Glycine max strain:Soybean 41 accessions
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA248222 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR1297380_1.fastq.gz | Fastqsanger.gz | |||
| SRR1297380_2.fastq.gz | Fastqsanger.gz | |||
| SRR1297390_1.fastq.gz | Fastqsanger.gz | |||
| SRR1297390_2.fastq.gz | Fastqsanger.gz | |||
| SRR1297400_1.fastq.gz | Fastqsanger.gz |
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Project description:Soybean (Glycine max) seeds are an important source of seed storage compounds, including protein, oil, and sugar used for food, feed, chemical, and biofuel production. We assessed detailed temporal transcriptional and metabolic changes in developing soybean embryos to gain a systems biology view of developmental and metabolic changes and to identify potential targets for metabolic engineering. Two major developmental and metabolic transitions were captured enabling identification of potential metabolic engineering targets specific to seed filling and to desiccation. The first transition involved a switch between different types of metabolism in dividing and elongating cells. The second transition involved the onset of maturation and desiccation tolerance during seed filling and a switch from photoheterotrophic to heterotrophic metabolism. Clustering analyses of metabolite and transcript data revealed clusters of functionally related metabolites and transcripts active in these different developmental and metabolic programs. The gene clusters provide a resource to generate predictions about the associations and interactions of unknown regulators with their targets based on “guilt-by-association” relationships. The inferred regulators also represent potential targets for future metabolic engineering of relevant pathways and steps in central carbon and nitrogen metabolism in soybean embryos and drought and desiccation tolerance in plants. SUBMITTER_CITATION: Biology 2013, 2(4), 1311-1337; doi:10.3390/biology2041311 Changes in RNA Splicing in Developing Soybean (Glycine max) Embryos Delasa Aghamirzaie, Mahdi Nabiyouni, Yihui Fang, Curtis Klumas, Lenwood S. Heath, Ruth Grene and Eva Collakova SUBMITTER_CITATION: Metabolites 2013, 3(2), 347-372; doi:10.3390/metabo3020347 Metabolic and Transcriptional Reprogramming in Developing Soybean (Glycine max) Embryos Eva Collakova, Delasa Aghamirzaie, Yihui Fang, Curtis Klumas, Farzaneh Tabataba, Akshay Kakumanu, Elijah Myers, Lenwood S. Heath and Ruth Grene Total mRNA profiles of 10 time course samples of Soybean developing embryos with three replicates per sample were generated by deep sequencing, using Illumina HiSeq 2000
2013-12-13 | E-GEOD-46153 | biostudies-arrayexpress
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Project description:Two Near Isogenic soybean (Glycine max) lines were grown in hydroponic conditions with either 50uM ferric nitrate or 100uM ferric nitrate. After 10 days, half the plants were harvested (total root tissue). At 12 days after planting, iron was added to plants grown in low iron conditions bringing them up to sufficient iron growth conditions. Root tissue was harvested for the remaining plants at 14 days after planting. Gene expression analysis from root tissue of two Near Isogenic Lines (NILs), Clark (PI548553) and IsoClark (PI547430), grown in iron stress or iron stress recovered conditions.
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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).
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Project description:Soybean (Glycine max) seeds are an important source of seed storage compounds, including protein, oil, and sugar used for food, feed, chemical, and biofuel production. We assessed detailed temporal transcriptional and metabolic changes in developing soybean embryos to gain a systems biology view of developmental and metabolic changes and to identify potential targets for metabolic engineering. Two major developmental and metabolic transitions were captured enabling identification of potential metabolic engineering targets specific to seed filling and to desiccation. The first transition involved a switch between different types of metabolism in dividing and elongating cells. The second transition involved the onset of maturation and desiccation tolerance during seed filling and a switch from photoheterotrophic to heterotrophic metabolism. Clustering analyses of metabolite and transcript data revealed clusters of functionally related metabolites and transcripts active in these different developmental and metabolic programs. The gene clusters provide a resource to generate predictions about the associations and interactions of unknown regulators with their targets based on guilt-by-association relationships. The inferred regulators also represent potential targets for future metabolic engineering of relevant pathways and steps in central carbon and nitrogen metabolism in soybean embryos and drought and desiccation tolerance in plants.
2013-12-13 | GSE46153 | GEO
Project description:Glycine max cultivar:Soybean Transcriptome or Gene expression
| PRJNA728044 | ENA
Project description:Two Near Isogenic soybean (Glycine max) lines were grown in hydroponic conditions with either 50uM ferric nitrate or 100uM ferric nitrate. After 10 days, half the plants were harvested (total root tissue). At 12 days after planting, iron was added to plants grown in low iron conditions bringing them up to sufficient iron growth conditions. Root tissue was harvested for the remaining plants at 14 days after planting. Gene expression analysis from root tissue of two Near Isogenic Lines (NILs), Clark (PI548553) and IsoClark (PI547430), grown in iron stress or iron stress recovered conditions. A total of 24 samples from four growth conditions, three biological replicates per treatment
2010-09-06 | E-GEOD-22227 | biostudies-arrayexpress
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
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Project description:Chilling stress is a major factor limiting the yield and quality of vegetable soybean (Glycine max L.) on a global scale. Systematic identification and function analysis of miRNA under chilling stress could be helpful to clarify the molecular mechanism of chilling resistance. In the present study, two independent small RNA libraries from leaves of vegetable soybean were constructed, and sequenced with the high-throughput Illumina Solexa system. A total of 434 known miRNAs and three novel miRNAs were identified. Moreover, the expression patterns of these miRNAs have been verified by qRT-PCR analysis. Furthermore, we identified their gene targets by high-throughput degradome sequencing and validated using 5'-RACE. A total of 898 transcripts were targeted by 54 miRNA families attributed to five categories. More importantly, we identified 55 miRNAs that differentially expressed between chilling stress and the control. The targets of these miRNAs were enriched in oxidation-reduction, signal transduction, and metabolic process functional categories. The qRT-PCR confirmed that there was a negative relationship among the miRNAs and their targets under chilling stress. Our work provides comprehensive molecular evidence for the possible involvement of miRNAs in the process of chilling-stress responses in vegetable soybean.
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