Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

16 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Microarray analysis of developing fruits from transgenic lines with increased or reduced SlARF9 mRNA levels in tomato.

ABSTRACT: 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). To explore the physiological role of SlARF9 in tomato fruit set and development, we generated transgenic tomato lines in which the gene was overexpressed or silenced, and used microarray analysis to identify possible transcriptomic changes associated with the fruit developmental phenotypes observed in the transgenic lines. The transcript profiling analysis was done using pericarp tissue from fruits, 3-4mm in diameter, with each sample containing the pericarp of two fruits. For each seperate transgenic line, tissues were pooled from 2-3 plants (T2), resulting in a total of 6 samples for SlARF9-OE, 7 samples for SlARF9-RNAi, and 2 samples for wild type. The transcript profiling analysis was carried out using affymetrix EUTOM3 tomato exon array.

ORGANISM(S): Solanum lycopersicum

SUBMITTER: Yury Tikunov

PROVIDER: E-GEOD-63637 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Global transcriptome profiling of AtJUB1-OX and WT fruits at mature green (MG) and breaker+7 developmental stages.

Project description:To understand the AtJUB1 mediated regulation of tomato fruit development. To test how the NAC transcription factor JUNGBRUNNEN1 from Arabidopsis thaliana (AtJUB1, identical to ANAC042; At2g43000) affects the development of tomato fruits, AtJUB1-GFP was expressed in transgenic tomato plants under the control of the CaMV 35S promoter. AtJUB1-GFP fusion protein was previously shown to encode a functionally active transcription factor in Arabidopsis (Wu et al., 2012). We then performed gene expression profiling of fruits from AtJUB1-GFP lines (AtJUB1-OX plants) and non-modified wild-type (WT) plants. Fruits at two developmental stages, namely mature green (MG) and Breaker+7 days (B+7), were analysed. To this end, the pericarp was separated from the rest of the fruits and quickly frozen in liquid nitrogen for subsequent RNA extraction. Gene expression analysis was performed using GeneChip Tomato Genome Arrays (Affymetrix). Probe preparation and microarray hybridizations were performed by ATLAS Biolabs (Berlin, Germany).

2017-03-31 | GSE87507 | GEO

Gene expression in three stages of ripening tomato fruit

Project description:Gene expression in three stages of ripening tomato fruit (variety Ailsa Craig) was determined with the EUTOM3 Affymetrix array in order to compare with degradrome sequencing data from study GSE42661, treated as RNAseq. three replicates of each stage (MG, mature green; T, turning/breaker; RR, red ripe) were hybridized; Expression values were normalized for each sample and reported by iTAG2.3 cDNA identifier in the accompanying matrix table.

2013-04-05 | E-GEOD-42783 | biostudies-arrayexpress

Microarray analysis of gene expression under different light conditions

Project description: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. 20 samples were analyzed (14 leaf samples and 6 pericarp samples); 2-3 biological replicates were used.

2012-05-01 | E-GEOD-35020 | biostudies-arrayexpress

Expression data from MCF-7 breast cancer cells treated with Wild Type Tomato fruit extract (WT) and transgenic lines tomato fruit extract (L6 and L7)

Project description: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.

2017-06-12 | GSE94548 | GEO

Transcriptional Profiling of high pigment-2dg Tomato Mutant Fruit

Project description:Phenotypes of the tomato (Solanum lycopersicum L.) high pigment-2dg (hp-2dg) mutant are caused by a mutation in the gene encoding DEETIOLATED1, a negative regulator of light signaling. Homozygous hp-2dg plants display a plethora of distinctive developmental and metabolic phenotypes in comparison to their normal isogenic counterparts. This mutant is however best known for the increased levels of lycopene and other plastid-accumulating functional metabolites. In this study we analyzed the transcriptional alterations in mature-green, breaker and early-red fruits of hp-2dg/hp-2dg plants in relation to their normal counterparts using microarray technology. Results show that a large portion of the genes that are affected by hp-2dg mutation, display a tendency for up- rather than down-regulation. Ontology assignment of these differentially regulated transcripts, revealed a consistent upregulation of those related to chloroplast biogenesis and photosynthesis in hp-2dg mutants throughout fruit ripening. A tendency of upregulation was also observed in structural genes involved in phytonutrient biosynthesis. However, this upregulation was not as consistent, positioning plastid biogenesis as an important determinant of phytonutrient overproduction in hp-2dg mutant fruits. Microscopic observations revealed a highly significant increase in chloroplasts size and number in pericarp cells of mature-green hp-2dg/hp-2dg fruits in comparison to their normal counterparts. This increase could be observed from early stages of fruit development. Therefore, the molecular trigger that drives phytonutrient overproduction in hp-2dg mutant fruits should be initially traced at early stages of fruit development. Keywords: Comparative Transcriptional Profiling of tomato fruit pericarp tissue

