E-GEOD-98817
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ABSTRACT:
PROVIDER: E-GEOD-98817 | ExpressionAtlas | 2020-04-30
REPOSITORIES: ExpressionAtlas
Similar Datasets
Project description:Bioenergy sorghum accumulates 75% of shoot biomass in stem internodes. Grass stem internodes are formed during vegetative growth and elongate in response to developmental and environmental signals. To identify genes and molecular mechanisms that modulate the extent of internode growth, we conducted microscopic and transcriptomic analysis of four successive sub-apical vegetative internodes representing different stages of internode development of the bioenergy sorghum genotype R.07020.
2017-08-17 | GSE98817 | GEO
Project description:Dynamics of gene expression during devepolement and expansion of vegetative stem internodes of bioenergy sorghum
| PRJNA386306 | ENA
Project description:Sorghum is multipurpose crop worldwide serving as food, feed, and feedstock for biofuels, whose floral transition and vegetative growth heavily depend on photoperiod. Although multiple sorghum maturity loci (Ma1-Ma6) have been associated with photoperiod sensitivity in previous QTL studies, the underlying molecular mechanisms remain poorly understood. By functional characterizing sorghum SbGhd7 (Ma6) and integrating RNA-seq analysis of Ghd7 overexpression sorghum, ChIP-seq analysis of SbGhd7 binding sites in protoplasts and molecular studies, we discovered that SbEhd1 and SbFT10 are the direct targets of SbGhd7. SbGhd7 is a transcriptional repressor and inhibits florigen-induced floral transition by repressing SbEhd1 and SbFT10 expression.
2024-01-30 | GSE238094 | GEO
Project description:In this study, we aim to present a global view of transcriptome dynamics during flower development in chickpea. We generated around 234 million high-quality reads for eight flower development stages (ranging from 16 to 40 million reads for each stage) and 91 million high-quality reads from three vegetative tissues using Illumina high-throughput sequencing GAII platform. Because of non-availability of reference genome sequence, we mapped the reads to chickpea transcriptome comprised of 34,760 transcripts for estimation of their transcriptional activity in different tissue samples. The transcriptome dynamics was studied by comparison of gene expression during flower development stages with vegetative tissues.
2014-01-09 | GSE42679 | GEO
Project description:In this study, we aim to present a global view of transcriptome dynamics during flower development in chickpea. We generated around 234 million high-quality reads for eight flower development stages (ranging from 16 to 40 million reads for each stage) and 91 million high-quality reads from three vegetative tissues using Illumina high-throughput sequencing GAII platform. Because of non-availability of reference genome sequence, we mapped the reads to chickpea transcriptome comprised of 34,760 transcripts for estimation of their transcriptional activity in different tissue samples. The transcriptome dynamics was studied by comparison of gene expression during flower development stages with vegetative tissues. We collected different tissue samples used in this study and total RNA isolated was subjected to Illumina sequencing. The sequenced data was further filtered using NGS QC Toolkit to obtain high-quality reads. The filtered reads were mapped to 34760 chickpea transcripts and reads per kilobase per million (RPKM) was calculated for each gene in all the sample to measure their gene expression. Differential expression analysis was performed using DESeq software. The genes preferentially expression during various stages of flower development as compared to vegetative stages and those with speciifc expression were identified.
2014-01-09 | E-GEOD-42679 | biostudies-arrayexpress
Project description:During in vitro differentiation, pluripotent stem cells undergo extensive remodeling of their gene expression profiles. While studied extensively at the transcriptome level, much less is known about protein dynamics, which might differ significantly from their mRNA counterparts. Here, we present deep proteome-wide measurements of protein levels during the differentiation of embryonic stem cells.
2017-01-10 | MSV000080461 | MassIVE
Project description:Sorghum is multipurpose crop worldwide serving as food, feed, and feedstock for biofuels, whose floral transition and vegetative growth heavily depend on photoperiod. Although multiple sorghum maturity loci (Ma1-Ma6) have been associated with photoperiod sensitivity in previous QTL studies, the underlying molecular mechanisms remain poorly understood. By functional characterizing sorghum SbGhd7 (Ma6) and integrating RNA-seq analysis of Ghd7 overexpression sorghum, ChIP-seq analysis of SbGhd7 binding sites in protoplasts and molecular studies, we discovered that SbEhd1 and SbFT10 are the direct targets of SbGhd7. SbGhd7 is a transcriptional repressor and inhibits florigen-induced floral transition by repressing SbEhd1 and SbFT10 expression.
2024-01-30 | GSE237989 | 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:Sorghum (Sorghum bicolor L. Moench) is a C4 species sensitive to the cold spring conditions that occur at northern latitudes, usually coupled with excessive light, and that greatly affects the photosynthetic rate. The objective of this study was to discover genes/genomic regions that control the capacity to cope with excessive energy under low temperature conditions during the vegetative growth period. A genome-wide association study (GWAS) was conducted for eight photosynthesis and chlorophyll fluorescence traits under three consecutive temperature treatments: control (28°C/24°C), cold (15°C/15°C) and recovery (28°C/24°C). Cold stress significantly reduced the photosynthetic capacity of sorghum plants and a total of 204 genomic regions were discovered associated with at least one trait in a particular treatment or in the time integrated response to cold. If no GBS markers were available for the targeted candidate genes, new SNPs were developed and genotyped using a SNPtype™ Assay (Fluidigm) on the Fluidigm BioMarkHD system and GT 96.96 Dynamic Array Integrated Fluidic Circuits of Fluidigm.
2017-08-10 | GSE102452 | GEO