GEO DataSets

(Submitter supplied) Using RNA-seq to study the transcription level of genes in WT and slnor mutant

Organism:

Solanum lycopersicum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25655

12 Samples

Download data: TXT

(Submitter supplied) Using WGBS-seq to study the methylation level of genes in WT, slnor, and sldml2 mutants

Organism:

Solanum lycopersicum

Type:

Methylation profiling by high throughput sequencing

Platforms:

GPL25655 GPL19694

14 Samples

Download data: BW

(Submitter supplied) DNA affinity purification sequencing for WUSCHEL in tomato flower abscission zone

Organism:

Solanum lycopersicum

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL25655

2 Samples

Download data: BW, NARROWPEAK

(Submitter supplied) Tomato seedlings with coated seeds of 12days responding to an Artemissia Absinthium essential oil shows increased tolarance to Fusarium

Organism:

Solanum lycopersicum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25655

24 Samples

Download data: TXT

(Submitter supplied) Postharvest fungal pathogens benefit from the increased host susceptibility that occurs during fruit ripening. In unripe fruit, pathogens often remain quiescent and unable to cause disease until ripening begins, emerging at this point into destructive necrotrophic lifestyles that quickly result in fruit decay. Here, we demonstrate that one such pathogen, Botrytis cinerea, actively induces ripening processes in order to facilitate infections and promote disease. more...

Organism:

Botrytis cinerea; Solanum lycopersicum

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL28361 GPL25655

18 Samples

Download data: CSV

(Submitter supplied) We report that Moniliophthora perniciosa biotype-S, which infects Solanaceae, manipulates the tomato Micro-Tom (MT) cytokinin (CK) metabolism. We evaluated the transcriptome of wild-type MT plants and of the transgenic line that overexpresses the Arabidopsis CYTOKININ OXIDASE-2 gene (35S::AtCKX2) inoculated or not with M. perniciosa at 12, 24, and 48 hours after inoculation (hai), and 5, 10, 20, and 30 days after inoculation (dai).

Organism:

Solanum lycopersicum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25655

130 Samples

Download data: TXT

(Submitter supplied) Combinational analyses of genome-wide transcription, binding sites and histone H3K4 trimethylation profiles revealed that SlJMJ7 directly binds and represses the expression of a series of key ripening-associated factors, including ethylene biosynthesis genes ACS2/4/8 and ACO2, DNA demethylase DML2, as well as the ripening-related transcription factors RIN and NOR by removal the mark of H3K4-trimethylation. more...

Organism:

Solanum lycopersicum

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL25655

6 Samples

Download data: BW

(Submitter supplied) This study evaluates the transcriptional response of Solanum lycopersicum cv. Fla. 8000 (wild-type and dmr6 mutants) to the pathogen Xanthomonas gardneri 153.

Organism:

Solanum lycopersicum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25655

24 Samples

Download data: TXT

(Submitter supplied) Plants communicate with each other using specific volatiles to warn of attacks and thus are able to activate defense mechanisms that make them more robust against external aggressions. In this research, we have activated defense responses of tomato plants by exposing them to two synthetic Herbivore Induced Plant Volatiles (HIPVs): (Z)-3-hexenyl propanoate (HP) [(Z)-3-HP] and methyl salicylate (MeSA). more...

Organism:

Solanum lycopersicum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25655

12 Samples

Download data: GTF, TAB, TXT

(Submitter supplied) Plant species have evolved specialized cell types and regulatory programs. To understand this diversity, we profiled tomato cell type translatomes and chromatin accessibility. While cell type expression signatures are diverse, some genes exhibit robust cell type expression across time and environments. Using xylem differentiation as a model, newly described, repurposed and conserved genes illustrate this spatial variation. more...

Organism:

Solanum lycopersicum; Oryza sativa Japonica Group

Type:

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

Platforms:

GPL21762 GPL25655 GPL21812

145 Samples

Download data: BED, BW, CSV

(Submitter supplied) The study of climacteric fruit ripening in tomato has been facilitated by the spontaneous ripening mutants Colorless non-ripening (Cnr), non-ripening (nor), and ripening inhibitor (rin). These mutants effect the genes encoding ripening transcription factors (TFs) SPL-CNR, NAC-NOR, and MADS-RIN causing pleiotropic defects to the ripening program. Here, we demonstrate that some ripening processes occur in the mutant fruit but at later stages of development compared to the wild type. more...

