GEO DataSets

(Submitter supplied) Large number of genes whose expression cycles are controlled by circadian rhythm. Circadian period and phase changes were positively selected during domestication in tomato. However, the effect of RNA metabolism on circadian gene oscillations remains largely unclear. In this study, we performed transcriptome and degradome termed genome-wide mapping of uncapped and cleavage transcripts (GMUCT) in tomato leaves at 6 time points in one circadian period. more...

Organism:

Solanum lycopersicum

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL16345

36 Samples

Download data: TXT

(Submitter supplied) Phosphate is a necessary macronutrient for basic biological processes, plant growth, and agriculture. Plants modulate their root system architecture and cellular processes to adapt to phosphate deprivation albeit with a growth penalty. Excess application of phosphate in the form of fertilizer can lead to eutrophication and has negative environmental impact. Moreover, phosphate mined from rock reserves is a finite and non-recyclable resource and its levels are nearing complete depletion. more...

Organism:

Solanum lycopersicum; Solanum pennellii

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL22467 GPL16345

32 Samples

Download data: CSV

(Submitter supplied) In order to study the role of SlLBD40 and WRKY37 in seed germination, we established two gene knockout lines respectively. We then used RNA-seq data from seeds 6 h after imbibition of WT and two gene knockout lines for gene expression profiling.

Organism:

Solanum lycopersicum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16345

9 Samples

Download data: TXT

(Submitter supplied) This study assayed the gene expression changes in response to chilling stress in the shoots and roots of tomato seedlings. Both a pretreatment and a concurrent ambient control were sampled to contrast gene expression.

Organism:

Solanum lycopersicum

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL16345 GPL27957

27 Samples

Download data: TXT

(Submitter supplied) Purpose: Grafting is a commonly used cultural practice to counteract salt stress and is especially important for vegetable production. However, it is not clear which metabolic processes and genes are involved in the response of tomato rootstocks to salt stress. Our goals is to elucidate the regulatory mechanism through which grafting enhances salt tolerance. Methods: The salt-sensitive tomato variety Zhongza 9 and the strongly salt-tolerant tomato rootstock variety QZ-006 (selected by the research group in the early stage) were used as experimental materials and were purchased from the Vegetable and Flower Institute of the Chinese Academy of Agricultural Sciences (Beijing, CHN) and Beijing Kaixingelin Agricultural Technology Co., Ltd. more...

Organism:

Solanum lycopersicum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16345

36 Samples

Download data: TXT

(Submitter supplied) Adverse environmental conditions, such as salinity, heat waves, or water scarcity have a devastating impact on plant productivity. In nature, multiple abiotic stresses occur simultaneously and plants evolved unique responses to cope against combination stress that are not induced under a single stress condition. Here we coupled genome-wide transcriptional profiling and untargeted metabolomics with physiological and biochemical analyses to characterize the effect of salinity and heat applied jointly in the metabolism of tomato plants. more...

Organism:

Solanum lycopersicum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16345

12 Samples

Download data: CSV

(Submitter supplied) We report transcripts from tomato:tomato and pepper:pepper self-grafts, and tomato:pepper and pepper:tomato hetergrafts over 4 time points: 24 hours after grafting, 3 days after grafting, 5 day after grafting, and 2 weeks after grafting Examination of 4 graft combinations over 4 time points

Organism:

Capsicum annuum; Solanum lycopersicum

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL16195 GPL26701 GPL16345

58 Samples

Download data: TXT

(Submitter supplied) We report the effect of chalcone isomerase deficiency on gene expression of glandular cells of type VI trichome in tomato leaves.

Organism:

Solanum lycopersicum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16345

24 Samples

Download data: TXT

(Submitter supplied) We report the transcriptome difference between glandular cells of type VI trichome and leaf cells of trichome shaved leaf.

Organism:

Solanum lycopersicum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16345

8 Samples

Download data: TXT

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Solanum lycopersicum

Type:

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

Platform:

GPL16345

10 Samples

Download data: TAR, TXT

(Submitter supplied) Purpose: To identify genes regulated by SlDOF1 during fruit ripening, we performed RNAseq experiments with three biological replicates and compared the transcriptom profiles of SlDOF1-RNAi and wild-type fruit at breaker stage. Methods: Expression profiles of wild-type (wt) and SlDof1-RNAi fruits (SlDof-8-RNAi) at 38 days after poliation (dpa) were generated by deep sequencing with three replicates using Illumina HiSeqTM 2000. more...

