GEO DataSets

(Submitter supplied) Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goal of this study is genome wide association mapping for cold tolerance and yield studies in tomato (Solanum spp.) by phenotyping the genotypes under six diffrent temporal arrangments. Also for conducting quantitative reverse transcription polymerase chain reaction (qRT–PCR) assay of cold tolerant genes.

Organism:

Solanum chilense; Solanum lycopersicum var. cerasiforme; Solanum peruvianum; Solanum pimpinellifolium; Solanum lycopersicum; Solanum habrochaites

Type:

Genome variation profiling by high throughput sequencing

6 related Platforms

50 Samples

Download data: VCF

(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) This study is to decipher the effect of SUN overexpressed NIL on gene expression during fruit development in tomato. RNA libraries were sequenced through Illumina Nextseq500 at Georgia Genomics and Bioinformatics Core (GGBC) of University of Georgia for 75 bp single end sequencing. Clean reads were mapped to ITAG3.2. Processed data are normalized into TPM.

Organism:

Solanum pimpinellifolium

Type:

Expression profiling by high throughput sequencing

Platform:

GPL27047

56 Samples

Download data: TXT

(Submitter supplied) The goal of this study is to decipher the effect of the lc and fas mutations on gene expression during floral development in tomato as well as determining the effect of strongly downregulating tomato CLV3 using the RNAi strategy. The strand-specific RNA libraries were sequenced through Illumina HiSeq2000 at Genomic Resources Core Facility at Weill Cornell Medical College for 50 bp single–end sequencing. more...

Organism:

Solanum pimpinellifolium

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16804

72 Samples

Download data: CSV

(Submitter supplied) The goal of this study is to decipher the effect of the tomato lc and fas mutation on gene expression during floral development in tomato. The 3'Tag RNA libraries were sequenced on a Illumina HiSeq2500 at Genomic Resources Core Facility at Weill Cornell Medical College for 100 bp single–end sequencing. Total raw reads for each sample ranged between 5 to 10 million per sample.

Organism:

Solanum pimpinellifolium

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20002

60 Samples

Download data: CSV

(Submitter supplied) Six stages of flower and fruit materials from S. lycopersicum var. Moneymaker (MM), S. lycopersicum var. cerasiforme LA1310 (CC) and Solanum pimpinellifolium PI365967 (PP) including 5DPA, 20DPA, mature green, break stage and red ripen fruits and -2DPA flower

Organism:

Solanum pimpinellifolium; Solanum lycopersicum var. cerasiforme; Solanum lycopersicum

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL19694 GPL21115 GPL20002

3 Samples

Download data: BW

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

Organism:

Solanum lycopersicum; Solanum pimpinellifolium; Solanum lycopersicum x Solanum pennellii; Solanum pennellii

Type:

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

8 related Platforms

39 Samples

Download data: TXT

(Submitter supplied) By using DNA methylation of introgression lines as a marker of past paramutation, we characterise in details the paramutation of the \textit{H06} locus in crosses between Solanum lycopersicum and a range of tomato relatives and cultivars. Paramutation of H06 depends on the timing of sRNA production and conforms to the RNA-directed model of paramutation. By scanning the methylomes of tomato introgression lines for shared regions of differential methylation, thousands of candidate regions for paramutation are identified. more...

Organism:

Solanum pennellii; Solanum pimpinellifolium; Solanum lycopersicum; Solanum lycopersicum x Solanum pennellii

Type:

Non-coding RNA profiling by high throughput sequencing

6 related Platforms

31 Samples

Download data: TXT

(Submitter supplied) MicroRNAs (miRNAs) are 19-24 nucleotide (nt) noncoding RNAs that play important roles in abiotic stress responses in plants. High temperatures have been the subject of considerable attention due to their negative effects on plant growth and development. Heat-responsive miRNAs have been identified in some plants. However, there have been no reports on the global identification of miRNAs and their targets in tomato at high temperatures, especially at different elevated temperatures. more...

Organism:

Solanum pimpinellifolium

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL20002

6 Samples

Download data: XLS

(Submitter supplied) Abscisic acid (ABA) regulates plant development and adaptation to environmental conditions. The ABA biosynthesis pathway in plants has been thoroughly elucidated; however, very few transcription factors directly regulating the expression of ABA biosynthetic genes have been identified. Here we show that the tomato (Solanum lycopersicum) zinc finger transcription factor SlZFP2, which is mainly expressed in developing fruits and axillary buds, negatively regulates ABA biosynthesis. more...

Organism:

Solanum pimpinellifolium

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19491

6 Samples

Download data: TXT

(Submitter supplied) Background: Tomato (Solanum lycopersicum) self-compatibility (SC) is defined as self-pollen tubes that can penetrate their own stigma, elongate in the style and fertilize their own ovules. Self-incompatibility (SI) is defined as self-pollen tubes that are prevented from developing in the style. To determine the influence of gene expression on style self-pollination, a transcriptome-wide comparative analysis of SC and SI tomato unpollinated/pollinated styles was performed using RNA-sequencing (RNA-seq) data. more...

Organism:

Solanum chilense; Solanum pimpinellifolium

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL20002 GPL20003

12 Samples

Download data: XLSX

(Submitter supplied) we found the expression levels of 76 known miRNAs were highly variable between the reciprocal hybrids through the high-throughput sequencing of small RNAs

Organism:

Solanum lycopersicum; Solanum pimpinellifolium; Solanum lycopersicum x Solanum pimpinellifolium

Type:

Non-coding RNA profiling by high throughput sequencing

Platforms:

GPL19278 GPL16804 GPL16345

4 Samples

Download data: FA

(Submitter supplied) Abscisic acid (ABA) regulates seed and bud dormancy. We show by forward and reverse genetic analysis that the tomato transcription factor SlZFP2 is required for release of bud and seed dormancy through negative regulation of ABA biosynthesis. We also demonstrated that ABA promotes growth and represses flowering in tomato both through transcriptional control on the florigen-encoding gene SINGLE FLOWER TRUSS (SFT) in tomato. more...

Organism:

Solanum pimpinellifolium

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16804

4 Samples

Download data: TXT

(Submitter supplied) Understanding the genetic basis of plants’ response to environmental stresses such as drought and salinity is vital for improving the future crop productivity and for deciphering the evolutionary mechanisms of adaptation and speciation. Here, we screened for genes and functional groups that are potentially involved in drought tolerance in tomato by comparing genome-wide transcriptome profiles of drought-sensitive S. more...

Organism:

Solanum lycopersicum; Solanum pimpinellifolium

Type:

Expression profiling by array

Platform:

GPL4741

46 Samples

Download data: CEL

(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 pennellii; Solanum habrochaites; Solanum lycopersicum; Solanum pimpinellifolium

Type:

Expression profiling by high throughput sequencing

4 related Platforms

52 Samples

Download data: TXT

(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 lycopersicum; Solanum pimpinellifolium

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL14847 GPL14848

9 Samples

Download data: TXT

(Submitter supplied) Universally accepted landmark stages are necessary to highlight key events in tomato reproductive development. In this study, we provide a description of floral and fruit development in a red-fruited closely related wild relative of tomato, Solanum pimpinellifolium accession LA1589. We use established and propose new landmarks as the framework for the characterization of the tomato fruit shape gene SUN in fruit development. more...

Organism:

Solanum pimpinellifolium; Solanum lycopersicum

Type:

Expression profiling by array

Platform:

GPL8362

18 Samples

Download data: FTR