GEO DataSets

(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 pimpinellifolium; Solanum lycopersicum; Solanum pennellii; Solanum habrochaites

Type:

Expression profiling by high throughput sequencing

4 related Platforms

52 Samples

Download data: TXT

(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 arcanum; Solanum lycopersicum

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL24124 GPL28683

18 Samples

Download data: FASTA, TAB

(Submitter supplied) Wild halophytic tomato has long been considered as an ideal gene donor for improving salt tolerance in tomato cultivars. Here, a wild tomato genotype, Solanum pimpinellifolium ‘PI365967’ is significantly more salt-tolerant than a cultivar, Solanum lycopersicom ‘moneymaker’. Affymetrix Tomato Genome Arrays was used to compare the transcriptome change of PI365967 and Moneymaker by salt treatment.After treatment with 200 mM NaCl for 5 h, PI365967 showed relatively fewer responsive genes compared to Moneymaker. more...

Organism:

Solanum lycopersicum

Type:

Expression profiling by array

Platform:

GPL4741

12 Samples

Download data: CEL, CHP, XLS

(Submitter supplied) We explored the transcriptomic alterations associated with domestication by interrogating a developmental time course of cotton fibers from the wild G. hirsutum var. yucatanense and a representative of an elite domesticated line.

Organism:

Gossypium; Gossypium hirsutum

Type:

Expression profiling by array

Platform:

GPL6989

30 Samples

Download data: TXT

(Submitter supplied) BACKGROUND: The tomato psyllid, Bactericera cockerelli Šulc (Hemiptera: Triozidae), is a pest of solanaceous crops such as tomato (Solanum lycopersicum L.) in the U.S. and vectors the disease-causing pathogen ‘Candidatus Liberibacter solanacearum’. Currently, the only effective strategies for controlling the diseases associated with this pathogen involve regular pesticide applications to manage psyllid population density. more...

Organism:

Solanum lycopersicum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19694

6 Samples

Download data: TXT

(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 lycopersicum; Solanum pennellii

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL19694 GPL24633 GPL22916

48 Samples

Download data: XLSX

(Submitter supplied) We used Bio-Rad laboratories, lnc. PCR assay panel to analyze expression levels of bZIP genes in various biotci stress and plant hormone treatments. Tomato (Solanum lycopersicum) cv. Suhong 2003 were reared in growth chambers at 24 ± 1 °C with a photoperiod of 14 h light/10 h dark and light intensity of 200 μE m2 s-1. For analysis of gene expression, 4-week-old tomato plants were treated by foliar spraying with 100 μM methyl jasmonate (MeJA), 100 μM 1-amino cyclopropane-1-carboxylic acid (ACC), 100 μM SA or 0.1% ethanol as a control and samples were collected at indicated time points after treatment. more...

Organism:

Solanum lycopersicum

Type:

Expression profiling by RT-PCR

Platform:

GPL20829

13 Samples

Download data: TXT

(Submitter supplied) We used Bio-Rad laboratories, lnc. PCR assay panel to analyze expression levels of bZIP genes in various tissues or organs. Tomato (Solanum lycopersicum) cv. Suhong 2003 were reared in growth chambers at 24 ± 1 °C with a photoperiod of 14 h light/10 h dark and light intensity of 200 μE m2 s-1. The roots, stem,leaves, flower, and fruits were collected from flowering plants for tissue expression analysis.

Organism:

Solanum lycopersicum

Type:

Expression profiling by RT-PCR

Platform:

GPL20824

5 Samples

Download data: TXT

(Submitter supplied) [original title] Understanding the complexity of fruit ripening by transcriptome analysis of rin mutant fruit and in silico analysis of promoters of differentially regulated genes A tomato MADS-box transcription factor, LeMADS-RIN, controls fruit ripening and mutation in this gene results in non-ripening phenotype of fruit. This mutation down-regulates certain ripening related ethylene responses, however, other ethylene responses are normal. more...

Organism:

Solanum lycopersicum

Type:

Expression profiling by array

Platform:

GPL4741

18 Samples

Download data: CEL

(Submitter supplied) The size of tomato fruits are largely dependent on growth conditions. To obtain insights on how light intensity contributes to translocation from a leaf and a fruit, we developed a plant irradiation system based on light-emitting diodes (LEDs) to a leaf. By using this system, we investigated the changes of transcript profiles of tomato leaves and fruits grown under different light conditions.

Organism:

Solanum lycopersicum

Type:

Expression profiling by array

Platform:

GPL4741

20 Samples

Download data: CEL, CHP

(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) Transcriptome analysis of 7 tissues of commercial tomato (S. lycopersicum cv MoneyMaker) and its wild red-fruited ancestor (S. pimpinellifolium LA0722) genotypes performed to assess expression level of tomato transcriptome and to aid whole genome annotation. Sequencing of fruit at 3 different developmental stages will help to assess gene regulation through ripening.

Organism:

Solanum pimpinellifolium; Solanum lycopersicum

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL14847 GPL14848

9 Samples

Download data: TXT

(Submitter supplied) Small RNAs (21-24 nt) are pivotal regulators of gene expression that guide both transcriptional and post-transcriptional silencing mechanisms in diverse eukaryotes, including most if not all plants. MicroRNAs (miRNAs) and short interfering RNAs (siRNAs) are the two major types, both of which have a demonstrated and important role in plant development, stress responses and pathogen resistance. In this work, we used a deep sequencing approach (Sequencing-By-Synthesis, or SBS) to develop sequence resources of small RNAs from Solanum tuberosum tissues (including leaves, flowers and stolon). more...

Organism:

Solanum tuberosum

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL13899

3 Samples

Download data: TXT

(Submitter supplied) Small RNAs (21-24 nt) are pivotal regulators of gene expression that guide both transcriptional and post-transcriptional silencing mechanisms in diverse eukaryotes, including most if not all plants. MicroRNAs (miRNAs) and short interfering RNAs (siRNAs) are the two major types, both of which have a demonstrated and important role in plant development, stress responses and pathogen resistance. In this work, we used a deep sequencing approach (Sequencing-By-Synthesis, or SBS) to develop sequence resources of small RNAs from Solanum licopersicum tissues (including leaves, flowers and fruit). more...

Organism:

Solanum lycopersicum

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL10518

3 Samples

Download data: TXT