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Unknown,Transcriptomics,Genomics,Proteomics

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Transcription analysis on difference of copper body concentrations in Crassostrea angulate

ABSTRACT: The aim of this study was to gain insight into the molecular mechanisms of intraspecies difference of copper accumulation in Crassostrea angulata. In this attempt, we have performed a comprehensive analysis of the transcriptome of oyster (gill and mantle). Digital gene expression (DGE) technology was applied to analyze the relationships between gene expression and differential Cu body burden. Digital gene expression (DGE) technology was applied to analyze the relationships between gene expression and differential Cu body burden

ORGANISM(S): Crassostrea angulata

SUBMITTER: Huang zekun

PROVIDER: E-GEOD-65653 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Transcription analysis on difference of copper body concentrations in Crassostrea angulate

Project description:The aim of this study was to gain insight into the molecular mechanisms of intraspecies difference of copper accumulation in Crassostrea angulata. In this attempt, we have performed a comprehensive analysis of the transcriptome of oyster (gill and mantle). Digital gene expression (DGE) technology was applied to analyze the relationships between gene expression and differential Cu body burden.

2016-06-30 | GSE65653 | GEO

Homeobox transcription factors involved in fruiting body development of Volvariella volvacea

Project description:The genome of V. volvacea revealed 47 genes encoding homeobox transcription factors. Of them, 8 differentially expressed homeobox transcription factors were obtained by comparing the gene expression during primordia and elongation formation. Furthermore, quantitative real-time PCR was performed on selected genes with different expression levels to demonstrate the utility of digital gene expression for gene expression profiles during fruiting body formation. The results showed that five homeobox transcription factors were up-regulated during primordia formation, and three homeobox transcription factors were down-regulated from the egg stage to elongation stage. Overall, a critical role for homeobox transcription factor was believed to contribute to the fruiting body formation. Using the 3'-tag digital gene expression (DGE), we compared the gene expression profiles in fruiting body development of V. volvacea.

2014-12-19 | E-GEOD-43297 | biostudies-arrayexpress

Whole transcriptome profiling of successful immune response to Vibrio infections in the oyster Crassostrea gigas by digital gene expression analysis

Project description:The cultivated Pacific oyster Crassostrea gigas has suffered for decades large scale summer mortality phenomenon resulting from the interaction between the environment parameters, the oyster physiological and/or genetic status and the presence of pathogenic microorganisms including Vibrio species. To obtain a general picture of the molecular mechanisms implicated in C. gigas immune responsiveness to circumvent Vibrio infections, we have developed the first deep sequencing study of the transcriptome of hemocytes, the immunocompetent cells. Using Digital Gene Expression (DGE), we generated a transcript catalog of up-regulated genes from oysters surviving infection with virulent Vibrio strains (Vibrio splendidus LGP32 and V. aestuarianus LPi 02/41) compared to an avirulent one, V. tasmaniensis LMG 20012(T). For that an original experimental infection protocol was developed in which only animals that were able to survive infections were considered for the DGE approach. We report the identification of cellular and immune functions that characterize the oyster capability to survive pathogenic Vibrio infections. Functional annotations highlight genes related to signal transduction of immune response, cell adhesion and communication as well as cellular processes and defence mechanisms of phagocytosis, actin cytosqueleton reorganization, cell trafficking and autophagy, but also antioxidant and anti-apoptotic reactions. In addition, quantitative PCR analysis reveals the first identification of pathogen-specific signatures in oyster gene regulation, which opens the way for in depth molecular studies of oyster-pathogen interaction and pathogenesis. This work is a prerequisite for the identification of those physiological traits controlling oyster capacity to survive a Vibrio infection and, subsequently, for a better understanding of the phenomenon of summer mortality. 4 Samples.

2011-11-01 | E-GEOD-33390 | biostudies-arrayexpress

Transcription profiling of Danio rerio livers following exposure to combinations of copper, sodium and calcium

Project description:Zebrafish (n=420; 70/treatment) were weighed and placed in 8L aerated tanks, served with flow-through soft-water at 25ml/min. A combination of Mariotte bottles were used to dose tanks with Cu (concentrated Cu solution made from CuSO4 dissolved in 0.05% HNO3), Na (concentrated NaCl solution), and Ca (concentrated CaCl2 solution) to 6 treatment regimes of either control (Ctrl), Cu only (Cu), high Ca only (Ca), Ca + Cu (CaCu), high Na only (Na), and Na + Cu (NaCu; See Table 1 for ion concentrations). Nitric acid had no measurable impact on water pH. Fish were fed 2% body weight of commercial tropical fish food, once per day. Tanks were monitored daily for mortality and cleaned of any food or waste that had accumulated. Water samples (10 ml) were taken from each tank, filtered though a 0.45?m filtration disc (Pall Corporation, East Hills, NY), added to a plastic tube containing 100?l HNO3 and kept at 4oC for analysis of ion content and Cu concentration. Throughout the experiment, there were no mortalities in any of the tanks. At the end of the exposure period, fish were quickly euthanized by overdose of buffered aesthetic (MS-222, Sigma) and sampled for gill, liver, and gut, which were immediately frozen in liquid N2 for further analysis of Cu burden, gene expression, and enzyme activity.

