Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

17 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Transcription profiling of Arabidopsis sulfur-starvation time series 3h to 168h

ABSTRACT: Comparison of sulfur-starved Arabidopsis vs. sulfur-sufficient (control) Arabidopsis, a time course (3h, 6h, 12h, 24h, 48h and 168h)

ORGANISM(S): Arabidopsis thaliana

SUBMITTER: Masahiko Kitayama

PROVIDER: E-MEXP-211 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Publications

Elucidation of gene-to-gene and metabolite-to-gene networks in arabidopsis by integration of metabolomics and transcriptomics.

Hirai Masami Yokota MY Klein Marion M Fujikawa Yuuta Y Yano Mitsuru M Goodenowe Dayan B DB Yamazaki Yasuyo Y Kanaya Shigehiko S Nakamura Yukiko Y Kitayama Masahiko M Suzuki Hideyuki H Sakurai Nozomu N Shibata Daisuke D Tokuhisa Jim J Reichelt Michael M Gershenzon Jonathan J Papenbrock Jutta J Saito Kazuki K

The Journal of biological chemistry 20050502 27

Since the completion of genome sequences of model organisms, functional identification of unknown genes has become a principal challenge in biology. Post-genomics sciences such as transcriptomics, proteomics, and metabolomics are expected to discover gene functions. This report outlines the elucidation of gene-to-gene and metabolite-to-gene networks via integration of metabolomics with transcriptomics and presents a strategy for the identification of novel gene functions. Metabolomics and transc ...[more]

PMID: 15866872

Similar Datasets

Transcription profiling of Arabidopsis HSI2 and HSI2-L1 double mutant

Project description:The effect of HSI2 and HSI2-L1 double mutant on plant gene expression.

2007-02-02 | E-MEXP-542 | biostudies-arrayexpress

Transcription profiling of Arabidopsis lba1 mutant vs Col-0 wild type under sucrose treatment

Project description:Comparison of lba1 mutant vs Col-0 wild-type under sucrose treatment.

2006-10-25 | E-MEXP-541 | biostudies-arrayexpress

Expression data from roots of Arabidopsis grown under sulfur, iron or potassium limitation

Project description:Deprivation of mineral nutrients causes significant retardation of plant growth. This slow growth is assumed to be associated with both nutrient specific transcriptional responses and additionally with common transcription patterns. In this study we adjusted the external supply of iron, potassium and sulfur to cause a similar retardation of growth. Global transcriptome analyses were performed to investigate whether the growth limitation by the different nutrient deficiencies triggered specific or similar transcriptional responses. The global transcriptome responded specifically to sulfur, iron or potassium deprivation. Arabidopsis thaliana plants were grown hydroponically under short-day conditions (8h light / 16h dark cycles) under full nutrient supply or under the limitation of sulfur, iron or potassium. Arabidopsis root material was harvested when the plants reached the age of 7 weeks (from sowing) and used for RNA extraction and hybridization on Affymetrix microarrays. Four biological replicates from each condition were analyzed.

2016-07-21 | E-GEOD-77602 | biostudies-arrayexpress

short-term effect of N and S supply shifts on gene expression in wheat grain

Project description:Nitrogen and Sulfur supply play an important role in modulating wheat grain development. We studied the short-term effect of shifting N and S supply levels at mid-way through grain filling on gene expression by microarray analysis. Please note: Factor Value[sampling time]: indicates when the samples were sampled, e.g. 3 hours after we shift the treatment as explained in the protocol TREATMENT and indicated in the protocol SAMPLING. Factor Value[growth condition] (a, b, c, d, e, f) corresponds to the treatments explained in the protocol TREATMENT: a) 3mM nitrogen and 0.02mM sulfur; b) 15mM nitrogen and 0.02mM sulfur; c) 3mM nitrogen and 2mM sulfur. At mid-way through grain filling, three additional N and S supply levels were introduced as follows: d) shifting treatment a) to 15mM nitrogen and 0.02mM sulfur; e) shifting treatment b)to 15mM nitrogen and 2mM sulfur; f) shifting treatment c) to 15mM nitrogen and 2mM sulphur.

