Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Transcriptome analysis using customized AZ microarray on tomato Flower Abscission zone of transgeneic line TAPG::antisense TPRPgene

ABSTRACT: To extend our previous knowledge from our gene expression studies on Flower pedicel Abscission zone using Affymetrix microarray chip we have employed whole transcriptome analysis by NGS as a discovery platform to identify and add the transcripts to pre-existing database. We designed the Customized AZ Microarray chip with the transcripts obtained from NGS (includes novel transcripts), pre existing Agilent probes, and some additional transcripts from previous databases. we developed transgenic lines by antisense silenciencing the genes, which are expressed in the AZ to study the functional role in abscission process. In the current stuty we silenced TPRP gene by antisense technology under abscisson promoter (TAPG::antsisense TPRP). The flower pedicel AZ tissue tissue was sampled at six time points (0, 4, 8, 12, 16 and 20 h), following flower removal, and analyzed for their gene expression profiles using the customized AZ microarray.

ORGANISM(S): Solanum lycopersicum

PROVIDER: GSE64606 | GEO | 2018/01/01

SECONDARY ACCESSION(S): PRJNA271401

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Transcriptome analysis using customized AZ microarray on tomato Flower Abscission zone of transgeneic line TAPG::antisense KD gene

Project description:To extend our previous knowledge from our gene expression studies on Flower pedicel Abscission zone using Affymetrix microarray chip we have employed whole transcriptome analysis by NGS as a discovery platform to identify and add the transcripts to pre-existing database. We designed the Customized AZ Microarray chip with the transcripts obtained from NGS (includes novel transcripts), pre existing Agilent probes, and some additional transcripts from previous databases. We developed transgenic lines by antisense silencing the genes, which are expressed in the AZ to study the functional role in abscission process. In the current stuty we silenced KD gene by antisense technology under abscisson promoter (TAPG::antsisense KD). The flower pedicel AZ tissue tissue was sampled at six time points (0, 4, 8, 12, 16 and 20 h), following flower removal, and analyzed for their gene expression profiles using the customized AZ microarray.

2018-01-01 | GSE64564 | GEO

Transcriptome Analysis using customized AZ microarray on Flower pedicel Abscission and non abscission zones in Tomato (Solanum lycopersicum c.v New Yorker) Plants.

Project description:To extend our previous knowledge from our gene expression studies on Flower pedicel Abscission zone using Affymetrix microarray chip we have employed whole transcriptome analysis by NGS as a discovery platform to identify and add the transcripts to pre-existing database. We designed the Customized AZ Microarray chip with the transcripts obtained from NGS (includes novel transcripts), pre existing Agilent probes, and some additional transcripts from previous databases. The flower pedicel AZ tissue and non abscission(NAZ) pedicel tissues was sampled at six time points (0, 4, 8, 12, 16 and 20 h), following flower removal, and analyzed for their gene expression profiles using the customized AZ microarray.

2017-01-19 | GSE64221 | GEO

NGS and Transcriptome Analyses using AZ customized microarray on Flower Abscission zone in Tomato (Solanum lycopersicum) Plants

Project description:To extend our previous knowledge from our gene expression studies on Flower Abscission zone using Affymetrix microarray chip we have employed whole transcriptome analysis by NGS as a discovery platform to identify and add the transcripts to pre-existing database. We designed the Customized AZ Microarray chip with the transcripts obtained from NGS (includes novel transcripts), pre existing Agilent probes, and some additional transcripts from previous databases. The flower AZ tissue was sampled at five time points (0, 2, 4, 8, and 14 h), following flower removal and analyzed for their gene expression profiles using the customized AZ microarray.

2017-01-19 | GSE45355 | GEO

NGS and Transcriptome Analyses using AZ customized microarray on Leaf Abscission zone in Tomato (Solanum lycopersicum) Plants

Project description:To extend our previous knowledge from our gene expression studies on Leaf Abscission zone using Affymetrix microarray chip we have employed whole transcriptome analysis by NGS as a discovery platform to identify and add the transcripts to pre-existing database. We designed the Customized AZ Microarray chip with the transcripts obtained from NGS (includes novel transcripts), pre existing Agilent probes, and some additional transcripts from previous databases. The leaf AZ tissue was sampled at five time points (0, 24, 48, 72, and 96 h), following leaf deblading and ethylene (10ppm) treated for 24h and analyzed for their gene expression profiles using the customized AZ microarray.

