GEO DataSets

(Submitter supplied) 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.

Organism:

Sorghum bicolor

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13779

24 Samples

Download data: CSV

(Submitter supplied) Sorghum is an important crop often subjected to simultaneous high temperatures and drought in the field. We examined the gene expression response to heat and drought stress both individually, and in combination, with the aim of identifying important stress tolerance mechanisms.

Organism:

Sorghum bicolor

Type:

Expression profiling by array

Platform:

GPL17335

12 Samples

Download data: TXT

(Submitter supplied) We sequenced mRNA of WT, p35S:AtBBD1 (OX) and atbbd1 (KO) plants. Plants were grown in soil for three weeks at 23 ℃ with 60% relative humidity. mRNA was isolated 6 hours after threating with 20% PEG.

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19580

4 Samples

Download data: XLSX

(Submitter supplied) To dissect the molecular mechanisms underlying drought tolerance (DT) in rice, transcriptome differences of a DT introgression line H471, the DT donor P28 and the drought sensitive recurrent parent HHZ under drought stress were investigated using deep transcriptome sequencing. Results revealed a differential constitutive gene expression prior to stress and distinct global transcriptome reprogramming among three genotypes under time-series drought stress, consistent with their differential genotypes and DT phenotypes.

Organism:

Oryza sativa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13160

18 Samples

Download data: TXT

(Submitter supplied) Background: Drought stress is the major environmental stress that affects plant growth and productivity. It triggers in plants a wide range of responses detectable at different scales: molecular, biochemical and physiological levels. At the molecular level the response to drought stress results in the differential expression of several metabolic pathways. For this reason, explore the subtle differences existing in gene expression of drought sensitive and drought tolerant genotypes allows to identify drought-related genes that could be used for selection of drought tolerance traits. more...

Organism:

Sorghum bicolor

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13779

12 Samples

Download data: TXT

(Submitter supplied) To understand the role of the Arabidopsis type-B Response Regulators ARR1, ARR10 and ARR12 in water stress response, we have carried out comparative expression analysis of the arr1,10,12 mutant and WT plants under dehydration and well-watered (control) conditions. Agilent’s whole Arabidopsis Gene Expression Microarray (G2519F-021169, V4, 4x44K) was used.

Organism:

Arabidopsis thaliana

Type:

Expression profiling by array

Platform:

GPL12621

18 Samples

Download data: TXT

(Submitter supplied) Purpose: To study the effects of drought at the transcriptomic level on two different actively dividing maize tissue: the ovaries, and the leaf meristem Methods: The Illumina reads were mapped to the maize B73 reference genome using Tophat followed by transcriptome reconstruction using Cufflinks. The FPKM valuse were extracted from cufflinks output and an R package called Limma was used to identify differentially expressed genes under drought under both tissues Results and Conclusions: Different processes which were differentially expressed under drought in both tissues were identified and analyzed in detail. more...

Organism:

Zea mays

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13977

8 Samples

Download data: TXT

(Submitter supplied) Purpose: to screen the candidate genes involved in the peanut drought stress response, we conducted global transcriptome analysis of peanut plants challenged with water deficit and ABA, using the Illumina HiSeq2000 sequencing platform. Methods: a sequences library of Yueyou7 were constructed at first. Then the profile of diffentialy expressed genes (DEGs) under three different treatments (control, water deficit without ABA, and water deficit with ABA) were conducted based on above sequence library. more...

Organism:

Arachis hypogaea

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18517

3 Samples

Download data: FASTA, TXT, XLSX

(Submitter supplied) Sorghum is an important cereal crop, which requires large quantities of nitrogen fertilizer for achieving commercial yields. Identification of the genes responsible for low-N tolerance in sorghum will facilitate understanding of the molecular mechanisms of low-N tolerance, and also facilitate the genetic improvement of sorghum through marker-assisted selection or gene transformation. In this study we compared the transcriptomes of root tissues from seven sorghum genotypes having different genetic backgrounds with contrasting low-N tolerance by the RNAseq deep sequencing data. more...

Organism:

Sorghum bicolor

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13779

28 Samples

Download data: TXT

(Submitter supplied) Background: The investigation of extremophile plant species growing in their natural environment offers certain advantages, chiefly that plants adapted to severe habitats have a repertoire of stress tolerance genes that are regulated to maximize plant performance under physiologically challenging conditions. Accordingly, transcriptome sequencing offers a powerful approach to address questions concerning the influence of natural habitat on the physiology of an organism. more...