2015-06-01 | E-MTAB-1920 | biostudies-arrayexpress

Transcription profiling of whole blood from women exposed to hormone replacement therapy and those with no treatment

Project description:The American Women's Health Initiative study published in July 2002 caused considerable concern among hormone replacement therapy (HRT) users and prescribers in many countries. This study is an exploratory research comparing the genome wide expression profile in whole blood samples according to HRT use. Within the Norwegian Women and Cancer study, 100 postmenopausal women (50 HRT users and 50 non-HRT users) born between 1943 and 1949 with normal to high body mass index and no other medication use were selected. After total RNA extraction, amplification and labelling, the samples were hybridized together with a common reference (Universal human reference RNA, Stratagen) to Agilent Human 1A oligoarrays (G4110b, Agilent Technologies, Palo Alto, CA) containing 20,173 unique genes. Differentially expressed genes were used to build a classifier using the nearest shrunken centroids method (PAM). Then, we tested the significant changes in single genes by different methods like t-test, Significance Analysis of Microarrays (SAM) and Bayesian ANOVA analysis (BAM). Results did not reveal any distinct gene list which predicted accurately HRT exposure (error rate = 0.45). Classifier performance slightly improved (error rate = 0.29) including only women who were using continuous combined HRT treatment. According to the small amplitude of expression alterations observed after HRT use in whole blood, large sample sizes are needed to identify significant single genes differentially expressed. However, significant enrichments in biologic process of genes with small changes after HRT use were observed (e.g. receptor and transporter activities, immune response, frizzled signalling pathway, actin filament organization, glycogen metabolism). Experiment Overall Design: Indirect design with Stratagene reference Experiment Overall Design: 47 non HRT users and 42 HRT users Experiment Overall Design: No technical replicates

2007-11-28 | E-GEOD-3492 | biostudies-arrayexpress

Transcription profiling of Arabidopsis wild type seeds grown under sulfur-deficient conditions

Project description:Comparison of Arabidopsis wild-type developing seeds grown under sulfur-deficient condition vs Arabidopsis wild-type developing seeds grown under control condition.

2007-06-01 | E-ATMX-1 | biostudies-arrayexpress

Transcription profiling of yeast strains lacking Met4 or Met4 cofactors at time points after sulfur limitation

Project description:All yeast strains used in this study (Table 1) are in the W303 background (ade2-1 can1-100, his3-1,15 leu2-3,112 trp1-1 ura3). For sulfur limitation microarray studies, WT, met4 delete, met31 delete met32 delete, cbf1 delete, and met28 delete strains were grown in minimal B-media [see Cherest, H., and Surdin-Kerjan, Y. (1992). Genetic analysis of a new mutation conferring cysteine auxotrophy in Saccharomyces cerevisiae: updating of the sulfur metabolism pathway. Genetics 130, p51-58 for B-media composition] supplemented with 0.5mM methionine as the sole sulfur source. An aliquot of cells was harvested for a t=0 time point while the remainder were filtered through a .22um Stericup filter (Millipore), then washed and resuspended in pre-warmed (30 C) B-media lacking any source of sulfur. Cells were harvested after 20, 40, and 80 minutes.

2009-11-30 | E-MEXP-2429 | biostudies-arrayexpress

Transcription profiling of Arabidopsis roots from wild type and stop1 mutant plants treated with Al or low pH

Project description:Comparison of stop1 mutant vs. wild type treated with Al or low pH, and gene expression responses to rhizotoxic ions (Al, low pH) in Arabidopsis roots.

2009-05-04 | E-MEXP-1908 | biostudies-arrayexpress

BIOLAN

Project description:Identification of expression profiles in colorectal cancer using tumoral and non-tumoral tissue samples

2011-01-11 | E-MTAB-476 | biostudies-arrayexpress

BIOLAN2

Project description:validation of 7 genes biomarker profile in colorectal cancer using tumoral and non-tumoral tissue samples

2012-02-02 | E-MTAB-770 | biostudies-arrayexpress