GEO DataSets

(Submitter supplied) Tomato is one of the most important crops for human consumption. Unfortunately, its production is affected by diseases caused by pathogens such as the actynomicete Clavibacter michiganensis subsp. michiganens (Cmm). This pathogen is the causal agent of the bacterial canker of tomato, considered one of the most devastating tomato diseases. To date, there are not resistant varieties of commercial tomato against Cmm. more...

Organism:

Solanum lycopersicum; Solanum arcanum

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL28683 GPL24124

18 Samples

Download data: FASTA, TAB

(Submitter supplied) The gram- positive bacterial pathogen Clavibacter michiganensis subsp. michiganensis (Cmm) causes huge economic losses by infecting tomato plants worldwide. Cmm can be spread by contaminated seeds and transplants, penetrating the plant through natural openings or wounds and is transferred through the plant xylem. While in recent years significant progress has been made to elucidate plant responses to pathogenic gram-negative bacteria by gene expression studies, the molecular mechanisms that lead to disease symptoms caused by gram-positive bacteria like Cmm remain elusive. more...

Organism:

Solanum lycopersicum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26877

4 Samples

Download data: XLS

(Submitter supplied) Purpose: Investigate genes associated to resistance of Xanthomonas perforans race T4 in tomato line with different resistance level Methods: Resistant and susceptible tomato breeding lines were subjected to the inoculation with Xanthomonas perforans race T4 followed by sample collection at 48 hpi and RNA-seq analysis for screening differential expressed genes associated with inoculation of pathogen. more...

Organism:

Solanum lycopersicum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19694

12 Samples

Download data: TXT

(Submitter supplied) ‘Candidatus Liberibacter solanacearum’ (Lso) has emerged as a major pathogen of crops worldwide. This bacterial pathogen is transmitted by Bactericera cockerelli, tomato psyllid, to solanaceous crops. In this study, the transcriptome profiles of Solanum lycopersicum exposed to B. cockerelli infestation and to Lso infection were evaluated at one, two and four weeks following colonization and/or infection. more...

Organism:

Solanum lycopersicum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19694

26 Samples

Download data: GTF, XLS

(Submitter supplied) The leaf miner, Tuta absoluta, is a notorious destructive pest of tomato that causes important losses worldwide. Breeding of resistant/tolerant tomato cultivars could be an effective strategy for T. absoluta management but, despite the economic importance of tomato, very limited information is available about its response to this treat. To elucidate the defense mechanisms to the herbivore feeding a comparative analysis was performed between a tolerant and susceptible cultivated tomato at both morphological and at transcriptome level to highlight constitutive leaf barriers, molecular and biochemical mechanisms to counter the effect of T. more...

Organism:

Solanum lycopersicum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26313

8 Samples

Download data: TXT

(Submitter supplied) Bacterial wilt caused by Ralstonia solanacearum is a lethal, soil-borne disease of tomato. Control of the disease with chemicals and crop rotation is insufficient, because the pathogen is particularly well adapted for surviving in the soil and rhizosphere. Therefore, cultivar resistance is the most effective means for controlling bacterial wilt, but the molecular mechanisms of resistance responses remain unclear. more...

Organism:

Solanum lycopersicum

Type:

Expression profiling by array

Platform:

GPL4741

12 Samples

Download data: CEL

(Submitter supplied) Leaf mold disease caused by Cladosporium fulvum is a major disease in cultivated tomato plants and affects global tomato production. Some Cf genes, of which Cf-16 is an effective gene for resisting tomato leaf mold, are associated with leaf mold resistance; however, the molecular mechanism is largely unknown. We used comparative transcriptome analysis of C. fulvum-resistant (cv. Ontario7816, including the Cf-16 gene) and C. more...

Organism:

Solanum lycopersicum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26877

24 Samples

Download data: TXT

(Submitter supplied) To test the hypothesis that gene expression by the fungal partner in this beneficial interaction is modulated by the plant host, Trichoderma virens was co-cultured with maize or tomato in a hydroponic system allowing interaction with the roots. The transcriptomes for T. virens alone were compared with fungus-inoculated tomato or maize roots by hybridization on oligonucleotide microarrays Based on the relevant role of Trichoderma virens as a biological control agent this study provides a better knowledge of its crosstalk with plants in a host-specific manner.