2017-01-19 | GSE45356 | GEO

Expression profiling of tomato pre-abscission pedicels

Project description:Organ abscission is a general activity found in plants and its regulation is an important agronomical concern because the trait directly affects the harvesting efficiency of fruits or grains and the yields. Generally, abscission takes place at a specialized cell layer, which is called abscission zones (AZs). So far, investigations on organ abscission have been focused mainly on the cell activities during organ detachment. By contrast, little attention has been paid to the properties of AZ cells at the pre-abscission stage. The pre-abscission cells are at a turning point for initiating abscission; until an abscission initiating signal is provided, the AZ cells keep their physiological state, while once the signal occurs, the cells immediately change their state into the onset of abscission. In this study, to screen the genes involved in the regulation of abscission at the pre-abscission state, we investigated the gene expression profiles of tomato flower pedicels at anthesis. The screening revealed many genes that characterize cell identities in each pedicel region. We harvested tomato flower pedicels at the anthesis stage and divided them into three parts: the abscission zone (AZ) and the flanking proximal- (Prox) and distal- (Dis) regions. RNA was isolated and subjected to DNA microarray analyses. Experiments were performed three times with independently prepared samples.

2012-07-19 | E-GEOD-39519 | biostudies-arrayexpress

Global gene expression analysis in the pedicel abscission zone of tomato flowers by DNA microarray

Project description:In tomato, the mutants that lack the abscission zone (AZ) within pedicels are called a ‘jointless’ and are agronomically significant in that they increase the tomato fruit yield for industrial processing. We have employed DNA microarray expression analysis to identify genes with the potential to play a role in development of the pedicel abscission zone of tomato, and identified several classes of differentially regulated genes between pedicels of the AZ-forming line (wild-type) and pedicels of the non AZ-forming lines (jointless mutant and MC-suppressed transformant). Tomato flower pedicels were harvested at anthesis stage from the AZ-forming line (wild-type) and the non AZ-forming lines (jointless mutant and MC-suppressed transformant), and subjected to DNA microarray analyses. Experiments were performed twice with independently prepared samples.

2010-07-03 | E-GEOD-22682 | biostudies-arrayexpress

Expression profiling of tomato pre-abscission pedicels

2012-07-20 | GSE39519 | GEO

Global gene expression analysis in the pedicel abscission zone of tomato flowers by DNA microarray

2010-07-03 | GSE22682 | GEO

Discovering differentially expressed genes in early floral buds of SlREVRis overexpression line and wild type in tomato

Project description:Versatile roles of REVOLUTA (REV), a Class III homeodomain-leucine zipper (HD-ZIP III) transcription factor, have been mainly depicted in Arabidopsis and Populus. In this study, we investigated the functions of its tomato homolog, namely SlREV. Over-expression of a microRNA166-resistant version of SlREV (35S::REVRis) not only resulted in vegetative abnormities such as curly leaves and fasciated stems, but also caused dramatic reproductive alterations including continuous production of flowers at pedicel abscission zone (AZ) and ectopic fruit formation on receptacles. Microscopic analysis showed that meristem-like structures continuously emerged out from the exodermises of pedicel AZs and ectopic carpels formed between the first and the second whorl of floral buds in 35S::REVRis plants. Therefore, we performed Illumina’s digital gene expression (DGE) system, a tag-based transcriptome sequencing methodTranscriptional data to dicover differential expressed genes in early buds (1-2 mm floral buds at stage 6-8) of overexpression line SlREVRis-1. The result suggests that SlREV may regulate genes related to meristem maintenance and cell differentiation in the development of flower pedicel abscission zone, and modulate genes in homodomain and MADS-box families and hormone pathways during fruit formation. These results reveal important roles of SlREV in tomato.

2014-06-10 | GSE58305 | GEO

Discovering differentially expressed genes in early floral buds of SlREVRis overexpression line and wild type in tomato

2014-06-10 | E-GEOD-58305 | biostudies-arrayexpress

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