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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Transcriptome analysis during the shift from dark to blue light in Arabidopsis wild type Col-0 plants.

ABSTRACT: RNA-seq was performed in three-day-old wild-type Col-0 plants grown on filter paper in the dark that were exposed to blue light and harvested after one-hour exposure.

INSTRUMENT(S): Illumina HiSeq 2000

ORGANISM(S): Arabidopsis thaliana

SUBMITTER: Minami Matsui

PROVIDER: E-MTAB-5188 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Next-generation sequencing of genomic DNA fragments bound to a transcription factor in vitro reveals its regulatory potential.

Kurihara Yukio Y Makita Yuko Y Kawashima Mika M Hamasaki Hidefumi H Yamamoto Yoshiharu Y YY Matsui Minami M

Genes 20141219 4

Several transcription factors (TFs) coordinate to regulate expression of specific genes at the transcriptional level. In Arabidopsis thaliana it is estimated that approximately 10% of all genes encode TFs or TF-like proteins. It is important to identify target genes that are directly regulated by TFs in order to understand the complete picture of a plant's transcriptome profile. Here, we investigate the role of the LONG HYPOCOTYL5 (HY5) transcription factor that acts as a regulator of photomorph ...[more]

PMID: 25534860

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TTV018 RORC IBD associated genotype effects on RORgT expression and function in ex vivo T cells

Project description:RNA sequencing of peripheral immune cells from patients +/- an IBD risk variant. Peripheral immune cells +/- in vitro test compound treatment.This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/

2016-07-11 | E-ERAD-443 | biostudies-arrayexpress

Study of low dose gamma irradiation effects in esophageal epithelial cell fate

Project description:Effect of low-doses of ionizing radiation on the behaviour of epithelial cells. The aim of the study is to check whether a single exposure of 50 mGy of ioninzing radiation promotes changes in RNA transcription levels and/or mutations.

2016-02-23 | E-ERAD-429 | 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.

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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.

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

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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.

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Oryza sativa Transcriptome or Gene expression

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

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

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

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