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Sample GSM239252 Query DataSets for GSM239252
Status Public on Nov 01, 2007
Title Columbia glabrous (C24) wild type stamen
Sample type RNA
 
Source name Arabidopsis (C24 ecotype) stamens from stages 13 and 14 flowers
Organism Arabidopsis thaliana
Characteristics Arabidopsis Columbia glabrous ecotype (C24)
Growth protocol Plants were grown in standard green house conditions using a 16:8 light-dark cycle.
Extracted molecule polyA RNA
Extraction protocol Total RNA was extracted using TRIzol (Invitrogen) and poly(A)+ RNA was selected using Dynabeads mRNA Purification kit (Dynal Inc) according to the manufacturers.
Label biotin
Label protocol Fifteen micrograms of total RNA was poly(A)+ selected using Dynabeads mRNA purification kit (Dynal Inc.). Double-stranded cDNAs were generated using Superscript Choice System (Invitrogen). Biotinylated cRNAs were synthesized with the ENZO BioArray High Yield RNA Transcript Labeling Kit (Enzo Life Sciences).
 
Hybridization protocol Following fragmentation, fifteen micrograms of cRNA were hybridized for 16 hr at 45°C with the GeneChip ATH1 Array. GeneChips were washed and stained using the EukGE-WS2V4_450 protocol in the Affymetrix Fluidics Station 450.
Scan protocol GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G System.
Description Wild type Columbia glabrous stamens
Data processing The data were analyzed with the Affymetrix GeneChip Operating System 1.3 (GCOS 1.3) using default analysis settings and global scaling as a normalization method. The trimmed mean target intensity of each array was set to 500.
 
Submission date Oct 23, 2007
Last update date Aug 28, 2018
Contact name Bob Goldberg
E-mail(s) bobglab@mcdb.ucla.edu
Phone 310-825-3270
Organization name University of California, Los Angeles
Department Molecular, Cell and Developmental Biology
Street address 610 Charles E Young Drive East
City Los Angeles
State/province CA
ZIP/Postal code 90095
Country USA
 
Platform ID GPL198
Series (1)
GSE9408 Identification of putative Arabidopsis DEMETER target genes by GeneChip Analysis
Relations
Reanalyzed by GSE119083

Data table header descriptions
ID_REF
VALUE GCOS 1.3 generated signal intensity.
ABS_CALL The call from the GCOS1.3 software analysis indicates if the transcript was present (P), absent (A), or marginal (M).
DETECTION P-VALUE p-value indicates the detection call significance level.

Data table
ID_REF VALUE ABS_CALL DETECTION P-VALUE
AFFX-BioB-5_at 317.8 P 0.001593
AFFX-BioB-M_at 482.5 P 0.000044
AFFX-BioB-3_at 300.5 P 0.000044
AFFX-BioC-5_at 1063.2 P 0.000044
AFFX-BioC-3_at 919.7 P 0.000044
AFFX-BioDn-5_at 2108.2 P 0.000044
AFFX-BioDn-3_at 3171.1 P 0.000052
AFFX-CreX-5_at 8517.9 P 0.000044
AFFX-CreX-3_at 11487.8 P 0.000044
AFFX-DapX-5_at 10.1 A 0.470241
AFFX-DapX-M_at 2.1 A 0.949771
AFFX-DapX-3_at 2.3 A 0.953518
AFFX-LysX-5_at 1.6 A 0.891021
AFFX-LysX-M_at 20.8 A 0.368438
AFFX-LysX-3_at 4.5 A 0.794268
AFFX-PheX-5_at 1.8 A 0.979978
AFFX-PheX-M_at 1.9 A 0.868639
AFFX-PheX-3_at 5.8 A 0.699394
AFFX-ThrX-5_at 2.3 A 0.996788
AFFX-ThrX-M_at 2.9 A 0.574038

Total number of rows: 22810

Table truncated, full table size 586 Kbytes.




Supplementary file Size Download File type/resource
GSM239252.CEL.gz 3.3 Mb (ftp)(http) CEL
Processed data included within Sample table

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