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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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RNAseq of patients with Ewings sarcoma

ABSTRACT: Cancer is driven my mutations in the genome. We will uncover the mutations that give rise to Ewings sarcoma, a bone tumour that largely affects children. We will use second generation Illumina massively parallel sequencing, and bespoke software, to characterise the genomes and transcriptomes of Ewings sarcoma tumours.

INSTRUMENT(S): Illumina HiSeq 2000

ORGANISM(S): Homo sapiens

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PROVIDER: E-ERAD-65 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Ewings Sarcoma RNA seq drug sensitivity

Project description:Illumina RNA-Seq will be performed on four Ewing’s sarcoma cell lines and two control cell lines. RNA was extracted from all the lines using a basic Trizol extraction protocol.

2013-01-30 | E-ERAD-144 | biostudies-arrayexpress

Transcriptome and Metabolite Profiling of the Infection Cycle of Zymoseptoria tritici on Wheat Reveals a Biphasic Interaction with Plant Immunity Involving Differential Pathogen Chromosomal Contributions and a Variation on the Hemibiotrophic Lifestyle Definition.

Project description:The hemibiotrophic fungus Zymoseptoria tritici causes Septoria tritici blotch disease of wheat (Triticum aestivum). Pathogen reproduction on wheat occurs without cell penetration, suggesting that dynamic and intimate intercellular communication occurs between fungus and plant throughout the disease cycle. We used deep RNA sequencing and metabolomics to investigate the physiology of plant and pathogen throughout an asexual reproductive cycle of Z. tritici on wheat leaves. Over 3,000 pathogen genes, more than 7,000 wheat genes, and more than 300 metabolites were differentially regulated. Intriguingly, individual fungal chromosomes contributed unequally to the overall gene expression changes. Early transcriptional down-regulation of putative host defense genes was detected in inoculated leaves. There was little evidence for fungal nutrient acquisition from the plant throughout symptomless colonization by Z. tritici, which may instead be utilizing lipid and fatty acid stores for growth. However, the fungus then subsequently manipulated specific plant carbohydrates, including fructan metabolites, during the switch to necrotrophic growth and reproduction. This switch coincided with increased expression of jasmonic acid biosynthesis genes and large-scale activation of other plant defense responses. Fungal genes encoding putative secondary metabolite clusters and secreted effector proteins were identified with distinct infection phase-specific expression patterns, although functional analysis suggested that many have overlapping/redundant functions in virulence. The pathogenic lifestyle of Z. tritici on wheat revealed through this study, involving initial defense suppression by a slow-growing extracellular and nutritionally limited pathogen followed by defense (hyper) activation during reproduction, reveals a subtle modification of the conceptual definition of hemibiotrophic plant infection.

2015-03-12 | E-MTAB-4116 | biostudies-arrayexpress

Oryza sativa strain:Nipponbare Transcriptome or Gene expression

Project description: Not available

2014-11-04 | E-MTAB-4123 | biostudies-arrayexpress

Populus trichocarpa Transcriptome or Gene expression

Project description:Our analysis provides a comprehensive picture of how P. trichocarpa responds to drought stress at physiological and transcriptome levels which may help to understand molecular mechanisms associated with drought response and could be useful for genetic engineering of woody plants. Drought stress treatment was performed dividing P. trichocarpa plants into the well-watered (WW) group (soil volumetric water content of 40â45 %) and the water-limited group (soil volumetric water content of 10â15 %). Two cDNA libraries constructed separately from the WW and WL groups were subjected to high-throughput Illumina sequencing.

2013-11-20 | E-MTAB-4126 | biostudies-arrayexpress

Genome-wide transcript analysis of early maize leaf development reveals gene cohorts associated with the differentiation of C4 Kranz anatomy

Project description:Photosynthesis underpins the viability of most ecosystems, with C4 plants that exhibit âKranzâ anatomy being the most efficient primary producers. Kranz anatomy is characterized by closely spaced veins that are encircled by two morphologically distinct photosynthetic cell types. Although Kranz anatomy evolved multiple times, the underlying genetic mechanisms remain largely elusive, with only the maize scarecrow gene so far implicated in Kranz patterning. To provide a broader insight into the regulation of Kranz differentiation, we performed a genome-wide comparative analysis of developmental trajectories in Kranz (foliar leaf blade) and non-Kranz (husk leaf sheath) leaves of the C4 plant maize. Using profile classification of gene expression in early leaf primordia, we identified cohorts of genes associated with procambium initiation and vascular patterning. In addition, we used supervised classification criteria inferred from anatomical and developmental analyses of five developmental stages to identify candidate regulators of cell-type specification. Our analysis supports the suggestion that Kranz anatomy is patterned, at least in part, by a SCARECROW/SHORTROOT regulatory network, and suggests likely components of that network. Furthermore, the data imply a role for additional pathways in the development of Kranz leaves.

