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Sample GSM1179574 Query DataSets for GSM1179574
Status Public on Jun 03, 2014
Title wild type-control_rep1
Sample type RNA
 
Source name wild type, control, replicate 1
Organism Arabidopsis
Characteristics ecotype: Col-0
tissue: leaf
genotype/variation: wild-type
Treatment protocol To conduct drought stress treatment, 2-week-old WT and transgenic plants in soil were subjected to drought condition (soil water deficit) by withholding water for 21 d and then re-watered.
Growth protocol Two transgenic Arabidopsis lines (nNOS-2 and nNOS-25) with the nNOS gene under the control of the cauliflower mosaic virus (CaMV) 35S promoter (Shi et al., 2012c), as well as Col-0 (WT), were used in this research. After stratificated in deionized water at 4°C for 3 days in darkness, the Arabidopsis seeds were sown in the plastic container filled with soil in the growth chamber. The growth chamber was controlled at an irradiance of about 120-150 µmol quanta m-2 s-1, 22-25°C, with 65% relative humidity under 16 h light and 8 h dark cycles. To keep the well growth condition, nutrient solution was irrigated twice every week.
Extracted molecule total RNA
Extraction protocol For RNA isolation, 2-week-old WT and transgenic plants (nNOS-25) in pots were subjected to control condition (well-watered) and drought condition (soil water deficit) by withholding water for 14 d, respectively. The leaf samples of two replications at 14 d under control and drought conditions were harvested from at least 20 seedlings per genotype. Total RNA was extracted with TRIzol reagent (Invitrogen) and quantified as previously described (Shi et al., 2012c), .then RNA was quantified and RNA quality was also determined using formaldehyde agarose gel and a 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA) according to the manufacturer’s protocol.
Label biotin
Label protocol For array hybridization, 200 ng of total RNA was used for first-strand cDNA synthesis and second-strand cDNA synthesis. Then aRNA cRNA was labeled with biotinylated ribonucleotide analog and was fragmented with fragmentation buffer using MessageAmpTM Premier RNA Amplification Kit (Ambion, #1792).
 
Hybridization protocol After purification, 12.5 μg of labeled and fragmented cRNA probes were hybridized to the Arabidopsis arrays with Hybrization, Wash and Stain Kit (Affymetrix, #900720) according to manufacturer’s instruction.
Scan protocol The arrays were scanned using GeneChip® Scanner 3000 (Affymetrix, #3000). The scanned images were saved as DAT files and transformed to JPG image. The signal intensities were extracted from the JPG image with Affymetrix® GeneChip® Command Console® Software (AGCC software) and saved as CEL files.
Description wild type without drought treatment rep1
Data processing affylmGUI package (Wettenhall et al., 2006) rooted in R (Gentleman et al., 2004) Significant analysis of microarray (SAM) R software (Irizarry et al., 2003) was used to calculate the intensity ratios and fold changes. All the differential expressed genes with p-value below 0.05 and log2 fold change above 1 or below -1 were chosen for further analysis.
 
Submission date Jul 02, 2013
Last update date Jun 03, 2014
Contact name Zhulong Chan
E-mail(s) zhulongch@wbgcas.cn
Organization name Chinese Academy of Sciences
Department Wuhan Botanic Garden
Street address Moshan, Wuchang District
City Wuhan, Hubei Province
ZIP/Postal code 430074
Country China
 
Platform ID GPL198
Series (1)
GSE48474 Dissecting physiological and transcriptional responses of nitric oxide to drought stress by increasing in vivo nitric oxide content in Arabidopsis

Data table header descriptions
ID_REF
VALUE log2 value, RMA signal intensity

Data table
ID_REF VALUE
244901_at 3.186271679
244902_at 3.213417999
244903_at 6.667511151
244904_at 6.425463038
244905_at 2.742841165
244906_at 6.705157555
244907_at 2.666821425
244908_at 2.385223875
244909_at 3.324178267
244910_s_at 2.540063346
244911_at 1.880322569
244912_at 7.035708102
244913_at 3.770393466
244914_at 2.567225596
244915_s_at 3.155815605
244916_at 3.978167655
244917_at 2.767293905
244918_at 2.245190879
244919_at 3.519745234
244920_s_at 4.807592145

Total number of rows: 22810

Table truncated, full table size 490 Kbytes.




Supplementary file Size Download File type/resource
GSM1179574_121215-121240A_T-C-1_ATH1-121501_-WT-control.CEL.gz 1.7 Mb (ftp)(http) CEL
Processed data included within Sample table

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