NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM761701 Query DataSets for GSM761701
Status Public on Aug 02, 2011
Title seedling in dark treated with mock, biological rep3
Sample type RNA
 
Source name Arabidopsis thaliana seedlings growing in dark for 4 days and treated with mock for 2 hours
Organism Arabidopsis thaliana
Characteristics developmental stage: seedling
age: 4 days
genotype/variation: FHY3p:FHY3-GR fhy3-4 transgenic line
Treatment protocol treated with 10 μM dexamethasone (DEX) or MOCK (equal volume of ethanol) for 2 h
Growth protocol FHY3p:FHY3-GR fhy3-4 transgenic seedlings grown in D or continuous FR light for 4 d
Extracted molecule total RNA
Extraction protocol total RNA was isolated using the RNeasy Plant Mini Kit (Qiagen)
Label biotin
Label protocol RNA quality was assessed with an Agilent 2100 Bioanalyzer, and hybridization to the Affymetrix GeneChip Arabidopsis ATH1 Genome Arrays was performed according to the manufacturer’s instructions.
 
Hybridization protocol Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
Scan protocol GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.
Data processing Raw microarray data were normalized using the robust multiarray analysis (RMA) algorithm in the BIOCONDUCTOR affy package. Then the microarray data were analyzed using Significance Analysis of Microarrays (SAM) method with default parameters as well as a manual setting of false discovery threshold (FDR) < 0.027 in D and <0.022 in FR.
 
Submission date Jul 15, 2011
Last update date Aug 15, 2018
Contact name Bosheng Li
E-mail(s) libs@sustc.edu.cn
Organization name SUSTC (current, may different with previous institution )
Department MCDB
Street address SUStech Huiyuan #1 406
City Shenzhen
State/province Guangdong
ZIP/Postal code 581055
Country China
 
Platform ID GPL198
Series (2)
GSE30712 Expression data from Arabidopsis thaliana under dark and far-red light
GSE30713 Genome-wide Binding Site Analysis of FAR-RED ELONGATED HYPOCOTYL 3 Reveals Its Novel Function in Arabidopsis Development
Relations
Reanalyzed by GSE118579

Data table header descriptions
ID_REF
VALUE RMA signal intensity

Data table
ID_REF VALUE
244901_at 5.203282994
244902_at 4.700358896
244903_at 8.839349812
244904_at 5.836820844
244905_at 3.887059513
244906_at 5.586114036
244907_at 3.586241713
244908_at 3.788919504
244909_at 3.923719677
244910_s_at 4.142706982
244911_at 3.214945541
244912_at 9.579077483
244913_at 3.903455639
244914_at 3.413370771
244915_s_at 4.131738597
244916_at 4.031178884
244917_at 3.838252009
244918_at 3.221541836
244919_at 5.09926628
244920_s_at 6.014184079

Total number of rows: 22810

Table truncated, full table size 490 Kbytes.




Supplementary file Size Download File type/resource
GSM761701.CEL.gz 2.0 Mb (ftp)(http) CEL
Processed data included within Sample table

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap