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Sample GSM385710 Query DataSets for GSM385710
Status Public on Mar 26, 2009
Title Deep-sowing 10d treatment TIBA, biological rep2
Sample type RNA
Source name Mesocotyl, TIBA
Organism Zea mays
Characteristics genotype: Maize inbred line 3681-4
age: 10d after sowing
tissue: mesocotyls
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 Mar 24, 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 (1)
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 142.89 P 0.000340305
AFFX-BioB-M_at 153.18 P 9.4506e-05
AFFX-BioB-3_at 130.609 P 7.00668e-05
AFFX-BioC-5_at 381.263 P 5.16732e-05
AFFX-BioC-3_at 463.469 P 4.42873e-05
AFFX-BioDn-5_at 761.534 P 4.42873e-05
AFFX-BioDn-3_at 2355.55 P 6.02111e-05
AFFX-CreX-5_at 5460.92 P 5.16732e-05
AFFX-CreX-3_at 7172.42 P 4.42873e-05
AFFX-DapX-5_at 430.986 P 4.42873e-05
AFFX-DapX-M_at 835.221 P 8.14279e-05
AFFX-DapX-3_at 1332.66 P 4.42873e-05
AFFX-LysX-5_at 61.0918 P 4.42873e-05
AFFX-LysX-M_at 85.3965 P 0.000509415
AFFX-LysX-3_at 310.956 P 4.42873e-05
AFFX-PheX-5_at 115.291 P 5.16732e-05
AFFX-PheX-M_at 98.4124 P 0.000258358
AFFX-PheX-3_at 130.327 P 4.42873e-05
AFFX-ThrX-5_at 127.51 P 0.000296708
AFFX-ThrX-M_at 199.948 P 4.42873e-05

Total number of rows: 17734

Table truncated, full table size 653 Kbytes.

Supplementary file Size Download File type/resource
GSM385710.CEL.gz 2.1 Mb (ftp)(http) CEL
GSM385710.CHP.gz 97.4 Kb (ftp)(http) CHP
Processed data provided as supplementary file
Processed data included within Sample table

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