Organism:

Trichoderma virens

Type:

Expression profiling by array

Platform:

GPL19568

11 Samples

Download data: TXT

(Submitter supplied) RNA sequencing in tomato for detect mRNA expression of Solanum lycopersicum flower.The two cultivars (monomaker, raceme) had three different flowering stages (budlet, Flower bud, Full bloom) for transcriptome sequencing

Organism:

Solanum lycopersicum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26877

18 Samples

Download data: XLS

(Submitter supplied) The simultaneous gene fungal-fruit expression at appressoria, quiescence and necrotrophic stages in C. gloeosporioides-tomato fruit interaction were characterized by Illumina NGS. Fungal appressoria stage on green fruit showed stage-specific transcription and was accompanied by massive fruit transcriptional defense response. The quiescent fungal transcriptome showed activation of chromatin remodeling genes while the fruit response continued a highly integrated and massive up-regulation of defense genes. more...

Organism:

Colletotrichum gloeosporioides; Solanum lycopersicum

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL16345 GPL18373

5 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) 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) RNA-seq of seedlings of four tomato species Solanum habrochaites, Solanum lycopersicum, Solanum pimpinelliolium, and Solanum pennellii. An additional panel of samples include many tissues from Solanum lycopersicum and Solanum pennellii in two light conditions

Organism:

Solanum lycopersicum; Solanum pennellii; Solanum habrochaites; Solanum pimpinellifolium

Type:

Expression profiling by high throughput sequencing

4 related Platforms

52 Samples

Download data: TXT

(Submitter supplied) To determine which genes were directly regulated by SlWRKY33 under cold stress, we performed ChIP-seq of SlWRKY33-OE plants with and without cold treatment.

Organism:

Solanum lycopersicum

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL27957

4 Samples

Download data: BW, FA

(Submitter supplied) We report the global wound-induced gene expression profile to compare the underlying transcriptional mechansims among S. lycopersicum, jasmonic acid–insensitive1 (jai1) and S. pennellii.

Organism:

Solanum pennellii; Solanum lycopersicum

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL19694 GPL22916 GPL24633

48 Samples

Download data: XLSX

(Submitter supplied) Gene-to-gene coexpression analysis is a powerful approach to infer function of uncharacterized genes. To perform non-targeted coexpression analysis of tomato genes, we collected a developmental gene expression dataset using various tissues of tomato plant. Expression data are collected from 24 different tissue types including root, hypocotyl, cotyledon, leaf at different stages, and fruit tissues at 4 different ripening stages from 4 different Solanum lycopersicum cultivars. more...

Organism:

Solanum lycopersicum

Type:

Expression profiling by array

Platform:

GPL4741

67 Samples

Download data: CEL, CHP

(Submitter supplied) Employing high-throughput sequencing and advanced microscopy techniques, we explored twenty-six histone modifications and Pol II distribution landscape in tomato (Solanum lycopersicum). Our findings revealed a comprehensive epigenetic landscape, uncovering distinct chromatin states associated with heterochromatin formation and gene silencing, allowing for the classification of genomic regions.

Organism:

Solanum lycopersicum

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL21762

8 Samples

Download data: BIGWIG

(Submitter supplied) Employing high-throughput sequencing and advanced microscopy techniques, we explored twenty-six histone modifications and Pol II distribution landscape in tomato (Solanum lycopersicum). Our findings revealed a comprehensive epigenetic landscape, uncovering distinct chromatin states associated with heterochromatin formation and gene silencing, allowing for the classification of genomic regions.

Organism:

Solanum lycopersicum

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL21762

4 Samples

Download data: BIGWIG

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

Organism:

Solanum lycopersicum

Type:

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

Platforms:

GPL27957 GPL21762

51 Samples

Download data: BIGWIG, BROADPEAK, NARROWPEAK

(Submitter supplied) Employing high-throughput sequencing and advanced microscopy techniques, we explored twenty-six histone modifications and Pol II distribution landscape in tomato (Solanum lycopersicum). Our findings revealed a comprehensive epigenetic landscape, uncovering distinct chromatin states associated with heterochromatin formation and gene silencing, allowing for the classification of genomic regions.

Organism:

Solanum lycopersicum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL27957

6 Samples

Download data: TXT