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Sample GSM239253 Query DataSets for GSM239253
Status Public on Nov 01, 2007
Title CaMV::DME pollen
Sample type RNA
 
Source name Arabidopsis (C24 ecotype) CaMV::DME pollen 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 CaMV::DME Columbia glabrous pollen
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 818.9 P 0.000225
AFFX-BioB-M_at 1111.8 P 0.00007
AFFX-BioB-3_at 816.1 P 0.000044
AFFX-BioC-5_at 2383.2 P 0.000052
AFFX-BioC-3_at 2108.8 P 0.000044
AFFX-BioDn-5_at 5750.1 P 0.000044
AFFX-BioDn-3_at 7722 P 0.000044
AFFX-CreX-5_at 21154.3 P 0.000044
AFFX-CreX-3_at 29575.2 P 0.000044
AFFX-DapX-5_at 78.9 A 0.185131
AFFX-DapX-M_at 13.8 A 0.48511
AFFX-DapX-3_at 10.3 A 0.804734
AFFX-LysX-5_at 5.4 A 0.916408
AFFX-LysX-M_at 61.8 A 0.300606
AFFX-LysX-3_at 9.4 A 0.824672
AFFX-PheX-5_at 5.5 A 0.976071
AFFX-PheX-M_at 34.7 A 0.559354
AFFX-PheX-3_at 17.7 A 0.824672
AFFX-ThrX-5_at 6.8 A 0.993813
AFFX-ThrX-M_at 12.3 A 0.645547

Total number of rows: 22810

Table truncated, full table size 583 Kbytes.




Supplementary file Size Download File type/resource
GSM239253.CEL.gz 3.2 Mb (ftp)(http) CEL
Processed data included within Sample table

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