Organism:

Solanum lycopersicum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16345

6 Samples

Download data: TXT

(Submitter supplied) We used the mode-based analysis of ChIP-seq (MACS) to identify a total of 18375, 14938, and 13680 peaks from the three biological replicates, respectively. SlDof1 target genes are involved in a variety of metabolic pathways and further analysis verified that SlDof1 direct regulates some well-known ripening-related genes.Our data suggest that SlDof1 acts as both activator and repressor, and these findings contribute to understanding the transcriptional regulatory networks underlying fruit ripening.

Organism:

Solanum lycopersicum

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL16345

4 Samples

Download data: TAR

(Submitter supplied) Purpose: We used transcriptome sequencing to study the regulated mechanism of VvSUC11,VvSUC12,or VvSUC27 on tomato fruit growth. Methods: the 35S:: VvSUC11, VvSUC12, and VvSUC27 constructs were introduced into transgenic tomatoes (Micro-Tom) by the Agrobacterium-mediated transformation, 5 DPA (days after anthesis) fruit was collected, 3 replicates per group. Extract total RNA, detect RNA quality, library preparation, sequencing, and analyze data. more...

Organism:

Solanum lycopersicum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16345

12 Samples

Download data: TXT

(Submitter supplied) Cyclophilin A/DIAGEOTROPICA (DGT) has been linked to auxin-regulated development in tomato and appears to affect multiple developmental pathways. Loss of DGT function results in a pleiotropic phenotype that is strongest in the roots, including shortened roots with no lateral branching. Here, we present an RNA-Seq dataset comparing the gene expression profiles of wildtype (Ailsa Craig variety) and dgt tissues from three spatially separated developmental stages of the root tip (differentiation zone, elongation zone, and meristem), with three replicates for each tissue and genotype.

Organism:

Solanum lycopersicum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16345

18 Samples

Download data: TXT

(Submitter supplied) Transcription factors (TFs) are important regulators of plant growth and development and responses to stresses. TFs themselves are also susceptible to multiple post-translational modifications (PTMs). Relatively, redox-mediated PTM of TFs in plants is not well elucidated. Here, we found that NON-RIPENING (NOR), a master TF regulating tomato fruit ripening, is a target of SlMsrE4 or SlMsrB2, the methionine sulfoxide reductase A and B in tomato, respectively. more...

Organism:

Solanum lycopersicum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16345

9 Samples

Download data: XLS

(Submitter supplied) In order to investigate the possible molecular mechanisms of SlMYB14 function in plant growth and stress responses, we employed the RNA-seq approach to identify the genes with altered expression levels in SlMYB14 transgenic plants.

Organism:

Solanum lycopersicum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16345

6 Samples

Download data: XLSX

(Submitter supplied) In response to biotic stress, plants produce suites of highly modified fatty acids that bear unusual chemical functionality. Despite their chemical complexity and proposed roles in pathogen defense, little is known about the biosynthesis of these decorated fatty acids in plants. Falcarindiol is a prototypical acetylenic lipid present in carrot, tomato, and celery that inhibits growth of fungi and human cancer cell lines. more...

Organism:

Solanum lycopersicum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16345

54 Samples

Download data: TXT

(Submitter supplied) A systems-level study identifies inter-specific translational regulation as important in the elevated CO2 response in two Solanum species

Organism:

Solanum pennellii; Solanum lycopersicum

Type:

Expression profiling by high throughput sequencing; Other

Platforms:

GPL16345 GPL22467

512 Samples

Download data: CSV, TXT

(Submitter supplied) Proteomics and transcriptomics data of tomato fruits (Solanum lycopersicum L. var. Moneymaker) at 9 developmental stages were used to calculate with a mathematical model the rate constants of synthesis and degradation for over 1,000 proteins. Proteome and transcriptome were extracted from the pericarp tissue and analyzed using label-free LC-MS/MS (Orbitrap Q-Exactive) and RNA Sequencing (Illumina), respectively. more...

Organism:

Solanum lycopersicum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16345

26 Samples

Download data: XLSX

(Submitter supplied) Global temperature increase poses a serious challenge for agricultural production worldwide, affecting yield in many crops including vegetable crops. While most crop plants can survive temperature increases during their vegetative growth periods, the reproduction phase is highly heat-stress (HS)-sensitive. Impaired pollen development and functioning under HS is implicated as the major cause for yield reduction. more...

Organism:

Solanum lycopersicum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16345

4 Samples

Download data: TXT