Organism:

Solanum lycopersicum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25655

8 Samples

Download data: TXT

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

Organism:

Arabidopsis thaliana; Solanum lycopersicum

Type:

Methylation profiling by high throughput sequencing; Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing

5 related Platforms

54 Samples

Download data: TXT

(Submitter supplied) Bisulfite (methylome) sequencing of progenies of Rutgers CV. Wild type grafted on Rutgers MSH1-RNAi line; Rutgers CV. Wild type grafted on Rutgers Wild type

Organism:

Solanum lycopersicum

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL25655

6 Samples

Download data: TXT

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

Organism:

Solanum lycopersicum

Type:

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

Platforms:

GPL25655 GPL27957

24 Samples

Download data: BW

(Submitter supplied) Here, we found that the tomato jmjC domain-containing gene SlJMJ6 encodes a histone lysine demethylase that specifically demethylates H3K27 methylation. Overexpression of SlJMJ6 accelerated fruit ripening in tomato, which is associated with the up-regulated expression of a large number of ripening-related genes. Integrated analysis of RNA-seq and ChIP-seq data identified 55 genes that are targeted directly by SlJMJ6 and transcriptionally up-regulated with decreased H3K27m3 in SlJMJ6 overexpressing (SlJMJ6-OE) fruits. more...

Organism:

Solanum lycopersicum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25655

6 Samples

Download data: TXT

(Submitter supplied) The increased susceptibility of ripe fruit to fungal pathogens poses a substantial threat to crop production and marketability. Here, we coupled transcriptomic analyses with mutant studies to uncover critical genes and processes governing ripening-associated susceptibility in tomato (Solanum lycopersicum) fruit. Using wild-type unripe and ripe fruit inoculated with three fungal pathogens—Botrytis cinerea, Fusarium acuminatum, and Rhizopus stolonifer—we identified common pathogen response genes reliant on chitinases, WRKY transcription factors, and reactive oxygen species detoxification. more...

Organism:

Solanum lycopersicum; Botrytis cinerea; Rhizopus stolonifer; Fusarium acuminatum

Type:

Expression profiling by high throughput sequencing

4 related Platforms

126 Samples

Download data: CSV

(Submitter supplied) Purpose: Circular RNAs (circRNAs) and microRNAs (miRNAs) play important roles in abiotic stress responses in plants. The aims of this study are to genome-widely identify the circRNAs, miRNAs and their targets in tomatoes at single heat, drought and their combination by high-throughput sequencing. Results: Following high-throughput sequencing, 765 miRNAs were identified in total with 335 conserved and 430 novel miRNAs in the 12 small-RNA libraries. more...

Organism:

Solanum lycopersicum

Type:

Non-coding RNA profiling by high throughput sequencing; Other

Platforms:

GPL25655 GPL19694

36 Samples

Download data: XLSX

(Submitter supplied) In this study, we identifyed the LncRNAs expressed in S. lycopersicum leaves under different para-hydroxybenzoic acid concentration treatments.

Organism:

Solanum lycopersicum

Type:

Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing

Platform:

GPL25655

9 Samples

Download data: FA, TXT

(Submitter supplied) We used Ribo-seq (Ribosome profiling) combining with RNA-seq to explore the translational landscape of tomato roots. We generated three biological replicates of RNA-seq and Ribo-seq data for tomato roots. We next used the RNA-seq result for de novo transcriptome assembly and Ribo-seq to identify novel translated open reading frames (ORFs). Our data revealed more than three hundreds of novel translated ORFs on previously unannotated transcripts. more...

Organism:

Solanum lycopersicum

Type:

Other

Platform:

GPL25655

6 Samples

Download data: BED, GTF

(Submitter supplied) Worldwide, 20-25% of all harvested fruit and vegetables are lost annually in the field and throughout the postharvest supply handling chain due to spoilage by fungal pathogens. Most impactful postharvest pathogens exhibit necrotrophic lifestyles, resulting in rotting of the host tissues and complete loss of marketable commodities. Necrotrophic fungi can readily infect ripe fruit leading to the rapid establishment of disease symptoms. more...

Organism:

Rhizopus stolonifer; Fusarium acuminatum; Solanum lycopersicum; Botrytis cinerea

Type:

Expression profiling by high throughput sequencing

4 related Platforms

52 Samples

Download data: CSV, FASTA