2013-07-29 | E-MTAB-4134 | biostudies-arrayexpress

Zea mays Transcriptome or Gene expression

Project description:The classical maize mutant lazy1 (la1), displayed prostrate growth with reduced shoot gravitropism. We compared the transcriptome profile of the third node in la1-ref mutants with those in wild-type plants using RNA-SEQ to examine the genome-wide effect of the ZmLA1 gene. We generated 14.6 and 36.5 million paired-end reads from two biological samples of wild-type and la1-ref mutant plants, respectively.

2013-11-20 | E-MTAB-4196 | biostudies-arrayexpress

Oryza sativa Transcriptome or Gene expression

Project description:Nitrogen (N), a critical macronutrient for plant growth and development, is a major limiting factor in most agricultural systems. Microarray analyses have been conducted to investigate genome-wide gene expression in response to changes in N concentrations. Although RNA-Seq analysis can provide a more precise determination of transcript levels, it has not previously been employed to investigate the expression of N-starvation-induced genes. We constructed cDNA libraries from leaf sheaths and roots of rice plants grown under N-deficient or -sufficient conditions for 12 h. Sequencing the libraries resulted in identification of 33,782 annotated genes. A comparison of abundances revealed 1,650 transcripts that were differentially expressed (fold-changeââ¥â2) due to an N-deficiency. Among them, 1,158 were differentially expressed in the leaf sheaths (548 up-regulated and 610 down-regulated) and 492 in the roots (276 up, 216 down).

2015-08-30 | E-MTAB-4195 | biostudies-arrayexpress

mRNA-seq of Zea mays B73 early-prophase meiocytes, anthers, and seedling control

Project description:A major step in the higher plant life cycle is the decision to leave the mitotic cell cycle and begin the progression through the meiotic cell cycle that leads to the formation of gametes. The molecular mechanisms that regulate this transition and early meiosis remain largely unknown. To gain insight into gene expression features during the initiation of meiotic recombination, we profiled early prophase I meiocytes from maize (Zea mays) using capillary collection to isolate meiocytes, followed by RNA-seq.

2013-07-25 | E-MTAB-4210 | biostudies-arrayexpress

Zea mays Transcriptome or Gene expression

Project description:To discover the transcriptional dynamics during seed germination we have obtained the time course transcriptomes for embryonic shoot apical meristem (SAM) every six hours, starting from dry seeds to hour 72 (3 days).

2013-04-02 | E-MTAB-4205 | biostudies-arrayexpress

RNA-seq Analysis of an Apical Meristem Time Series Reveals a Critical Point in Arabidopsis thaliana Flower Initiation

Project description:Floral transition is a critical event in the life cycle of a flowering plant as it determines its reproductive success. Despite extensive studies of specific genes that regulate this process, the global changes in transcript expression profiles at the point when a vegetative meristem transitions into an inflorescence have not been described. In this study we analyzed gene expression during Arabidopsis thaliana meristem development from day 7 to 16 after germination in one-day increments. The dynamics of the expression of the main flowering regulators were consistent with previous reports: notably, the expression of FLOWERING LOCUS C (FLC) decreased over the course of the time series while expression of LEAFY (LFY) increased. This analysis revealed a developmental time point between 10 and 12 days after germination where FLC expression had decreased but LFY expression had not yet increased, which was characterized by a peak in the number of differentially expressed genes. GO enrichment analysis of these genes identified an overrepresentation of genes related to the cell cycle, suggesting that during transition to the flowering stage a change in dynamics of cell division takes place. In particular, we hypothesize that a subset of the meristematic cells experiences a forced exit from G0 at day 10. Finally, we observed an acceleration of the cell cycle at day 11, which may be linked to meristem reorganization preceding activation of LFY.

2015-07-21 | E-MTAB-4202 | biostudies-arrayexpress

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