Sorghum bicolor
Ontology highlight
ABSTRACT:
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| DRR153321_1.fastq.gz | Fastqsanger.gz | |||
| DRR153321_2.fastq.gz | Fastqsanger.gz | |||
| DRR153322_1.fastq.gz | Fastqsanger.gz | |||
| DRR153322_2.fastq.gz | Fastqsanger.gz | |||
| DRR153323_1.fastq.gz | Fastqsanger.gz |
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Project description:This study utilized next generation sequencing technology (RNA-Seq and BS-Seq) to examine the transcriptome and methylome of various tissues within sorghum plants with the ultimate goal of improving the Sorghum bicolor annotation We examined the mRNA of various Sorghum bicolor (BTx623) tissues (flowers, vegitative and floral meristems, embryos, roots and shoots) and bisulfite treated DNA from two root samples
2014-08-29 | E-GEOD-50464 | biostudies-arrayexpress
Project description:* The high sequence and structural similarities between BRI1 brassinosteroid receptors of Arabidopsis (AtBRI1) and sorghum (SbBRI1) prompted us to study the functionally conserved roles of BRI in both organisms. * Introducing sorghum SbBRI1 in Arabidopsis bri1 mutants restores defective growth and complements developmental phenotypes to WT levels. * Sorghum mutants for SbBRI1 receptors show defective BR sensitivity and results in impaired growth and development throughout the entire sorghum life cycle. Embryonic analysis of sorghum primary roots traced the root growth and development at the early stages, revealing the role of SbBRI1 in BR perception during cell division and BR sensing. RNA-seq of SbBRI1 mutants support the roles of SbBRI1 in cell wall biosynthesis and remodeling. * Together, these results uncover that sorghum SbBRI1 receptor protein play functionally conserved roles in plant growth and development.
2025-01-15 | GSE265868 | GEO
Project description:This study used with RNA-Seq to examine the tissue specific expression data within sorghum plants for improving the Sorghum bicolor gene annotation. We examined the RNA from tissues (spikelet, seed and stem) in Sorghum bicolor (BTx623).Total RNAs form each tissues were extracted using SDS/phenol method followed by LiCl purification
2015-03-11 | E-MTAB-4273 | biostudies-arrayexpress
Project description:This study utilized next generation sequencing technology (RNA-Seq and BS-Seq) to examine the transcriptome and methylome of various tissues within sorghum plants with the ultimate goal of improving the Sorghum bicolor annotation
2014-08-29 | GSE50464 | GEO
Project description:Sorghum is a C4 cereal important not only as food, but also as forage and a bioenergy resource. Its resistance to harsh environments has made it an agriculturally important research subject. Recent accumulation of genomic and transcriptomic information has facilitated genetic studies. Yet genome-wide translational profiles in sorghum are still missing, although increasing evidence has demonstrated that translation is an important regulatory step, and the transcriptome does not necessarily reflect the profile of functional protein production in some organisms. Deep sequencing of ribosome-protected mRNA fragments (ribosome profiling, or Ribo-seq) has enabled genome-wide analysis of translation. In this study, we took advantage of Ribo-seq and identified actively translated reading frames throughout the genome. We detected translation of 7,304 main ORFs annotated in the sorghum reference genome version 3.1 and revealed a number of unannotated translational events. A comparison of the transcriptome and translatome between sorghums grown under normal and sulfur-deficient conditions revealed that gene expression is modulated independently at transcript levels and translation levels. Our study revealed the translational landscape of sorghum’s response to sulfur and provides datasets that could serve as a fundamental resource to extend research on sorghum, including translational studies.
2022-11-16 | GSE184725 | GEO
Project description:This experiment contains the subset of data corresponding to sorghum RNA-Seq data from experiment E-GEOD-50464 (http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-50464/), which goal is to examine the transcriptome of various Sorghum bicolor (BTx623) tissues: flowers, vegetative and floral meristems, embryos, roots and shoots. Thus, we expanded the existing transcriptome atlas for sorghum by conducting RNA-Seq analysis on meristematic tissues, florets, and embryos, and these data sets have been used to improve on the existing community structural annotations.
2014-08-29 | E-MTAB-3839 | biostudies-arrayexpress
Project description:To verify whether phosphorus deficiency can induce sorghum to produce and secrete SLs, we conducted RNA-sequencing (RNA-seq) analyses in sorghum plants grown under phosphorus deficiency conditions; to verify which genes induced by SL treatment, we conducted RNA-sequencing (RNA-seq) analyses in sorghum plants grown under SL treatment.
2024-10-01 | GSE245050 | GEO
Project description:After experiencing drought, Sorghum bicolor generates substantial root pressure, which varies with genotype and re-watering amount.
2020-06-10 | GSE152143 | GEO
Project description:This study examines the proteomic responses in tissues of etiolated Sorghum bicolor BTx623 seedlings to salt stress (100 mM NaCl). The aim of the experiment is to investigate the induction and posssible role of Membrane Steroid Binding Protein 1 to salt tolerance in Sorghum.
2025-12-05 | PXD058939 | Pride
Project description:Plant secondary cell walls constitute the majority of plant biomass and are an important source of biomaterials. Secondary cell walls are particularly prominent in xylem cells present in the vascular tissue. Although the process of vascularization has been extensively studied in the dicot Arabidopsis thaliana, remarkably little is known about these processes in grass species despite their emerging importance as biomass feedstocks. The targeted biofuel crop Sorghum bicolor has a sequenced and well-annotated genome, making it an ideal monocot model for addressing vascularization and biomass deposition. Here we generated tissue-specific transcriptome data using laser capture microdissection in the developing vascular and non-vascular tissues of the sorghum root. Many sorghum genes with enriched expression in developing vasculature were orthologous to genes previously associated with vascular development in other species. However, a number of transcription factor families, including NAC domain, MYB and ARF varied in their complement of vascular expressed genes to a considerable degree in sorghum compared to Arabidopsis and/or maize. Differential expression of genes associated with DNA methylation and chromatin modification were identified between vascular and non-vascular cell types, implying that changes in DNA methylation may be a feature of sorghum root vascularization. To profile DNA methylation in these tissues, sodium bisulfite sequencing of laser capture microdissected tissue was performed. DNA methylation was enriched in genic regions of genes demonstrating higher expression in non-vascular tissues. Methylation in genic and intergenic regions varied by tissue type and gene expression level. Furthermore, genes involved in cell elongation showed differences in methylation levels concomitant with expression between non-vascular and vascular tissue types suggesting a novel mode by which root growth in distinct tissues may be modulated. Our results provide both a genetic and epigenetic framework for studying vascularization and secondary cell wall development in sorghum.
2016-12-30 | GSE70903 | GEO