Not diagnosed with any long-term medical condition; <br>?Or have not (in the previous 4 months) donated blood, received any inoculations and are not taking regular prescribed medicine (including HRT and oral contraception) <br>Prior to inclusion in this study volunteers were screened for general health and had a blood sample taken for routine screening of Hb content etc. Only those volunteers who were in good general health were allowed to participate in the study. <br>The age of all volunteers has been reported here as being 20-45 years in order to preserve the anonymity of the data, and so that the individuals involved may not be able to track down their own specific data. Please contact us if the details of volunteers' ages are required.

2013-01-30 | E-TABM-7 | biostudies-arrayexpress

RNA-Seq of round spermatids comparing WT (FVBNJ) to H2A.B3 knock-out mice

Project description:The histone variant H2A.B3 (H2A.Bbd/H2A.Lap1) has a tissue-specific expression pattern and is found to be most highly expressed during spermatogenesis. In order to investigate the role of H2A.B3 in chromatin packaging and regulation of spermatogenesis we created a line of TALEN-edited FVBN mice in which a deletion was introduced into the single exon of the H2AFB3 gene. The deletion was confirmed by Sanger sequencing and off-target effects investigated using exome sequencing. The deletion is visible in the RNA-Seq data of KO mouse, and the deleterious effect on the H2A.B3 protein has been confirmed using immunohistochemistry.

2019-01-04 | E-MTAB-7277 | biostudies-arrayexpress

BIGenomics_Agilent_15k_templates

Project description:Hybridization of ligation probes to a zipcode (tag) microarray. The purpose of the experiment was to establish functionality and target specificity of the ligation probes by using pools of synthetic templates with all of the probes. The templates are 80-mer synthetic dsDNA molecules, each specific for a single probe. Each probe is a ssDNA molecule containing target recognition sequences, PCR primer binding sequences and a unique tag sequence. If a matching target sequence is present in the mixture, the probes is ligated into a circular molecule, which can be PCR amplified and hybrized on a microarray harbouring complementary tag sequences.

2012-02-24 | E-MEXP-3538 | biostudies-arrayexpress

Quantitative Proteomics of Enriched Esophageal and Gut Tissues from the Human Blood Fluke Schistosoma mansoni

Project description:Schistosomes are blood-dwelling helminth parasites causing a debilitating disease in the tropics. Major challenges to control persist and vaccines would provide an additional tool, but finding protective antigens is not trivial. It's known that the self-cure response of Rhesus macaques targets proteins from the tegument, gut and esophagus, the last of which is the least investigated. Here we applied proteomics to characterise esophageal antigens with potential utility for vaccine development. This dataset was generated by partial reanalysis of our published MS-data (PXD014872; 10.1021/acs.jproteome.9b00531). Originally, we have shown that shotgun proteomics applied to dissected esophageal fragments identified 13 MEG proteins, eleven of which are uniquely located in the esophageal glands. Antigenic variation by alternative splicing of MEG proteins was confirmed together with a specialised machinery for protein glycosylation in the esophagus. Moreover some gastrodermal secretions were highly enriched in the gut, while others were more uniformly distributed, potentially as markers of lysosomal activity. In contrast to PXD014872, this reanalysis allowed semi-specific trypsin cleavage during database search. This has proven to increase N-terminal sequence coverage of proteins processed for signal peptide removal, including esophageal MEG proteins.

2024-06-20 | PXD037384 | Pride

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