Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Gene expression in melanocytes and metastases melanoma cells from the pig

ABSTRACT: Melanoblastoma-bearing Libechov minipigs (MeLiM) provide an animal model for the study of spontaneous cutaneous melanoma. We compared the serial analysis of gene expression (SAGE) profile between normal skin melanocytes and melanoma cells from a pulmonary metastasis of MeLiM. Keywords: disease state study To minimise the contribution of cells other than melanocytes, we constructed SAGE libraries from a primary culture of melanoma cells derived from a pulmonary melanoma metastasis of a young MeLiM and from a pigmented melanocyte cell line, PigMel, derived from the skin of a healthy Meishan pig.

ORGANISM(S): Sus scrofa

SUBMITTER: Giorgia Egidy

PROVIDER: E-GEOD-5982 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Transcription analysis in the MeLiM swine model identifies RACK1 as a potential marker of malignancy for human melanocytic proliferation.

Egidy Giorgia G Julé Sophia S Bossé Philippe P Bernex Florence F Geffrotin Claudine C Vincent-Naulleau Silvia S Horak Vratislav V Sastre-Garau Xavier X Panthier Jean-Jacques JJ

Molecular cancer 20080428

<h4>Background</h4>Metastatic melanoma is a severe disease. Few experimental animal models of metastatic melanoma exist. MeLiM minipigs exhibit spontaneous melanoma. Cutaneous and metastatic lesions are histologically similar to human's. However, most of them eventually spontaneously regress. Our purpose was to investigate whether the MeLiM model could reveal markers of malignancy in human melanocytic proliferations.<h4>Results</h4>We compared the serial analysis of gene expression (SAGE) betwee ...[more]

PMID: 18442364

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Project description:19 bronchial epithelial SAGE libraries were constructed and analyzed in this study. Discussed in the study: IDENTIFICATION OF NOVEL LUNG GENES IN BRONCHIAL EPITHELIUM BY SERIAL ANALYSIS OF GENE EXPRESSION Kim M. Lonergan1, Raj Chari1, Ronald J. deLeeuw1, Ashleen Shadeo1, Bryan Chi1, Ming-Sound Tsao2, Steven Jones3, Marco Marra3, Victor Ling1, Raymond Ng1,4, Calum MacAulay5, Stephen Lam5 and Wan L. Lam1 From the 1Department of Cancer Genetics & Developmental Biology, 5Department of Cancer Imaging, 3Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Research Centre, Vancouver, BC, Canada, 2Ontario Cancer Institute / Princess Margaret Hospital, Toronto, ON, Canada, 4the Department of Computer Science, University of British Columbia, Vancouver, BC, Canada A description of the transcriptome of human bronchial epithelium should provide a basis for studying lung diseases including cancer. We demonstrate here that minute epithelial specimens obtained by bronchial brushings afford reliable profiling by serial analysis of gene expression (SAGE) leading to lung gene discovery. We have deduced global gene expression profiles of bronchial epithelium and lung parenchyma, based upon a vast data set of nearly two million sequence tags from 21 SAGE libraries generated from individuals with a history of smoking. Cluster and linear regression analysis demonstrate the repeatability and reproducibility of bronchial SAGE libraries, and suggest that the transcriptome of the bronchial epithelium is distinct from that of lung parenchyma and other tissue types. This distinction is highlighted by the abundant expression of signature genes that reflect tissue-specific and region-specific functions. Through our analysis we have identified novel bronchial-enriched genes and a novel transcript variant for surfactant, pulmonary-associated protein B in lung parenchyma. Conspicuously, gene expression associated with ciliogenesis is evident in bronchial epithelium. Additionally, it is noted that a large number of unmapped tags awaits further investigation. This study represents a comprehensive delineation of the bronchial and parenchyma transcriptomes, identifying more than 20,000 known and hypothetical genes expressed in the human lung, constituting one of the largest human SAGE studies reported to date. Keywords: bronchial epithelium 19 bronchial epithelial SAGE libraries were constructed and analyzed in this study.

Project description:Perennial ryegrass (Lolium perenne L.) is a major grass species used for forage and turf throughout the world, and gains by conventional breeding have reached a plateau. Perennial ryegrass is an outcrossing, self-incompatible diploid (2n = 2x = 14) with a relatively large genome (4067 Mbp/diploid genome; Evans, G.M., Rees, H., Snell, C.L. and Sun, S. (1972). The relation between nuclear DNA amount and the duration of the mitotic cycle. Chrom. Today, 3, 24–31). Using tissues sourced from active pastures during the peak of the autumn, winter, spring and summer seasons, we analysed the ryegrass transcriptome employing a Serial Analysis of Gene Expression (SAGE™) protocol, with the dual goals of understanding the seasonal changes in perennial ryegrass gene expression and enhancing our ability to select genes for genetic manipulation. A total of 159 002 14-mer SAGE™ tags was sequenced and mapped to the perennial ryegrass DNA database, comprising methyl-filtered (GeneThresher®) and expressed sequence tag (EST) sequences. The analysis of 14 559 unique SAGE™ tags, which were present more than once in our SAGE™ library, revealed 964, 1331, 346 and 131 exclusive transcripts to autumn, winter, spring and summer, respectively. Intriguingly, our analysis of the SAGE™ tags revealed season-specific expression profiles for the small subunit of ribulose-1,5-bisphosphate carboxylase (Rubisco), LprbcS. The transcript level for LprbcS was highest in spring, and then decreased gradually between summer and winter. Five different copies of LprbcS were revealed in ryegrass, with one possibly producing splice variant transcripts. Two highly expressed LprbcS genes were reported, one of which was not active in autumn. Another LprbcS gene showed an inverse expression profile to the autumn inactive LprbcS in a manner to compensate the expression level. Keywords: paddock samples, pasture, perennial ryegrass, Serial Analysis of Gene Expression (SAGE™), season specific expression, monocot Ryegrass tissue Perennial ryegrass (Lolium perenne L.) cv. Bronsyn was used throughout this study. Field-grown samples, comprising mainly viable leaves and pseudostems, were collected at midday from livestock-active monocultural paddocks at Dexcel, Hamilton, New Zealand during the peak of each season, and frozen immediately in liquid nitrogen. Samples were transported in dry-ice and stored at ?80 oC until use. During spring and summer, care was taken not to include any floral stems in the tissue sample. Grass samples were collected from pregrazed (15–60 days post-grazing) and post-grazed (1 day post-grazing) ryegrass swards, which were visibly healthy and free of any pests. Construction of SAGE™ libraries RNA was extracted using TRIZOL® reagent (Invitrogen, Carlsbad,CA, USA). For each SAGE™ library, 100 ug of pre- and post-grazed sample-derived total RNA was employed, and the libraries were created using an I-SAGE™ or I-SAGE™Long Kit (Invitrogen) according to the manufacturer’s protocol. Pre- and post-grazed SAGE™ libraries were sequenced at the Australian Genome Research Facility (Brisbane, Australia), and the tags were extracted using SAGE2000 software and combined to produce the transcript profile for the season.

Dataset Information

Gene expression in melanocytes and metastases melanoma cells from the pig

Publications

Transcription analysis in the MeLiM swine model identifies RACK1 as a potential marker of malignancy for human melanocytic proliferation.

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