Dataset Information

E-MTAB-4045

ABSTRACT: Transcription profiling by high throughput sequencing of soybean seeds from globular to early-maturation stage

TISSUE(S): Inner Integument, Cotyledon Vasculature, Axis Epidermis, Cotyledon Abaxial Epidermis, Root Tip, Axis Shoot Apical Meristem, Embryo Proper, Embryo Proper Axis, Endosperm, Cotyledon Abaxial Parenchyma, Hilum, Axis Plumule, Suspensor, Embryo Proper Cotyledon, Outer Integument, Cotyledon Adaxial Parenchyma, Seed Coat Endothelium, Seed Coat Parenchyma, Cotyledon Adaxial Epidermis, Seed Coat Epidermis, Seed Coat Hourglass, Seed Coat Palisade, Axis Vasculature, Axis Stele, Axis Parenchyma

PROVIDER: E-MTAB-4045 | ExpressionAtlas | 2016-02-04

REPOSITORIES: ExpressionAtlas

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			Action	DRS
	E-MTAB-4045-analysis-methods.tsv	Tabular
	E-MTAB-4045-atlasExperimentSummary.Rdata	Rdata
	E-MTAB-4045-coexpressions.tsv.gz	Tabular
	E-MTAB-4045-configuration.xml	Xml
	E-MTAB-4045-factors.xml	Xml

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Project description:To understand gene expression networks leading to functional properties and compositional traits of the soybean seed, we have undertaken a detailed examination of soybean seed development from a few days post-fertilization to the mature seed using Illumina high-throughput transcriptome sequencing (RNA-Seq). RNA was sequenced from seven different stages of seed development, yielding between 12 million and 78 million sequenced transcripts. These have been aligned to the 79,000 gene models predicted from the soybean genome recently sequenced by the Department of Energy Joint Genome Institute. Over one hundred gene models were identified with high expression exclusively in young seed stages, starting at just four days after fertilization. These were annotated as being related to many basic components and processes such as histones and proline-rich proteins. Genes involved with some storage proteins such as glycinin and beta-conglycinin had their highest expression levels at the stages of largest fresh weight, confirming previous knowledge that these storage products are being rapidly accumulated before the seed begins the desiccation process. Other gene models showed high expression in the dry, mature seeds, perhaps indicating the preparation of pathways needed later, in the early stages of imbibition. Many highly-expressed gene models at the dry seed stage are, as expected, annotated as hydrophilic proteins associated with low water conditions, such as late embryogenesis abundant (LEA) proteins and dehydrins, which help preserve the cellular structures and nutrients within the seed during desiccation. Hundreds of transcription factors with notable expression in at least one stage of seed development were also identified and examined. Results from a second biological replicate demonstrate high reproducibility of these data. High-throughput sequencing using Illumina Genome Analyzer II and Illumina HiSeq 2000 (RNA-Seq) was performed on seven stages of soybean seeds, with two biological replicates per stage.

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E-MTAB-4045

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