GEO DataSets

(Submitter supplied) Tomatoes are one of the valuable sources of antioxidants such as carotenes, ascorbic acid (AsA), and phenolic compounds (flavonoids and hydroxycinnamic acid derivatives). These secondary metabolites have been proved to be beneficial for humans and animals because their involvement in the prevention of many proliferative and degenerative diseases. The aim of this work is to gain greater insights in the genetic control of phenylpropanoid accumulation in tomato fruit by using genomics-based strategies. more...

Organism:

Solanum lycopersicum

Type:

Expression profiling by array

Platform:

GPL15489

22 Samples

Download data: TXT

(Submitter supplied) We compared gene expression by microarray analysis between wild type and transgenic sibling progeny from two primary transgenic lines containing a construct for knocking down expression of both tomato fruitfull orthologs, FUL1/TDR4 and FUL2/MBP7.

Organism:

Solanum lycopersicum

Type:

Expression profiling by array

Platform:

GPL10570

8 Samples

Download data: TXT

(Submitter supplied) High levels of ascorbic acid (AsA) in tomato fruits provide health benefits for humans and also play an important role in several aspects of the plant life. Although AsA metabolism has been characterized in detail, the genetic mechanisms controlling AsA accumulation in tomatoes are poorly understood. We used an introgression line (IL 12-4) containing a QTL promoting AsA accumulation in the fruit and carried out a comparative transcriptomic analysis of fruit tissue using a parental cultivar (M82) with low AsA levels as a reference. more...

Organism:

Solanum lycopersicum

Type:

Expression profiling by array

Platform:

GPL9923

24 Samples

Download data: TXT

(Submitter supplied) 20,200 specific oligos (35-40mer) were designed on Tomato Gene Index Version 11 (LeGI v.11, June21, 2006) tentative consensus (TC) sequences by using the program design OligoArray 2.1 (Rouillard et al. 2003). As negative controls, nine bacterial oligonucleotides sequences provided by CombiMatrix were utilized. The 90K TomatArrayTM 1.0 was designed with four replicates of each probe randomly distributed across the array to allow measurement of the variability within the array. more...

Organism:

Solanum lycopersicum

3 Series

54 Samples

Download data

(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) Ascorbic acid (AsA), important for plant cell protection against oxidative stresses, is useful for human health. Among vegetables, tomato is the most important specie due to its significant consumption at worldwide level. Although AsA metabolism has been characterized in detail, the genetic mechanisms controlling AsA accumulation in tomatoes are poorly understood. We used an introgression line (IL 10-1) containing a QTL inducing a reduced AsA accumulation in the fruit and carried out a comparative transcriptomic analysis in fruit tissues using a parental cultivar (M82) with normal fruit AsA levels as a reference. more...

Organism:

Solanum lycopersicum

Type:

Expression profiling by array

Platform:

GPL9923

24 Samples

Download data: TXT

(Submitter supplied) The transformation of the ovary into a fruit after successful completion of pollination and fertilization has been associated with many changes at transcriptomic level. These changes are part of a dynamic and complex regulatory network that is controlled by phytohormones, with a major role for auxin. One of the auxin-related genes differentially expressed upon fruit set and early tomato fruit development is Solanum lycopersicum ARF9 (SlARF9). more...

Organism:

Solanum lycopersicum

Type:

Expression profiling by array

Platform:

GPL16358

15 Samples

Download data: CEL

(Submitter supplied) Purpose: Tomato (Solanum lycopersicum) serves as a research model for fruit development; however, while it is an important dietary source of antioxidant nutrients, the transcriptional regulation of genes that determine nutrient levels remains poorly understood. The goals of this study are to investigate dynamic changes of tomato genes during fruit development at transcription level and provides insight into the regulatory mechanism of fruit development and presents candidate transcription factors involved in secondary metabolism. more...

Organism:

Solanum lycopersicum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL15580

14 Samples

Download data: TXT

(Submitter supplied) We performed transcriptome analyses throughout fruit development using the tomato cultivar M82 and its near-isogenic line IL8-3, with interesting and useful traits such as a high content of soluble solids. To identify genes that show differential expression between M82 and IL8-3 fruits, we used a custom microarray containing 43,803 tomato probes. Some genes, such as cell wall invertase and sucrose synthase genes, which are encoded by LIN6 (Solyc10g083290) and TOMSSF (Solyc12g009300) respectively, are well known to play a key role in the sink function of fruit. more...