2007-10-08 | GSE6041 | GEO

Microarray analysis of ripening tomato fruits with RNAi knockdown of a direct RIN-target GRAS family gene

Project description:The tomato (Solanum lycopersicum) MADS-box transcription factor RIPENING INHIBITOR (RIN) acts as a master regulator of tomato fruit ripening. We previously identified a direct RIN target gene Solyc07g052960, which encodes a putative GRAS family protein belonging to the SHORT-ROOT (SHR) branch, but its role was unknown. RNA interference (RNAi)-mediated gene silencing reduced Solyc07g052960 expression in transgenic fruits, but the fruits appeared to ripen normally. However, the transgenic fruits at the ripening stage showed a marked decrease of the expression levels of several ripening-induced genes, especially involved in cell wall modification and secondary metabolism. This suggests that Solyc07g052960 participates in the regulation of these processes as one component of the RIN-activated transcriptional cascade regulating fruit ripening in tomato. For a preliminary screening, we monitored global gene expression in tomato fruits from untransformed control (Ailsa Craig [AC] cultivar) and three transgenic lines with Solyc07g052960 knockdown by RNAi (lines T-7, T-22 and T-23) at the ripening (pink coloring) stage using microarray without biological replication.

2014-03-01 | E-GEOD-45658 | biostudies-arrayexpress

Microarray analysis of developing fruits from transgenic lines with increased or reduced SlARF9 mRNA levels in tomato.

Project description: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). To explore the physiological role of SlARF9 in tomato fruit set and development, we generated transgenic tomato lines in which the gene was overexpressed or silenced, and used microarray analysis to identify possible transcriptomic changes associated with the fruit developmental phenotypes observed in the transgenic lines.

2014-11-26 | GSE63637 | GEO

Microarray analysis of ripening tomato fruits with RNAi knockdown of a direct RIN-target GRAS family gene

2014-03-01 | GSE45658 | GEO

Understanding the complexity of fruit ripening by transcriptome analysis of rin mutant fruit

Project description:[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. A complete understanding of this mutation and its effect on fruit transcriptome during ripening is not clear. In this study, microarray analysis has been used to investigate the influence of rin mutation on fruit transcriptome at different stages of ripening. A total of 2,398 genes were found to be differentially expressed in wild type fruit pericarp, which on cluster analysis indicated a major shift in their expression profiles in rin mutant fruit. A total of 1,802 genes were found to be differentially expressed between wild type and rin mutant fruits and 17% of these genes encoded regulatory elements, suggesting that mutation in LeMADS-RIN results in disturbance in the regulatory transcriptional networks during ripening. Since LeMADS-RIN has been reported to bind to the CArG box of LeACS2 promoter, in-silico analysis of 51 putative promoter sequences of the genes, that showed ripening associated up-regulation in wild type but showed impairment in up-regulation in rin mutant fruit during ripening, were searched for presence of CArG box along with ethylene and auxin responsive elements. The study revealed that only 24 putative promoter sequences harbor LeMADS-RIN specific CArG box suggesting an alternative mode of regulation by LeMADS-RIN for CArG box deficient genes. Three chronological stages of tomato (Solanum lycopersicon) fruit ripening were compared between wild type and rin mutant

2012-02-29 | E-GEOD-20720 | biostudies-arrayexpress

Gene regulation in parthenocarpic tomato fruit

Project description:To evaluate the role of seeds in fruit quality, we induced parthenocarpy in tomato by regulating ovule-specific auxin synthesis or responsiveness using the INO promoter from A. thaliana, which is expressed in the outer layer of the integuments during early stages of ovule development. We compared these to fruit where the same coding regions were expressed from the DeFH9 promoter which is expressed in carpel tissues during early stages of ovule development. Expression of auxin synthesis or responsiveness genes by both of these promoters produced seedless parthenocarpic tomato fruit. We compared fruit samples using the Affymetrix tomato GeneChip (GPL4741) to determine how gene regulation and expression differed between wild-type and transgenic fruit. Keywords: genetic modification

2009-08-31 | GSE14358 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data