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Sample GSM375788 Query DataSets for GSM375788
Status Public on Mar 07, 2009
Title Deep-sowing 10d treatment Control, biological rep1
Sample type RNA
Source name Mesocotyl, control
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 25, 2009
Contact name Guoying Wang
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 (2)
GSE15048 Gibberellin-induced gene expression in maize mesocotyl under deep-sowing condition
GSE15371 Auxin-induced gene expression in mesocotyl elongation of maize inbred line 3681-4 tolerant to deep-sowing

Data table header descriptions
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
AFFX-BioB-5_at 108.784 P 0.00255552
AFFX-BioB-M_at 145.021 P 0.000195116
AFFX-BioB-3_at 143.466 P 7.00668e-05
AFFX-BioC-5_at 269.699 P 7.00668e-05
AFFX-BioC-3_at 357.5 P 4.42873e-05
AFFX-BioDn-5_at 551.684 P 4.42873e-05
AFFX-BioDn-3_at 1770.06 P 8.14279e-05
AFFX-CreX-5_at 4451.38 P 5.16732e-05
AFFX-CreX-3_at 5845.65 P 4.42873e-05
AFFX-DapX-5_at 595.221 P 4.42873e-05
AFFX-DapX-M_at 1145.28 P 6.02111e-05
AFFX-DapX-3_at 1987.79 P 4.42873e-05
AFFX-LysX-5_at 80.3472 P 4.42873e-05
AFFX-LysX-M_at 133.551 P 0.000146581
AFFX-LysX-3_at 356.191 P 4.42873e-05
AFFX-PheX-5_at 214.243 P 5.16732e-05
AFFX-PheX-M_at 167.323 P 8.14279e-05
AFFX-PheX-3_at 215.853 P 4.42873e-05
AFFX-ThrX-5_at 163.58 P 7.00668e-05
AFFX-ThrX-M_at 280.198 P 4.42873e-05

Total number of rows: 17734

Table truncated, full table size 654 Kbytes.

Supplementary file Size Download File type/resource
GSM375788.CEL.gz 2.2 Mb (ftp)(http) CEL
GSM375788.CHP.gz 97.0 Kb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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