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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Pathogenic response of Glycine max to the stem parasitic plant Cuscuta

ABSTRACT: Little is known about plant pathogenic response to parasitic plants, although some parasitic plants affect crop production in certain areas. To study this, we chose Glycine max as the model host plant and investigated changes in expression patterns after parasitization by Cuscuta using microarrays. Transcriptional change of Glycine max stem with and without Cuscuta at 2 different stages were compared

ORGANISM(S): Glycine max

SUBMITTER: Takeshi Furuhashi

PROVIDER: E-GEOD-51328 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Pathogenic response of Glycine max to the stem parasitic plant Cuscuta

Project description:Little is known about plant pathogenic response to parasitic plants, although some parasitic plants affect crop production in certain areas. To study this, we chose Glycine max as the model host plant and investigated changes in expression patterns after parasitization by Cuscuta using microarrays.

2014-06-27 | GSE51328 | GEO

Expression data from human olfactory neurosphere derived cells (hONS) established from adult donors treated with coated and uncoated ZnO nanoparticles

Project description:ZnO nanoparticles can elicit a range of cytotoxic responses in different cells in vitro that may reflect either Zn2+ dissolution or nanoparticle-specific effects. Coating the ZnO nanoparticles may mitigate their cytotoxicity. We aimed to capture whole genome transcriptional profiles (up and down regulated) at time-points associated with distinct cytotoxic responses in cells treated with two types of uncoated (Nanosun, Z-COTE) or two types of coated (HP1, MAX) ZnO nanoparticles, compared to untreated cells. hONS cells were incubated with 25ug/ml ZnO nanoparticles (uncoated: Nanosun and Z-COTE; coated: MAX, HP1) for 2h and 6h and their expression profiles were compared to time-matched untreated cells.

2013-09-11 | E-GEOD-45322 | biostudies-arrayexpress

Transcriptome analysis during seed development provides insights into altered gene expression in Glycine max

Project description:The temporal expression profile of Glycine max seeds was carried out to identify genes that are differentially expressed (DE) during seed development. Using the Affymetrix chip, we have for the first time provided a holistic view of the transcriptional landscape during seed development in four different developmental stages in Glycine max. cv. Pusa 16. The analysis of the differential expression patterns and functional category enrichment of DE genes highlighted specific and common significant coordination and enrichment of various biological processes during seed development which have led to the identification of few candidate genes related to inositol metabolism and especially in phytate biosynthesis. In conclusion, we have shown here a logical approach to identify possible candidate genes for fine tuning the metabolic flux for phytate generation, which may be altered by metabolic engineering in developing a low phytate phenotype. Seeds of Glycine max grown at 28/26°C, 16h/8h light/dark were collected at different developmental stages( 0-4mm, 4-8mm, 8-12mm and 12-16mm ) and analyzed. Samples in triplicates from each developmental stage were used for data generation on Affymetrix Chip, each time the earlier developmental stage was considered as control Vs the treatment, corresponding to the later developmental stage. For each biological replicates, RNA was extracted from 20 seeds collected from 5 different plants, grown in the same conditions using the Trizol method. RNA integrity was analyzed using bio analyzer (with RIN value more than 8).

2015-08-11 | E-GEOD-69821 | biostudies-arrayexpress

Comparative physiology and transcriptional networks underlying the heat shock response in Populus trichocarpa, Arabidopsis thaliana and Glycine max

Project description:This SuperSeries is composed of the following subset Series: GSE26195: Comparative physiology and transcriptional networks underlying the heat shock response in Populus trichocarpa, Arabidopsis thaliana and Glycine max [Populus] GSE26197: Comparative physiology and transcriptional networks underlying the heat shock response in Populus trichocarpa, Arabidopsis thaliana and Glycine max [Arabidopsis] GSE26198: Comparative physiology and transcriptional networks underlying the heat shock response in Populus trichocarpa, Arabidopsis thaliana and Glycine max [Soy] Refer to individual Series

