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Items: 1 to 20 of 902

1.

A Multimodal Study of Wild Tomato Species Introgressions Unravels the Genetic Basis of Transcriptome and Metabolome Variation in Important Fruit Traits

(Submitter supplied) Here, we report RNAseq data from a Solanum lycopersicum-pennellii introgression population (IL) and a backcross introgression population (BIL), to establish the genetic basis of gene expression and chemical variation accompanying transfer of wild species-associated fruit traits. Transcriptome analysis of these lines resulted in the identification of genomic loci significantly linked with levels of hundreds of transcripts and metabolites. more...
Organism:
Solanum lycopersicum x Solanum pennellii
Type:
Expression profiling by high throughput sequencing
Platform:
GPL22468
523 Samples
Download data: TSV
Series
Accession:
GSE151451
ID:
200151451
2.

Deciphering the biological processes underlying tomato biomass production and composition.

(Submitter supplied) After tomato fruits harvesting huge amounts of biomass residues, including plant and immature fruit, remaining in the field can be utilized to produce bioenergy. Little is known about the molecular aspects underlying tomato plant biomass production and hydrolysis. To identify genes involved in the regulation of plant biomass accumulation and composition, two Solanum pennellii introgression lines (ILs) with contrasting phenotypes for plant architecture and biomass characteristics, were analyzed. more...
Organism:
Solanum lycopersicum; Solanum lycopersicum x Solanum pennellii
Type:
Expression profiling by high throughput sequencing; Other
Platforms:
GPL26313 GPL26312
7 Samples
Download data: TXT
Series
Accession:
GSE128409
ID:
200128409
3.

RNA-seq of Solanum lycopersicum cv. M82 and S. pennellii introgression line 3-5 day old root tip tissue

(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 lycopersicum; Solanum lycopersicum x Solanum pennellii; Solanum pennellii
Type:
Expression profiling by high throughput sequencing
Platforms:
GPL16345 GPL22468 GPL22467
305 Samples
Download data: TSV, TXT
Series
Accession:
GSE87162
ID:
200087162
4.

Paramutation of natural epialleles in tomato

(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
Series
Accession:
GSE97247
ID:
200097247
5.

Paramutation of natural epialleles in tomato [sRNA]

(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
Series
Accession:
GSE97206
ID:
200097206
6.

Paramutation of natural epialleles in tomato [BiSulfite-seq]

(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 lycopersicum; Solanum lycopersicum x Solanum pennellii
Type:
Methylation profiling by high throughput sequencing
4 related Platforms
8 Samples
Download data: TXT
Series
Accession:
GSE97192
ID:
200097192
7.

Post-pollination carpels of S. pennellii introgression lines

(Submitter supplied) Expression in carpels of three pennellii NILs were contrasted to the recurrent parent (S. lycopersicum)
Organism:
Solanum lycopersicum; Solanum lycopersicum x Solanum pennellii
Type:
Expression profiling by array
Platform:
GPL4741
17 Samples
Download data: CEL
Series
Accession:
GSE77235
ID:
200077235
8.

Pre-anthesis anthers of S. pennellii introgression lines

(Submitter supplied) Expression in pollen of four pennellii NILs were contrasted to the recurrent parent (S. lycopersicum)
Organism:
Solanum lycopersicum; Solanum lycopersicum x Solanum pennellii
Type:
Expression profiling by array
Platform:
GPL4741
21 Samples
Download data: CEL
Series
Accession:
GSE77232
ID:
200077232
9.

Small RNA profiling Tomato, wild tomato relative and series of introgression lines

(Submitter supplied) High throughput sequencing was used to investigate the production of small RNAs from cultivated tomato cultivar M82 and its wild relative Solanum pennellii. In order to understand the pattern of inheritance of the samll RNAs, interspecific hybrids (F1 and F2) along with series of introgressed lines comprising precise short genomic regions from S. pennellii in M82 background were used.
Organism:
Solanum lycopersicum; Solanum lycopersicum x Solanum pennellii; Solanum pennellii
Type:
Non-coding RNA profiling by high throughput sequencing
Platforms:
GPL10777 GPL10776 GPL9245
18 Samples
Download data: FASTA
Series
Accession:
GSE23562
ID:
200023562
10.

Illumina NovaSeq 6000 (Solanum lycopersicum x Solanum pennellii)

Organism:
Solanum lycopersicum x Solanum pennellii
Download data
Platform
Accession:
GPL33844
ID:
100033844
11.

Illumina HiSeq 1500 (Solanum lycopersicum x Solanum pennellii)

Organism:
Solanum lycopersicum x Solanum pennellii
1 Series
6 Samples
Download data
Platform
Accession:
GPL26312
ID:
100026312
12.

Illumina HiSeq 2500 (Solanum lycopersicum x Solanum pennellii)

Organism:
Solanum lycopersicum x Solanum pennellii
2 Series
4 Samples
Download data
Platform
Accession:
GPL23238
ID:
100023238
13.

Illumina HiSeq 2000 (Solanum lycopersicum x Solanum pennellii)

Organism:
Solanum lycopersicum x Solanum pennellii
5 Series
835 Samples
Download data
Platform
Accession:
GPL22468
ID:
100022468
14.

Illumina Genome Analyzer (Solanum lycopersicum x Solanum pennellii)

Organism:
Solanum lycopersicum x Solanum pennellii
3 Series
17 Samples
Download data
Platform
Accession:
GPL10777
ID:
100010777
15.

6261

Organism:
Solanum lycopersicum x Solanum pennellii
Source name:
Skin fruit tissue
Platform:
GPL22468
Series:
GSE151451
Download data
Sample
Accession:
GSM4578695
ID:
304578695
16.

6305

Organism:
Solanum lycopersicum x Solanum pennellii
Source name:
Skin fruit tissue
Platform:
GPL22468
Series:
GSE151451
Download data
Sample
Accession:
GSM4578694
ID:
304578694
17.

6494

Organism:
Solanum lycopersicum x Solanum pennellii
Source name:
Skin fruit tissue
Platform:
GPL22468
Series:
GSE151451
Download data
Sample
Accession:
GSM4578693
ID:
304578693
18.

6602

Organism:
Solanum lycopersicum x Solanum pennellii
Source name:
Skin fruit tissue
Platform:
GPL22468
Series:
GSE151451
Download data
Sample
Accession:
GSM4578692
ID:
304578692
19.

IL10-1

Organism:
Solanum lycopersicum x Solanum pennellii
Source name:
Skin fruit tissue
Platform:
GPL22468
Series:
GSE151451
Download data
Sample
Accession:
GSM4578691
ID:
304578691
20.

6319

Organism:
Solanum lycopersicum x Solanum pennellii
Source name:
Skin fruit tissue
Platform:
GPL22468
Series:
GSE151451
Download data
Sample
Accession:
GSM4578690
ID:
304578690
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