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Sample GSM1179570 Query DataSets for GSM1179570
Status Public on Jun 03, 2014
Title nNOS-control_rep1
Sample type RNA
Source name nNOS, control, replicate 1
Organism Arabidopsis
Characteristics ecotype: Col-0
tissue: leaf
genotype/variation: nNOS gene under the control of the cauliflower mosaic virus (CaMV) 35S promoter
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 transgenic 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
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
VALUE log2 value, RMA signal intensity

Data table
244901_at 3.682596341
244902_at 3.582911007
244903_at 7.847781805
244904_at 7.5476772
244905_at 2.72513795
244906_at 8.249806955
244907_at 2.524677907
244908_at 2.38967343
244909_at 3.601791949
244910_s_at 2.727156361
244911_at 1.878869757
244912_at 7.582120343
244913_at 3.661907304
244914_at 2.791598069
244915_s_at 3.239119291
244916_at 3.848665502
244917_at 2.889368529
244918_at 2.449555959
244919_at 4.264966092
244920_s_at 5.920422517

Total number of rows: 22810

Table truncated, full table size 490 Kbytes.

Supplementary file Size Download File type/resource
GSM1179570_121215-121240A_N-C-1_ATH1-121501_-transgenic-control.CEL.gz 1.7 Mb (ftp)(http) CEL
Processed data included within Sample table

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