Comment[GEAAccession]	E-GEAD-954
MAGE-TAB Version	1.1
Investigation Title	Comparing the transcriptomes of TPS1 transgenic and wild type potato plants (CBX76)
Experiment Description	Potato plants expressing the trehalose-6-phosphate synthase (TPS1) gene of yeast are improved in drought tolerance. TPS1-transgenic derivatives of the cultivar White Lady, however, grow slower and have a reduced carbon fixation and stomatal density than the wild-type, even under non stress conditions. To understand the molecular basis of this phenomenon, we have compared the transcriptomes of wild-type and TPS1-transgenic (line T2) plants grown under optimal condition, using the POCI microarray. Two independently grown biological repeats were used. Of each biological repeats three technical repeat microarray hybridisations were performed. 63 and 163 genes were up- or down-regulated more than two-fold, respectively, in the leaves of TPS1-transgenic plants compared to the wild-type. Using the MapMan software, these genes were assigned into functional groups. This assignment and an extensive literature search revealed that about half of the known genes can be connected to three major areas: carbon fixation and metabolism, stress, and regulatory functions. According to the literature, the majority of the genes in the carbon fixation and metabolism group are known to be regulated by light and the circadian clock. Members of the second group are regulated by biotic and/or abiotic stresses or by factors, such as hormones and reactive oxygen species, which are involved in stress related regulatory cascades. Genes with regulatory function include transcription factors and other proteins, which are involved in signalling cascades or in different transcriptional and translational regulatory mechanisms. To verify the microarray results, we used RNA gel blot analysis to examine the expression of eight genes and found that RNA gel blot and microarray data were correlated in each case.
Experimental Design	genetic modification design
Experimental Factor Name	sample_name
Experimental Factor Type	sample_name
Person Last Name	Mihaly	Ferenc	Zsofia
Person First Name	Kondrak	Marincs	Banfalvi
Person Affiliation	Plant Physiology Group,Agricultural Biotechnology Center		
Person Roles	submitter		
Public Release Date	2025-01-31
Protocol Name	P-GEAD-3922	P-GEAD-3923	P-GEAD-3924	P-GEAD-3925	P-GEAD-3926	P-GEAD-3927	P-GEAD-3928	P-GEAD-3929
Protocol Type	sample collection protocol	nucleic acid extraction protocol	nucleic acid labeling protocol	nucleic acid hybridization to array protocol	array scanning and feature extraction protocol	normalization data transformation protocol	growth protocol	treatment protocol
Protocol Description	All fully expanded leaves of three plants of both wild type (wt) and transgenic (T2) lines were collected, pooled and frozen in liquid nitrogen. RNA was isolated in three technical parallels., Raw signals were cross channel normalised using the local regression (Lowess) function of ArrayPro v. 4.5.1.73.	Leaf samples were frozen and grinded in liquid nitrogen. Total RNA was isolated from the powder by a phenol-sodium acetate-SDS-EDTA buffer and phenol-chloroform extraction, followed by lithium-chloride precipitation and purification using RNeasy MinElute Cleanup Kit from Qiagen.	Fluorescently labelled cDNA was synthesised from 20 microg total RNA using a SuperScript Plus Direct labelling kit (Invitrogen), according to the instruction of the manufacturer. Alexa Fluor 647 and 555 labelled dUTPs were used for the transgenic and wild type samples, respectively, and anchored oligo (dT) was used as primer. Labelled cDNA was purified using a MinElute PCR purification kit (Qiagen), and was quantified by NanoDrop spectrophotometer. cDNA yield varied between 1.06 and 2.31 microg, while specific dye incorporation was between 25 and 113 pmol dye/microg cDNA.	One microgram of each of the Alexa Fluor 647- and 555-labelled cDNAs was combined, dried in SpeedVac, and dissolved in 20 microl of water. The  hybridisation mixture was set up using a Gene Expression Hybridisation Kit (Agilent) and applied to the microarray, which then was hybridised at 65 C degrees for 17 h, followed by two subsequent washes in the appropriate Agilent wash solutions for one minute at RT and 37 C degrees, respectively.	Dried microarrays were scanned with a Genetix microarray scanner at 100% laser power and 50-70% gain settings.	Scan images were analysed using ArrayPro v. 4.5.1.73 software., Ratio data obtained with the ArrayPro software were transferred to Excel and average values were calculated. Genes with 2-fold up and down regulation were selected and their ratio values were transformed into log2 values. These genes were exported into MapMan software for functional assignment and to identify Arabidopsis thaliana orthologs.	Solanum tuberosum cv. Desiree and TPS1-transgenic plants were vegetatively propagated from single-node stem segments in tissue culture at 24 C degrees under a 16 h light / 8 h dark regime on RM medium. Six-week-old plants were transferred to pots containing A260 sterile soil and were grown in greenhouse for six weeks in Summer, under natural light, at 20-28degree C, and under 70% soil water content.	none
SDRF File	E-GEAD-954.sdrf.txt
Comment[Number of channel]	single-channel
Comment[Array Design REF]	A-GEAD-159
Comment[AEExperimentType]	transcription profiling by array
Comment[SecondaryAccession]	CBX76
Comment[BioProject]	PRJDB20053
Comment[CIBEX Accept Date]	2010-01-01
Comment[CIBEX Public Release Date]	2009-02-04
Comment[Last Update Date]	2025-01-31