Organism:

Solanum lycopersicum

Type:

Expression profiling by array

Platform:

GPL21511

24 Samples

Download data: TXT

(Submitter supplied) Ripening is an important stage of fruit development to determine its quality as a diet. A tomato (Solanum lycopersicum) MADS-box transcription factor, RIPENING INHIBITOR (RIN), has been believed to serve as a regulator of ripening lying upstream of ethylene-dependent and ethylene-independent pathways. Here, we have conducted global gene expression analysis to comprehensively identify tomato genes whose expressions are affected by the rin mutation using microarray with RNA samples from the normal and rin mutant tomato fruits at the pre-ripening (mature green) and ripening (pink coloring) stages. more...

Organism:

Solanum lycopersicum

Type:

Expression profiling by array

Platform:

GPL10570

12 Samples

Download data: TXT

(Submitter supplied) Colletotrichum coccodes secretes ammonium during germination and colonization of host tissue as a mechanism for dual activation of fungal pathogenicity factors and plant cell death via activation of host NADPH oxidase. Ammonium accumulation during colonization of tomato fruits by C. coccodes induced host nucleus integrity changes and program cell death (PCD). Transcriptome analysis at the leading edge of colonized tissue and ammonium treated tomato fruits revealed 82 and 237 common up-regulated and common down-regulated genes, respectively. more...

Organism:

Solanum lycopersicum

Type:

Expression profiling by array

Platform:

GPL4741

8 Samples

Download data: CEL

(Submitter supplied) The tomato (Solanum lycopersicum) MADS-box transcription factor RIN, one of the earliest-acting fruit-ripening regulators, is required for both ethylene-dependent and -independent regulatory pathways for fruit ripeing. Here, we performed chromatin immunoprecipitation coupled with a DNA microarray (ChIP-chip) for the putative promoters of whole tomato predicted genes (ITAG2) for the genome-wide identification of the direct RIN targets. more...

Organism:

Solanum lycopersicum

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL15968

3 Samples

Download data: PAIR, TXT

(Submitter supplied) Phenylpropanoids are derived from phenylalanine and comprise an important class of plant secondary metabolites that include specialized bioactives with medicinal properties, important phytonutrients, a broad range of natural colours, phytoanticipins, phytoalexins and phytoestrogens. A number of transcription factors have been used to upregulate specific branches of phenylpropanoid metabolism, but by far the most effective has been the fruit-specific expression of AtMYB12 in tomato, which resulted in an astonishing 10% of fruit dry weight accumulating as flavonoids and hydroxycinnamates. more...

Organism:

Solanum lycopersicum

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL16345

2 Samples

Download data: WIG

(Submitter supplied) Phenylpropanoids are derived from phenylalanine and comprise an important class of plant secondary metabolites that include specialized bioactives with medicinal properties, important phytonutrients, a broad range of natural colours, phytoanticipins, phytoalexins and phytoestrogens. A number of transcription factors have been used to upregulate specific branches of phenylpropanoid metabolism, but by far the most effective has been the fruit-specific expression of AtMYB12 in tomato, which resulted in an astonishing 10% of fruit dry weight accumulating as flavonoids and hydroxycinnamates. more...

Organism:

Solanum lycopersicum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL15580

17 Samples

Download data: TXT

(Submitter supplied) Southern tomato virus (STV) often infects healthy tomato plants (Solanum lycopersicum). In this study, we compared STV-free and STV-infected cultivar M82 plants to determine the effect of STV infection on the host plant. STV-free plants exhibited a short and bushy phenotype, whereas STV-infected plants exhibited increased height. STV-infected plants produced more fruit than STV-free plants, and the germination rate of seeds from STV-infected plants was higher than that of seeds from STV-free plants. more...

Organism:

Solanum lycopersicum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19694

6 Samples

Download data: TXT

(Submitter supplied) In this study, we explored the metabolome and transcriptome of the ripe fruit in nine landrace accessions representing the seven genetic groups and compared them to the mature fruit of the wild progenitor S. pimpinellifolium. The goal is to shed light in understanding the factors responsible for acquiring tomato fruit quality (taste and flavour) at molecular level during the domestication process.

Organism:

Solanum lycopersicum; Solanum pimpinellifolium

Type:

Expression profiling by array

Platform:

GPL4741

30 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) To investigate the effects of transgenic lines L6 and L7 tomato fruits on total expression profile of MCF-7 breast cancer cells, we treated MCF-7 cells with 1 ug/ml of tomato fruit extract for 24 hours and compare it with wild type tomato fruit extract Objectives for this study included the identification of genes that were up or down-regulated at the transcriptional level in MCF-7 cells treated with transgenic lines L6 and L7 tomatofruit extract and compare it to wild type tomato fruit extract.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL15207

8 Samples

Download data: CEL, CHP