Glycine max
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA156655 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR361418.fastq.gz | Fastqsanger.gz |
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Project description:Small RNAs, including microRNAs and their targets, as well as phased secondary siRNAs, were characterized in the soybean genome by deep sequencing of small RNA libraries from a wide range of tissues. The mRNA targets of many of these small RNAs were also validated from many of the same tissues using PARE (Parallel Analysis of RNA Ends) libraries.
2014-12-01 | GSE58779 | GEO
Project description:An overview of small RNAs sequences existing in seed development and contrasted with vegetative tissues of the soybean Four small RNA sequence populations from high throughput deep sequencing-by-synthesis and representing different tissues/organs of the soybean were characterized into small RNA classes, level of expresion, genes of origin and putative targeted genes
2012-10-09 | E-GEOD-36728 | biostudies-arrayexpress
Project description:RNA-seq was used to characterize gene expression in soybean from a wide range of tissues. The primary focus of the project was small RNAs, and the identification of microRNAs and phased siRNA-generating loci, but RNA-seq data were generated from the same samples. This project was supported by the United Soybean Board.
2020-05-09 | GSE150157 | GEO
Project description:An overview of small RNAs sequences existing in seed development and contrasted with vegetative tissues of the soybean
2012-10-09 | GSE36728 | GEO
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
Project description:This SuperSeries is composed of the following subset Series: GSE33378: Deep sequencing of small RNAs from different tissues in soybean GSE33379: Deep sequencing of the degradome cDNA library in soybean Refer to individual Series
2011-11-02 | E-GEOD-33380 | biostudies-arrayexpress
Project description:Tropospheric ozone (O3) is a secondary air pollutant and anthropogenic greenhouse gas. Concentrations of tropospheric O3 have more than doubled since the Industrial Revolution, and are high enough to damage plant productivity. Soybean (Glycine max L. Merr.) is the worldâs most important legume crop and is sensitive to O3. Current ground-level O3 are estimated to reduce global soybean yields by 6% to 16%. In order to understand transcriptional mechanisms of yield loss in soybean, we examined the transcriptome of soybean flower and pod tissues exposed to elevated O3 using RNA-Sequencing.
2015-01-31 | E-MTAB-5226 | biostudies-arrayexpress
Project description:We present results from deep sequencing of small RNA populations from several genotypes of soybean and demonstrate that the CHS siRNAs accumulated only in the seed coats of the yellow varieties having either the dominant I or i-i alleles and not in the pigmented seed coats with homozygous recessive i genotypes. However, the diagnostic CHS siRNAs did not accumulate in the cotyledons of genotypes with the dominant I or i-i alleles thus demonstrating the novelty of an endogenous inverted repeat region of CHS genes driving RNA silencing in trans of non-linked CHS family members in a tissue-specific manner. The phenomenon results in inhibition of a metabolic pathway by siRNAs in one tissue allowing expression of the flavonoid pathway and synthesis of secondary metabolites in other organs as the chalcone synthase small RNAs are found in the seed coats of yellow seeded soybean varieties but not in the cotyledons of the same genotype. In order to compare the population of chalcone synthase related small RNAs, we sequenced 3 to 6 million small RNAs using the Illumina Genome Analyzer from the following four soybean cultivars and tissues with specific genotypes at the I locus: Richland immature seed coats (homozygous for the dominant I allele that specifies yellow seed coat); Williams immature seed coats (homozygous for the dominant i-i allele that specifies yellow seed coat with pigmented hilum) Williams (i-i/i-i yellow) immature cotyledons (homozygous for the dominant i-i allele that specifies yellow seed coat with pigmented hilum); Williams 55 immature seed coats (a Williams isogenic line homozygous for the recessive i allele that specifics pigmented seed coats. All seed coats and cotyledons were dissected from green stage immature seeds within the fresh weight range of 50-75 mg.
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Project description:Two soybean isolines that differed in leaf phenotype were profiled by high throughput RNA and small RNA (sRNA) sequencing. A Clark isoline abbreviated as CF and homozygous for a dominant mutant allele, Lf1, that specifies a five-foliate compound leaf was compared to wild type Clark, designated CS, which is homozygous for the standard allele that produces trifoliate leaves. Although Lf1 is dominant, it presents variable expressivity as the young plantlets with the Lf1Lf1 genotype initially have trifoliate leaves in the first few weeks, after which they transition to five-foliate leaves. This study provides insight into the initial understanding of leaf development in soybean by revealing a number of small RNAs differentially expressed between the CS and CF. Out of over 200,000 unique sequences, 913 showed similarities to 122 known miRNAs in soybean.
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Project description:We present results from deep sequencing of small RNA populations from several genotypes of soybean and demonstrate that the CHS siRNAs accumulated only in the seed coats of the yellow varieties having either the dominant I or i-i alleles and not in the pigmented seed coats with homozygous recessive i genotypes. However, the diagnostic CHS siRNAs did not accumulate in the cotyledons of genotypes with the dominant I or i-i alleles thus demonstrating the novelty of an endogenous inverted repeat region of CHS genes driving RNA silencing in trans of non-linked CHS family members in a tissue-specific manner. The phenomenon results in inhibition of a metabolic pathway by siRNAs in one tissue allowing expression of the flavonoid pathway and synthesis of secondary metabolites in other organs as the chalcone synthase small RNAs are found in the seed coats of yellow seeded soybean varieties but not in the cotyledons of the same genotype.
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