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Sample GSM450490 Query DataSets for GSM450490
Status Public on Sep 09, 2009
Title WT Arabidopsis seedlings replicate 2
Sample type RNA
 
Source name WT
Organism Arabidopsis thaliana
Characteristics ecotype: Col0
age: 12 days old seedlings
Treatment protocol Samples were collected at Zeitgeber Time 15 (ZT15).
Growth protocol Seedlings were grown on MS3 medium under 12-hour light:12-hour dark (LD) cycles for 12 days.
Extracted molecule total RNA
Extraction protocol Total RNA extractions were performed with Pure Link Total RNA Purification System (Invitrogen).
Label biotin
Label protocol Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (Expression Analysis Technical Manual Rev. 3, 2005, Affymetrix).
 
Hybridization protocol Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on ATH1 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
Scan protocol GeneChips were scanned using the Affymetrix 7G Scanner using AGCC software version 1.1
Description Genome expression data from WT Arabidopsis seedlings
Data processing Carmaweb software (https://carmaweb.genome.tugraz.at) was used for data processing with the gcRMA algorythm for normalization. Differentially expressed genes were identified using the empirical Bayes moderated t statistics from the LiMMA package. Genes with an FDR < 5% were selected as misregulated in TOC1-ox
 
Submission date Sep 08, 2009
Last update date Sep 08, 2009
Contact name Paloma Mas
E-mail(s) pmmgmc@cid.csic.es
Phone 34-93-400-6100
Organization name Consorcio CSIC-IRTA-UAB (CRAG)
Department Genetica Molecular
Street address C/ Jordi Girona 18-26
City Barcelona
ZIP/Postal code 08034
Country Spain
 
Platform ID GPL198
Series (1)
GSE18007 Genome-wide analysis of TOC1-ox transcriptional networks

Data table header descriptions
ID_REF
VALUE log2 gcRMA signal

Data table
ID_REF VALUE
244901_at 4.262358611
244902_at 4.425089901
244903_at 6.027165681
244904_at 2.854520274
244905_at 1.981681224
244906_at 4.846206434
244907_at 2.439391869
244908_at 2.170567257
244909_at 2.128788935
244910_s_at 2.562659398
244911_at 2.69409363
244912_at 3.106040596
244913_at 1.837560845
244914_at 2.648965857
244915_s_at 2.091601849
244916_at 2.04337766
244917_at 2.049783763
244918_at 2.190894843
244919_at 2.101464315
244920_s_at 7.038941476

Total number of rows: 22810

Table truncated, full table size 490 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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