2011-04-01 | E-GEOD-26199 | biostudies-arrayexpress

Transcriptional Response to C1 and methylated compounds in Pelagibacter HTCC1062

Project description:Recent studies have shown that Pelagibacter oxidize a wide range of one carbon (C1) and methylated compounds that are ubiquitous in the oceans. However, the metabolic pathways used to oxidize and assimilate these compounds are complex and have been only partly described. To understand the metabolism of these compounds in Pelagibacter and to identify candidate genes involved in these pathways, we used microarray to study changes in gene expression in response to five different compounds (trimethylamine N-oxide (TMAO), methylamine, dimethylsulfoniopropionate (DMSP), methanol, and glycine betaine (GBT)) in Pelagibacter strain HTCC1062. This project will examine the transcriptional response of the marine microorganism Pelagibacter HTCC1062 to five methylated compounds. To do this, 18 flasks were innoculated with cells - 3 flasks without any methylated compounds and rest of 15 treated with different methylated compounds respectively (TMAO (trtmA), methylamine (trtmB), DMSP (trtmC), methanol (trtmD) and glycine betaine (trtmE)). Cells were all harvested at the same timepoint in the exponential phase.

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Expression data from primary human hepatic stellate cells treated with coated and uncoated ZnO nanoparticles, or ZnSO4

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2014-08-07 | E-GEOD-60159 | biostudies-arrayexpress

RIP-seq experiment to evaluate the role of methylation of the spliceosome component LSM4 in the regulation of alternative splicing

Project description:The RIP-seq experiment was designed to look for the direct targets of LSM4 U6snRNP component. For this plants were grown in Murashige and Skoog (MS) plates in continuous light (LL) for 12 days and were vacuum-infiltrated with 1% formaldehyde for 15 min followed by quenching with 125 mM glycine. A whole-cell extract was prepared in RIP-lysis buffer. The extract was pre-cleared with Sepharose beads and subjected to immunoprecipitation with GFP-Trap beads (Chromotek). After extensive washing with RIP washing buffer, co-precipitated RNAs were extracted with Trizol (Invitrogen) and treated with DNase (Promega). Libraries were prepared and sequenced at the Max Planck-Genome-Centre Cologne (MP-GC).

2023-05-31 | E-MTAB-12369 | biostudies-arrayexpress

Identifying conserved and novel miRNAs in germinating seeds of Glycine max using deep sequencing

Project description:MicroRNAs (miRNAs) are important post-transcriptional regulators of plant development. In soybean (Glycine max), an important edible oil crop, valuable lipids are synthesized and stored in the cotyledons during embryogenesis .This storage lipids are used as energy source of the emerging seeds, during the germination procces. Until now, there are no microRNAs related to lipid metabolism in soybean or any other plant. This work aims to describe the miRNAome of germinating seeds of B. napus by identifying plant-conserved and novel miRNAs and comparing miRNA abundance in mature versus germinating seeds. A total of 183 familes were detected through a computational analysis of a large number of reads obtained from deep sequencing from two small RNA libraries of (i) pooled germintaing seeds stages and (ii) mature soybean seeds. We have found 39 new mirna precursors which produce 41 new mature forms. The present work also have identified isomiRNAs and mirnas offset (moRNAs). This work presents a comprehensive study of the miRNA transcriptome of soybean germinating seeds and will provide a basis for future research on more targeted studies of individual miRNAs and their functions in lipid consumption in development soybean seeds. MicroRNA profiles in 2 different seed libraries (mature seeds and a pool of germinating seed stages) of Glycine max by deep sequencing (Illumina GAII).

2015-05-25 | E-GEOD-38373 | biostudies-arrayexpress

Alterations of RNA maps of IncP-7 plasmid pCAR1 in various Pseudomonas bacteria.

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2011-10-10 | E-GEOD-28568 | biostudies-arrayexpress

Gene expression of soybean roots inoculated with wild-type and type III secretion mutant strains of Bradyrhizobium elkanii

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2013-09-17 | E-GEOD-38520 | biostudies-arrayexpress

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