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Sample GSM375794 Query DataSets for GSM375794
Status Public on Mar 07, 2009
Title Deep-sowing 10d treatment UCZ, biological rep1
Sample type RNA
 
Source name Mesocotyl, UCZ
Organism Zea mays
Characteristics genotype: Maize inbred line 3681-4
age: 10d after sowing
Extracted molecule total RNA
Extraction protocol The total RNA was extracted by the TRIzol method (Invitrogen, USA). Mesocotyls were ground in liquid nitrogen, and 50-100 mg of frozen tissue was transferred into a tube with 1 ml TRIzol. Next, RNA was isolated, dried and dissolved in 50 µl DEPC-H2O. RNA quality and concentration were determined by 1.0% agarose gel electrophoresis and spectrophotometry.
Label biotin
Label protocol Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 µg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
 
Hybridization protocol Following fragmentation, 10 µg of cRNA were hybridized for 16 hr at 45℃ 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.
Description Gene expression data from maize mesocotyl
Data processing The data were analyzed with GCOS software (Microarray Suite version 5.0, MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.
 
Submission date Feb 28, 2009
Last update date Mar 06, 2009
Contact name Guoying Wang
E-mail(s) gywang@caas.net.cn
Phone 86-10-62162927
Organization name Chinese Academy of Agricultural Sciences
Department Institute of Crop Sciences
Lab Maize Molecular Biology
Street address Zhongguancun Nandajie 12
City Beijing
ZIP/Postal code 100081
Country China
 
Platform ID GPL4032
Series (1)
GSE15048 Gibberellin-induced gene expression in maize mesocotyl under deep-sowing condition

Data table header descriptions
ID_REF
VALUE MAS5-calculated Signal intensity
ABS_CALL the call in an absolute analysis that indicates if the transcript was present (P), absent (A), marginal (M), or no call (NC)
DETECTION P-VALUE 'detection p-value', p-value that indicates the significance level of the detection call

Data table
ID_REF VALUE ABS_CALL DETECTION P-VALUE
AFFX-BioB-5_at 135.016 P 0.000581214
AFFX-BioB-M_at 153.013 P 8.14279e-05
AFFX-BioB-3_at 152.191 P 5.16732e-05
AFFX-BioC-5_at 298.234 P 6.02111e-05
AFFX-BioC-3_at 398.301 P 5.16732e-05
AFFX-BioDn-5_at 615.195 P 4.42873e-05
AFFX-BioDn-3_at 1939.89 P 6.02111e-05
AFFX-CreX-5_at 4962.38 P 5.16732e-05
AFFX-CreX-3_at 6011.48 P 4.42873e-05
AFFX-DapX-5_at 872.52 P 4.42873e-05
AFFX-DapX-M_at 1709.34 P 5.16732e-05
AFFX-DapX-3_at 2847.69 P 4.42873e-05
AFFX-LysX-5_at 143.277 P 4.42873e-05
AFFX-LysX-M_at 177.089 P 7.00668e-05
AFFX-LysX-3_at 643.411 P 5.16732e-05
AFFX-PheX-5_at 292.722 P 4.42873e-05
AFFX-PheX-M_at 336.434 P 4.42873e-05
AFFX-PheX-3_at 376.727 P 4.42873e-05
AFFX-ThrX-5_at 224.01 P 4.42873e-05
AFFX-ThrX-M_at 496.424 P 4.42873e-05

Total number of rows: 17734

Table truncated, full table size 654 Kbytes.




Supplementary file Size Download File type/resource
GSM375794.CEL.gz 2.1 Mb (ftp)(http) CEL
GSM375794.CHP.gz 97.2 Kb (ftp)(http) CHP
Raw data provided as supplementary file
Processed data included within Sample table
Processed data provided as supplementary file

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