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Transcriptional Analysis of 1M Regions in Medicago truncatula Using Tiling Microarrays

ABSTRACT: We report here a transcriptonal analysis in six different organ types of a approximately 1 Mb region in legume plants barrel medic (Medicago truncatula) which is sytenic with soybean (Glycine max). We used oligonucleotide tiling microarrays to detecte transcription of over 80% of the predicted genes in both species. We detected differential gene expression in the six examined organ types. Keywords: RNA

ORGANISM(S): Medicago truncatula

PROVIDER: GSE10055 | GEO | 2008/01/15

SECONDARY ACCESSION(S): PRJNA109071

REPOSITORIES: GEO

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Transcriptional Analysis of 1M Regions in Medicago truncatula Using Tiling Microarrays

Project description:We report here a transcriptonal analysis in six different organ types of a approximately 1 Mb region in legume plants barrel medic (Medicago truncatula) which is sytenic with soybean (Glycine max). We used oligonucleotide tiling microarrays to detecte transcription of over 80% of the predicted genes in both species. We detected differential gene expression in the six examined organ types. Keywords: RNA Both the barrel medic and soybean tiling arrays were produced on the Maskless Array Synthesizer platform. Briefly, tiling-paths consisting of 36-mer oligonucleotides offset by five nucleotides were designed to represent both DNA strands of the selected barrel medic and soybean genome sequence. Probes were synthesized at a feature-density of 390,000 probes per array in a âchess boardâ design. Microarray production and storage were carried out. Total RNA and mRNA were sequentially isolated using the RNeasy Plant Mini kit (Qiagen, Valencia, CA) and the Oligotex mRNA kit (Qiagen) according to the manufacturerâs recommendations, respectively. mRNA from different organ types was reverse transcribed using a mixture of oligo(dT)18 and random nonamer primers, during which amino-allyl-modified dUTP (aa-dUTP) was incoporated. The aa-dUTP decorated cDNA was fluorescent labeled by conjugating the monofunctional Cy3 dye (GE Healthcare, Piscataway, NJ) to the amino-allyl functional groups in the cDNA. Two Î¼g dye-labeled targets were used for hybridization.

2010-05-26 | E-GEOD-10055 | biostudies-arrayexpress

Transcriptional Analysis of 1M Regions in Glycine max Using Tiling Microarrays

2008-01-15 | GSE10056 | GEO

Transcriptional Analysis of 1M Regions in Glycine max Using Tiling Microarrays

Project description:We report here a transcriptonal analysis in six different organ types of a approximately 1 Mb region in soybean (Glycine max) which is sytenic with legume (Medicago truncatula). We used oligonucleotide tiling microarrays to detecte transcription of over 80% of the predicted genes in both species. We detected differential gene expression in the six examined organ types. Keywords: RNA Both the barrel medic and soybean tiling arrays were produced on the Maskless Array Synthesizer platform. Briefly, tiling-paths consisting of 36-mer oligonucleotides offset by five nucleotides were designed to represent both DNA strands of the selected barrel medic and soybean genome sequence. Probes were synthesized at a feature-density of 390,000 probes per array in a âchess boardâ design. Microarray production and storage were carried out. Total RNA and mRNA were sequentially isolated using the RNeasy Plant Mini kit (Qiagen, Valencia, CA) and the Oligotex mRNA kit (Qiagen) according to the manufacturerâs recommendations, respectively. mRNA from different organ types was reverse transcribed using a mixture of oligo(dT)18 and random nonamer primers, during which amino-allyl-modified dUTP (aa-dUTP) was incoporated. The aa-dUTP decorated cDNA was fluorescent labeled by conjugating the monofunctional Cy3 dye (GE Healthcare, Piscataway, NJ) to the amino-allyl functional groups in the cDNA. Two Î¼g dye-labeled targets were used for hybridization.

2010-05-26 | E-GEOD-10056 | biostudies-arrayexpress

Medicago truncatula drought stress recovery

Project description:Molecular Elasticity and Adjustment of Drought Recovery Dynamics of 14N- and 15N-fertilized Legume Medicago truncatula. Climate change in conjunction with population growth necessitates a systems biology approach to characterize plant drought response and a more thorough understanding of the underlying molecular mechanisms. During drought stress and recovery, the metabolome and proteome regulate and are regulated through diverse mechanisms including synthesis and degradation. In order to study this complex regulation network, a front-end multilevel analysis is presented for the first time, investigating protein turnover, regulatory classes of proteins and metabolites as well as post translational ubiquitination of a target set of proteins during a severe stress and recovery scenario in the model legume Medicago truncatula. Evidence for enhanced translational proteome regulation was observed during drought recovery and functional clusters of differentially dynamic phases during the course of recovery were defined. The data give novel insights into molecular elasticity that enable recovery of drought stressed plants. Additionally, these results offer putative targets and metabolic pathways for future plant-bioengineering towards enhanced drought stress tolerance.

2016-03-29 | PXD001728 | Pride

Medicago truncatula seed development under greenhouse conditions

Project description:Transcriptional profiling of seeds of Medicago truncatula during maturation. To identify genes that are regulated during seed maturation in the model legume Medicago truncatula, plants at flowering stage were grown at variable light and temperature conditions under greenhouse environment (period March-June). Seeds were then collected at different stages of development. Using the Medicago NimbleGen chip, a transcriptomic analysis was performed to follow the differential expression of genes during seed maturation.

2019-09-11 | GSE137174 | GEO

High-throughput pyrosequencing of miRNAs from Medicago truncatula nodules and roots

Project description:We have used deep sequencing of small RNAs from nodules and root apexes of the model legume Medicago truncatula, to identify 113 novel candidate miRNAs. These miRNAs (legume or Mt-specific) are encoded by 278 putative hairpin precursors in the M. truncatula genome. Several miRNAs are differentially expressed in nodules and root tips and large variety of targets could be predicted for these genes. Specific miRNA isoforms showed contrasting expression patterns in these tissues Keywords: Transcriptome analysis

2009-07-07 | GSE15438 | GEO

Medicago truncatula seed development at under greenhouse conditions

2013-12-05 | GSE52833 | GEO

Medicago truncatula seed development at 21-19°C

Project description:Transcriptional profiling of seeds of Medicago truncatula during maturation. To identify genes that are regulated during seed maturation in the model legume Medicago truncatula, plants at flowering stage were grown at controlled temperature of 21-19°C, 16h light. Seeds were then collected at different stages of development. Using the Medicago NimbleGen chip, a transcriptomic analysis was performed to follow the differential expression of genes during seed maturation.

2013-07-31 | GSE49350 | GEO

Medicago truncatula roots infected (or not) with the oomycete Aphanomyces euteiches

Project description:The objective of this study was to evaluate the effect of the oomycete Aphanomyces euteiches (strain ATCC201684) on the legume model Medicago truncatula (F83005-5 line) transcritpome.

2018-03-15 | GSE109500 | GEO

The proteome of Medicago truncatula in response to ammonium and urea nutrition

Project description:comprehensive and quantitative proteomic study of the roots of the NH4+-tolerant legume Medicago truncatula grown with nitrate, NH4+ or urea as sole N source using the iTRAQ method.

2019-06-03 | PXD011074 | Pride

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