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Title: Expression Analysis of Carotenoid Biosynthesis Pathway Genes in Tomato      
dateReleased:
01-04-2011
description:
Tomato pericarp tissues at three different stages (green, breaker and ripening) of fruit development from both the above genotypes were collected using a sterile surgical blade and flash frozen in liquid nitrogen. High quality RNA was extracted from the frozen pericarp tissue using TRI Reagent (Ambion, INC. USA) and pooled at least from three independent samples and treated with DNase-I (QIAGEN GmbH, Germany). RNA cleanup was carried out using RNeasy Plant Mini Kit (QIAGEN GmbH, Germany) and 5ug of total RNA from each sample with three biological replications were reverse-transcribed to double stranded cDNA using the GeneChipR One-Cycle cDNA Synthesis Kit. The biotin-labelled cRNA was made using the GeneChipR IVT Labelling Kit (Affymetrix, CA, USA). 15 ug of cRNA samples was fragmented and was hybridized for 16 hours at 45C to the Affymetrix tomato GeneChip Array (Santa Clara, CA, USA). After washing and staining with R-phycoerythrin streptavidin in a Fluidics Station, using the GenechipR Fluidics Station 450, the arrays were scanned by the GenechipR 3000 Scanner. The chip images were scanned and extracted using default settings and the .CEL files were produced by using the Affymetrix GeneChip Operating Software (GCOS 1.2). Samples that passed through various quality checks (data not shown) were normalized with RMA algorithm using GeneSpring GX 10 (Agilent Technologies Inc., Santa Clara, CA, USA). Probes showing twofold up- or down-regulation (in Log2 transformed values) compared to corresponding control condition were taken only into consideration for further analysis
privacy:
not applicable
aggregation:
instance of dataset
ID:
E-MEXP-2934
refinement:
raw
dateSubmitted:
10-06-2010
keywords:
functional genomics
dateModified:
05-02-2014
creators:
SHUCHI SMITA
availability:
available
types:
gene expression
name:
Lycopersicon esculentum
ID:
A-AFFY-87
name:
Affymetrix GeneChip Tomato Genome Array [Tomato]
accessURL: https://www.ebi.ac.uk/arrayexpress/files/E-MEXP-2934/E-MEXP-2934.raw.1.zip
storedIn:
ArrayExpress
qualifier:
gzip compressed
format:
TXT
accessType:
download
authentication:
none
authorization:
none
accessURL: https://www.ebi.ac.uk/arrayexpress/files/E-MEXP-2934/E-MEXP-2934.processed.1.zip
storedIn:
ArrayExpress
qualifier:
gzip compressed
format:
TXT
accessType:
download
authentication:
none
authorization:
none
abbreviation:
EBI
homePage: http://www.ebi.ac.uk/
ID:
SCR:004727
name:
European Bioinformatics Institute
homePage: https://www.ebi.ac.uk/arrayexpress/
ID:
SCR:002964
name:
ArrayExpress