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Sample GSM947104 Query DataSets for GSM947104
Status Public on Sep 01, 2013
Title HAN-4h-rep3
Sample type RNA
 
Channel 1
Source name RNA from 4h DEX treatment
Organism Arabidopsis thaliana
Characteristics genotype/variation: HAN overexpression
time: 4h
Growth protocol Plants used for microarray experiments were 35S:HAN-GR lines in the Landsberg erecta (Ler) background.Plants were grown on a soil:vermiculite:perlite mixture under continuous illumination with a light intensity range of 80 to 100 µmol•m–2•s–1 at 20°C.
Extracted molecule total RNA
Extraction protocol Total RNA were extracted using Qiagen RNeasy according to the manufacturer's instructions
Label Cy3
Label protocol RNA was dye-labeled as previously described (Wellmer et al. (2006) PLoS Genetics 2, e117). In brief, first and second strand cDNA was synthesized using a poly(A)-primer with a T7 promoter sequence. Then, in vitro transcription was performed using the Megascript T7 kit (Ambion, Austin, TX). For the oligonucleotide array, dye molecules were coupled to the amplified RNA, and the dye-labeled RNA was fragmented before hybridization.
 
Channel 2
Source name RNA from 4h mock
Organism Arabidopsis thaliana
Characteristics genotype/variation: control
time: 4h
Growth protocol Plants used for microarray experiments were 35S:HAN-GR lines in the Landsberg erecta (Ler) background.Plants were grown on a soil:vermiculite:perlite mixture under continuous illumination with a light intensity range of 80 to 100 µmol•m–2•s–1 at 20°C.
Extracted molecule total RNA
Extraction protocol Total RNA were extracted using Qiagen RNeasy according to the manufacturer's instructions
Label Cy5
Label protocol RNA was dye-labeled as previously described (Wellmer et al. (2006) PLoS Genetics 2, e117). In brief, first and second strand cDNA was synthesized using a poly(A)-primer with a T7 promoter sequence. Then, in vitro transcription was performed using the Megascript T7 kit (Ambion, Austin, TX). For the oligonucleotide array, dye molecules were coupled to the amplified RNA, and the dye-labeled RNA was fragmented before hybridization.
 
 
Hybridization protocol Dye-labeled antisense RNA was hybridized to microarrays using a MAUI hybridization system (BioMicro Systems, Salt Lake City, UT, USA) as previously described (Wellmer et al. (2006) PLoS Genetics 2, e117). Specifically, hybridizations were done as follows: dye-labeled antisense RNA preparations were dried down and the resulting pellets were re-suspended in 5 ul 10 mM EDTA and 45 ul SlideHyb Buffer #1 (Ambion, Austin, Texas, United States) and hybridized for 14 h to microarrays at 48C using a MAUI hybridization system (BioMicro Systems, Salt Lake City, Utah, United States) according to the manufacturer's instructions.
Scan protocol Microarrays were scanned and the data acquired with an Axon GenePix 4200A scanner using GenePix v5.0 analysis software.
Description Biological replicate 3 of 4.
Data processing Data were processed using lowess normalization with the Resolver data analysis system (Rosetta Biosoftware, Seattle, WA).
 
Submission date Jun 12, 2012
Last update date Sep 01, 2013
Contact name Xiaolan Zhang
E-mail(s) zhxiaolan@cau.edu.cn
Organization name China Agricultural University
Department Vegetable Science
Street address No.2 Yuanmingyuan Xi Lu Haidian District
City Beijing
ZIP/Postal code 100193
Country China
 
Platform ID GPL5762
Series (1)
GSE38658 Transcription repressor HANABA TARANU (HAN) controls flower development via integrating multiple hormone actions, floral organ specification and GATA3 family auto-regulation

Data table header descriptions
ID_REF
VALUE lowess normalized log2 ratio (DEX/mock)

Data table
ID_REF VALUE
A000001_01 0.418928352
A000002_01 0.262897389
A000003_01 -0.433445178
A000004_01 0.01063017
A000005_01 0.080025248
A000006_01 0.35155965
A000007_01 -0.568182581
A000008_01 6.129056993
A000009_01
A000010_01 0.263063486
A000011_01 0.157193637
A000012_01 -0.01940006
A000013_01 0.366010037
A000014_01 -1.431285939
A000015_01 -0.088994454
A000016_01 0.114872274
A000017_01 0.501112853
A000018_01 6.64385619
A000019_01 -0.023951102
A000020_01 -0.135866859

Total number of rows: 26540

Table truncated, full table size 560 Kbytes.




Supplementary file Size Download File type/resource
GSM947104_HAN_4h_rep3.gpr.gz 3.2 Mb (ftp)(http) GPR
Processed data included within Sample table

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