GEO DataSets

(Submitter supplied) Phosphate is a necessary macronutrient for basic biological processes, plant growth, and agriculture. Plants modulate their root system architecture and cellular processes to adapt to phosphate deprivation albeit with a growth penalty. Excess application of phosphate in the form of fertilizer can lead to eutrophication and has negative environmental impact. Moreover, phosphate mined from rock reserves is a finite and non-recyclable resource and its levels are nearing complete depletion. more...

Organism:

Solanum pennellii; Solanum lycopersicum

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL22467 GPL16345

32 Samples

Download data: CSV

(Submitter supplied) A systems-level study identifies inter-specific translational regulation as important in the elevated CO2 response in two Solanum species

Organism:

Solanum lycopersicum; Solanum pennellii

Type:

Expression profiling by high throughput sequencing; Other

Platforms:

GPL22467 GPL16345

512 Samples

Download data: CSV, TXT

(Submitter supplied) The goal of this study was to perform RNA-seq expression analysis on Solanum lycopersicum cv. M82 X S. pennellii introgression lines, deriving expression Quantitative Trait Loci which were analyzed together with pre-existing genomic and phenotypic data to define genes and regulatory pathways controlling tomato root development and observed natural variation. We completed the RNAseq expression profiling analysis and developed a tool to display this information graphically in collaboration with Nicholas Provart at the University of Toronto: http://bar.utoronto.ca/efp_tomato/cgi-bin/efpWeb.cgi?dataSource=ILs_Root_Tip_Brady_Lab To identify candidate genes and pathways we focussed on one root growth trait, root growth angle, and identified two statistically significant genomic regions within tomato root growth angle QTL containing two candidate genes that likely control the gravitropic setpoint angle (CDC73 and PAP27), both of which are conserved between Arabidopsis and tomato, and which we tested using transgenic lines of the Arabidopsis orthologs. more...

Organism:

Solanum pennellii; Solanum lycopersicum; Solanum lycopersicum x Solanum pennellii

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL16345 GPL22468 GPL22467

305 Samples

Download data: TSV, TXT

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

Organism:

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

Type:

Non-coding RNA profiling by high throughput sequencing

6 related Platforms

31 Samples

Download data: TXT