{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Arto Soitamo"],"organism":["Arabidopsis thaliana"],"software":["QuantArray [PerkinElmer]"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MEXP-1068"],"description":["Eight-week old Arabidopsis plants were used to find out whether light has an effect on gene expression at low temperature."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Labeling - For Cy3 (control) cDNA labelling (Cy5 in dye swap), 1mg of poly(A) mRNA was labelled with (dT)12-18 primers (Amersham Biosciences, UK) with direct incorporation of either Cy3 or Cy5 dUTP using Superscript II Reverse Transcriptase (Invitrogen, USA). RNA was degraded and the labelled cDNA products were further purified using Microcon ® YM30 columns (Millipore, USA). The quantity of labelled cDNAs was measured using Nanodrop ND-1000 spectrophotometer (Nanodrop Technology’s, USA) and the quality was checked on 1% agarose gel prepared in TAE (Tris/Acetate/EDTA) buffer","Growth Protocol - Arabidopsis thaliana ecotype Colombia 0 seeds were germinated in 50 % vermiculite/50 % soil and grown in controlled-environment chambers at 23°C and under 100 mmol photons m-2 s-1 (8-hour-photoperiod) for 8 weeks. A short day photoperiod was used to prevent bolting (flower shoot formation) and thus keep the plants under vegetative growth. The relative humidity was controlled during growth and low temperature treatments and kept constantly at 60%. Cold treatments for 8 hours were performed at 3°C (measured from the bottom of the leaf using digital thermocouple).","Sample Processing - To allow full CO2 assimilation before the treatments, Arabidopsis plants were transferred after 2 hours of the beginning of light period directly from growth temperature (23°C ) to the low temperature (3°C )treatment . The cold treatments were performed either in the light (100 mmol photons m-2 s-1) or in the dark. The dark treatment at 23°C for 8 hours was also performed after 2 hours of the beginning of light period. Controls for Cold/Light, Cold/Dark and Dark samples were treated at 23°C in the light (100 mmol photons m-2 s-1) the same 8 hours. Internal variation in results was controlled by Blanc hybridizations of leaf material collected from growth conditions","Hybridization - Arabidopsis cDNA microarray slides are based on the GEM1 clone set purchased from InCyte Genomics, Palo Alto, CA, USA [4]. Slides were UV-cross linked (90mJ/cm-2) and prehybridized with 1% BSA (fraction V) in 5X SSC, 0.1% SDS for 30 min at 50°C and washed with 2X SSC and 0.2X SSC for 3 min. After centrifugation (500x g for 10 sec) the slides were used for the hybridizations during the same day. The labelled cDNAs were combined (10 to 20 pmol of labelled Cy3 and Cy5 cDNAs) and hybridized in the total volume of 80 ml (3X SSC, 0.65X Denhardt’s and 0.3% SDS). Hybridization was performed in a sealed chamber (Corning, USA) overnight at 65°C. The arrays were washed at room temperature with 0.5X SSC/0.1% SDS for 15 min, twice with 0.5X SSC/0.01% SDS for 5 min and twice with 0.06X S","Labeling - For Cy5 (treated) cDNA labelling (Cy3 in dye swap), 1mg of poly(A) mRNA was labelled with (dT)12-18 primers (Amersham Biosciences, UK) with direct incorporation of either Cy3 or Cy5 dUTP using Superscript II Reverse Transcriptase (Invitrogen, USA). RNA was degraded and the labelled cDNA products were further purified using Microcon ® YM30 columns (Millipore, USA). The quantity of labelled cDNAs was measured using Nanodrop ND-1000 spectrophotometer (Nanodrop Technology’s, USA) and the quality was checked on 1% agarose gel prepared in TAE (Tris/Acetate/EDTA) buffer","Nucleic Acid Extraction - Total RNA was first isolated using TriZol-reagent (Invitrogen, USA) according to manufacturers recommendations and used for further isolation of mRNA by Dynabeads mRNA Purification Kit (Dynal, Biotech, Norway). 250 mg of total RNA yielded 2.5-5 mg of mRNA."],"figure_sub":["MIAME Score","Raw Data","Organization","Assays and Data","Processed Data","Additional Files","MAGE-TAB Files","Array Designs"],"data_protocol":["Feature Extraction - The slides were scanned using ScanArray Express 5000 device (GSI Lumonics, USA) and the spot intensities were quantified using software provided by the same device (Scan Array Express Microarray Analysis System 2.0, Perkin-Elmer, USA).","Assay Data Transformation - Of Lowess normalized data, GeneSpring program calculated the ratios of up or down regulation of genes. Next the normalized values of up or down regulated genes were tested for statistical confidence. The induction or repression of a gene should be statistically significantly different from a ratio of 1.0 determined with Students t test in GeneSpring (termed as quality control). After Benjamini and Hochberg false discovery rate (FDR) correction for multiple testing, a false discovery rate of 0.05 or less was considered statistically significant. Dye swap experiments were also performed. Since there were only marginal differences between the normal and dye swap experiments, only a few dye swap experiments were included."],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["ScanArray [PerkinElmer]"],"pubmed_abstract":["<h4>Background</h4>Light and temperature are the key abiotic modulators of plant gene expression. In the present work the effect of light under low temperature treatment was analyzed by using microarrays. Specific attention was paid to the up and down regulated genes by using promoter analysis. This approach revealed putative regulatory networks of transcription factors behind the induction or repression of the genes.<h4>Results</h4>Induction of a few oxidative stress related genes occurred only under the Cold/Light treatment including genes encoding iron superoxide dismutase (FeSOD) and glutathione-dependent hydrogen peroxide peroxidases (GPX). The ascorbate dependent water-water cycle genes showed no response to Cold/Light or Cold/Dark treatments. Cold/Light specifically induced genes en"],"study_type":["transcription profiling by array"],"species":["Arabidopsis thaliana"],"pubmed_title":["Light has a specific role in modulating Arabidopsis gene expression at low temperature"],"pubmed_authors":["Arto Soitamo","Arto J Soitamo, Mirva Piippo, Yagut Allahverdiyeva, Natalia Battchikova and Eva-Mari Aro"],"additional_accession":[]},"is_claimable":false,"name":"Transcription profiling of Arabidopsis seedlings exposed to low temperatures in light and dark conditions","description":"Eight-week old Arabidopsis plants were used to find out whether light has an effect on gene expression at low temperature.","dates":{"release":"2008-02-05T00:00:00Z","modification":"2022-11-22T04:02:09.724Z","creation":"2021-10-04T17:37:38Z"},"accession":"E-MEXP-1068","cross_references":{"pubmed":["18230142"],"EFO":["EFO_0002768"],"doi":["18230142"]}}