Sorghum bicolor
Ontology highlight
ABSTRACT:
OTHER RELATED OMICS DATASETS IN: E-MTAB-4273
REPOSITORIES: ENA
Similar Datasets
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 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: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:Comparative RNA-seq analysis of MAMP triggered gene expression in two sorghum bicolor lines, BTx623 and SC155-14E, revealed a clear transcriptional response to elicitation with the microbe associated molecular pattern (MAMPs) flagellin (flg22) or chitin elicitation.
2020-06-06 | GSE151860 | GEO
Project description:This study utilized next generation sequencing technology (RNA-Seq) to examine the transcriptome of sorghum plants challenged with osmotic stress and exogenous abscisic acid (ABA) to elucidate those genes and gene networks that contribute to sorghum's tolerance to water-limiting environments with a long-term aim of developing strategies to improve plant productivity under drought. We examined the mRNA of 9 day old Sorghum bicolor (BTx623) from 2 tissue types (roots and shoots) for 2 treatments (20 uM ABA and 20% PEG) with corresponding controls (0.2M NaOH and H2O) for 27 hrs prior to harvesting, each done in triplicate biological replicates - resulting in 24 unique runs
2011-10-26 | E-GEOD-30249 | biostudies-arrayexpress
Project description:Sorghum plants (Btx623 background) were grown in a glasshouse between March and May 2014. At panicle emergence, two biological replicates of flag leaf tissue and two biological replicates of emerging panicle tissue were harvested and used for RNA extraction. Btx623 is a non-shattering Sorghum accession, thus in the future we would like to add additional samples from accessions with varying degrees of seed shattering. This dataset will be useful for future comparisons of 1) shattering individuals at these stages and 2) additional flowering developmental time points in a variety of accessions (http://www.rnaseqforthenextgeneration.org/profiles/carrie-thurber.html#research)
2015-08-19 | E-MTAB-4203 | biostudies-arrayexpress
Project description:Parallel Analysis of RNA Ends (PARE) sequencing reads were generated to validate putative microRNAs and identify cleavage sites in Sorghum bicolor and Setaria viridis.
2020-05-19 | GSE150798 | GEO
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:We selected 11 tissues from sorghum reference genome line BTX623 for comparative study between Maize and sorghum. These 11 tissues were selected at different development stages at Cold Spring Harbor Laboratory upland farm, RNA were extracted, library was made and sequenced on HiSeq2500 PE125 platform at Woodbury Genome Center.
2018-07-31 | E-MTAB-5956 | biostudies-arrayexpress
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