Organism:

Eutrema salsugineum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17514

10 Samples

Download data: TXT

(Submitter supplied) Our study provides the first comprehensive insight into the comparative transcriptome between shoot and rhizome in sorghum propinquum. Using the deep RNA sequencing technique, more than 70% of genes were identified to be expressed. Comparative analysis revealed that a strong difference in gene expression patterns between shoot and rhizome organs, especially a set of organ-specific TF genes and cis-elements were determined, implying a unique complicated molecular network controlling shoot or rhizome growth and development. more...

Organism:

Sorghum propinquum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16583

2 Samples

Download data: TXT

(Submitter supplied) We developed a commercially available whole-transcriptome sorghum microarray (Sorgh-WTa520972F) and generated this dataset to identify tissue and genotype-specific expression patterns for all identified Sorghum bicolor exons and UTRs. The genechip contains 1,026,373 probes covering 149,182 exons (27,577 genes) across the Sorghum bicolor nuclear, chloroplast and mitochondrial genomes. Specific probesets were also included for putative non-coding RNAs that may play a role in gene regulation (e.g., microRNAs), and confirmed functional small RNAs in related species (corn and sugarcane) were also included in our array design.

Organism:

Sorghum bicolor; Saccharum hybrid cultivar; Zea mays subsp. mays

Type:

Expression profiling by array; Non-coding RNA profiling by array

Platform:

GPL17576

78 Samples

Download data: CEL

(Submitter supplied) 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. more...

Organism:

Sorghum bicolor

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL20690

12 Samples

Download data: CSV

(Submitter supplied) We conducted a large-scale field experiment, imposing pre- and post-flowering drought stress on two genotypes of sorghum across a tightly-resolved time series, resulting in a data set of over 350 transcriptomes root and shoot tissue.

Organism:

Sorghum bicolor

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL21615 GPL20818

395 Samples

Download data: FA, GFF3, TXT

(Submitter supplied) As no commercial array is available for sorghum microarray analysis, we designed an array based on the annotation of Sbi1.4 gene set and the available 209,835 sorghum ESTs from the NCBI EST database. The array will be used for investigating the expression divergence between grain and sweet sorghum lines under normal and sucrose treatments

Organism:

Sorghum bicolor

Type:

Expression profiling by array

Platform:

GPL15369

12 Samples

Download data: TXT

(Submitter supplied) Sorghum (Sorghum bicolor) is one of the world's most important cereal crops. S. propinquum is a perennial wild relative of S. bicolor with well-developed rhizomes. Functional genomics analysis of S. propinquum, especially with respect to molecular mechanisms related to rhizome growth and development, can contribute to the development of more sustainable grain, forage, and bioenergy cropping systems. more...

Organism:

Oryza sativa; Sorghum propinquum

Type:

Expression profiling by array

Platform:

GPL6864

15 Samples

Download data: TXT

(Submitter supplied) Plant survival in adverse environmental conditions requires a substantial change in the metabolism, which is reflected by the extensive transcriptome rebuilding upon the occurrence of the stress. Therefore, transcriptomic studies offer an insight into the mechanisms of plant stress responses. Here, we present the results of global gene expression profiling of roots and leaves of two barley genotypes with contrasting ability to cope with drought stress. more...

Organism:

Hordeum vulgare

Type:

Expression profiling by array

Platform:

GPL14927

24 Samples

Download data: TXT

(Submitter supplied) We performed a transcriptomic analysis on two tomato genotypes, M82 and Tondo, in response to a PEG-mediated osmotic treatment, mimicking water stress. The analysis was conducted separately on leaves and roots to characterize the specific response of these two organs. A total of 6,267 differentially expressed transcripts related to osmotic stress response was detected. The construction of gene co-expression networks defined the metabolic and signaling pathways of the common and specific responses of leaf and root. more...

Organism:

Solanum lycopersicum

Type:

Expression profiling by array

Platform:

GPL33096

24 Samples

Download data: XLSX

(Submitter supplied) Crop resilience and yield stability are complex traits essential for food security. Sorghum bicolor is an important grain crop that shows promise for its natural resilience to drought and potential for marginal land production. We have developed sorghum lines in the Tx430 genetic background suppressed for MSH1 expression as a means of inducing de novo epigenetic variation and have used these materials to evaluate changes in plant growth vigor. more...

Organism:

Sorghum bicolor

Type:

Expression profiling by high throughput sequencing

Platform:

GPL31003

5 Samples

Download data: TXT

(Submitter supplied) Identify the change in transcriptomic and epigenetic profiles within the sorghum root system of the cultivar BTx623 in response to limiting phosphorus conditions. This data is from the 2022 publication "Sorghum root epigenetic landscape during limiting phosphorus conditions".

Organism:

Sorghum bicolor

Type:

Methylation profiling by high throughput sequencing; Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL21615 GPL20818

34 Samples

Download data: BW, CSV, TSV