Unknown,Transcriptomics,Genomics,Proteomics

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


ABSTRACT: 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 “chess board” 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 manufacturer’s 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 μg dye-labeled targets were used for hybridization.

ORGANISM(S): Glycine max

SUBMITTER: XingWang Deng 

PROVIDER: E-GEOD-10056 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Transcriptional analysis of highly syntenic regions between Medicago truncatula and Glycine max using tiling microarrays.

Li Lei L   He Hang H   Zhang Juan J   Wang Xiangfeng X   Bai Sulan S   Stolc Viktor V   Tongprasit Waraporn W   Young Nevin D ND   Yu Oliver O   Deng Xing-Wang XW  

Genome biology 20080319 3


<h4>Background</h4>Legumes are the third largest family of flowering plants and are unique among crop species in their ability to fix atmospheric nitrogen. As a result of recent genome sequencing efforts, legumes are now one of a few plant families with extensive genomic and transcriptomic data available in multiple species. The unprecedented complexity and impending completeness of these data create opportunities for new approaches to discovery.<h4>Results</h4>We report here a transcriptional a  ...[more]

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