2009-09-01 | E-MEXP-2288 | biostudies-arrayexpress

Gene expression profiling of primary acute lymphoblastic leukemia (ALL) cells

Project description:The aim of this study was to benchmark digital gene expression (DGE) profiling by massively parallel sequencing against the most commonly used method for gene expression analysis. We compared the DGE levels to expression levels from Affymetrix arrays. Data from Affymetrix Human Genome U133 plus 2.0 GeneChips was available for 12 of the 21 RNA samples from ALL patient cells analyzed by DGE.

2011-12-20 | GSE26865 | GEO

Transcriptomic Analysis of Differentially Expressed Genes during Larval Development of Rapana Venosa by Digital Gene Expression Profiling

Project description:In present study, digital gene expression (DGE) profiling was performed to obtain a general picture of the transcriptomic implicated in the early development of R. venosa. Eighteen DGE libraries at six developmental stages of R. venosa were constructed, sequenced by IIIumina HiSeq 2500 platform.

2016-07-22 | GSE70548 | GEO

Transcriptome Analysis of Immunity- and Reproduction-related Differential Gene Expression in Parasitized Locusta migratoria

Project description:The transcriptome and DGE analysis of the fat body and ovary of L. migratoria based on the Illumina short-read sequencing technology and De novo assembly. Research on the trade-offs between immunity and reproduction is contributing significantly to the understanding of the fitness of organisms in nature. The cDNA libraries for the mixed tissue samples of the fat body and ovary collected from the Sephadex group, the bacterial parasite group, and the dipteran parasite group at 4 hours and 6 days post-treatment were made for the DGE analysis. Every experimental treatment sample had one DGE-seq and one parallel replication.

2017-05-01 | E-GEOD-57437 | biostudies-arrayexpress

Tag-seq profiling in eye-antennal and wing imaginal discs of D. melanogaster, D. yakuba and D. virilis

Project description:The aim of this study is to identify a set of eye-specific genes across Drosophila species. Species are used as replicates to remove biological noise and identify a core set of conserved eye-developmental genes. We analyze this conserved core using the motif discovery tool i-cisTarget, and identify master regulators of retinal determination, including the Zinc Finger transcription factor Glass. Six samples were analyzed by Illumina Digital Gene Expression (DGE) using the NlaIII restriction enzyme, namely two different tissues (eye-antennal discs and wing discs) for each of the three species under study.

2012-09-21 | E-GEOD-39782 | biostudies-arrayexpress

Limitations and possibilities of small RNA digital gene expression profiling

Project description:Analysis of RNA samples by massive parallel sequencing holds the promise to assay gene expression in both a quantitative and qualitative fashion and therefore allows for digital gene expression (DGE) profiling. We assessed the effect of different experimental approaches by generating small RNA libraries from a biological sample as well as an equimolar pool of synthetic miRNAs and analyzed the results using capillary dideoxy sequencing and next-generation sequencing platforms (Roche/454, AB/SOLiD and Illumina/Solexa). Whereas different sequencing platforms provided highly similar results, large differences in DGE profiles were observed depending on the library preparation method used. Nevertheless, our results indicate that the preferential nature of the library preparation methods is systematic and highly reproducible and we show that DGE is well suited for the quantification of relative expression differences between samples. This SuperSeries is composed of the following subset Series: GSE16369: Limitations and possibilities of small RNA digital gene expression profiling: library preparation comparison (454) GSE16370: Limitations and possibilities of small RNA digital gene expression profiling: library preparation comparison (SOLiD) GSE16371: Limitations and possibilities of small RNA digital gene expression profiling: spleen and liver comparison (SOLiD) GSE16372: Limitations and possibilities of small RNA digital gene expression profiling: synthetic miRNAs replicates (SOLiD) GSE16373: Limitations and possibilities of small RNA digital gene expression profiling: synthetic miRNA replicates (Illumina) Refer to individual Series

2009-07-28 | E-GEOD-16374 | biostudies-arrayexpress

Transcriptome analysis of buckwheat seed developmental

Project description:Combining the Solexa/ Illumina RNA-seq high-throughput sequencing approach with Digital Gene Expression (DGE) analysis results in a powerful transcriptomic study. This publication reports the transcriptome profiling analysis of Fagopyrum esculentum Moench. using RNA-seq and DGE in order to better understand the molecular mechanisms underlying biological aspects of buckwheat, especially seed development and maturation.

2017-12-31 | GSE34314 | GEO

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