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Sample GSM258187 Query DataSets for GSM258187
Status Public on Jan 26, 2008
Title B84xB73 11-day seedling aerial tissue biological replicate 2
Sample type RNA
Source name Zea mays 11-day seedling aerial tissue genotype B84xB73
Organism Zea mays
Characteristics Genotype: B84xB73; Stage: 11-day old seedling, all aerial tissue
Growth protocol Seeds for maize inbreds and hybrids were sown and grown under greenhouse conditions for 11 days and then sampled for gene expression analysis. Three biological replicates were grown using standard greenhouse conditions (1:1 mix of autoclaved field soil and MetroMix; 16 hours light and 8 hours dark; daytime temperature of 30ºC and night temperature of 22ºC) and sampled between 8:00 and 9:00 am. The plants were cut immediately above the highest brace root, thus all above-ground tissues and meristems were collected. Each biological replicate consisted of pooled tissue from eight different seedlings of the same genotype. The sampled tissues were flash frozen in liquid nitrogen and stored at -80 C prior to RNA isolation.
Extracted molecule total RNA
Extraction protocol Total RNA samples were isolated using TRIzol (Invitrogen, Carlsbad, CA) and purified using the RNeasy system (QIAGEN, Valencia, CA).
Label biotin
Label protocol Eight ug of total RNA was labeled for each hybridization using the One-Cycle cDNA Synthesis Kit, according to the manufacturer’s instructions (Affymetrix, Santa Clara CA).
Hybridization protocol Hybridization was performed according to the recommended Affymetrix protocols at the University of Minnesota Microarray facility.
Scan protocol The Genechip 3000 scanner was used to scan each array
Description refer to PMID: 16702414
Data processing MAS5.0 values are reported; the .cel file is also available
Submission date Jan 22, 2008
Last update date Jan 25, 2008
Contact name Robert M Stupar
Organization name University of Minnesota
Department Agronomy and Plant Genetics
Street address 1991 Upper Buford Circle
City Saint Paul
State/province MN
ZIP/Postal code 55108
Country USA
Platform ID GPL4032
Series (1)
GSE10236 Similar patterns of additive and non-additive gene expression in maize hybrids with varying levels of heterosis

Data table header descriptions
VALUE MAS5.0 signal
ABS_CALL Present-Absent-Marginal Call

Data table
AFFX-BioB-5_at 138.768 P 0.000753643
AFFX-BioB-M_at 199.907 P 0.000169227
AFFX-BioB-3_at 169.17 P 5.16732e-05
AFFX-BioC-5_at 294.783 P 6.02111e-05
AFFX-BioC-3_at 289.53 P 4.42873e-05
AFFX-BioDn-5_at 344.178 P 4.42873e-05
AFFX-BioDn-3_at 1960.85 P 5.16732e-05
AFFX-CreX-5_at 3045.17 P 4.42873e-05
AFFX-CreX-3_at 5356.57 P 4.42873e-05
AFFX-DapX-5_at 216.315 P 7.00668e-05
AFFX-DapX-M_at 396.353 P 8.14279e-05
AFFX-DapX-3_at 482.413 P 5.16732e-05
AFFX-LysX-5_at 26.3358 P 0.0020226
AFFX-LysX-M_at 46.9684 P 0.0103112
AFFX-LysX-3_at 85.4704 P 0.00010954
AFFX-PheX-5_at 35.5089 P 0.000146581
AFFX-PheX-M_at 33.2871 P 0.000581214
AFFX-PheX-3_at 42.4284 P 0.000258358
AFFX-ThrX-5_at 80.9796 P 7.00668e-05
AFFX-ThrX-M_at 122.554 P 4.42873e-05

Total number of rows: 17734

Table truncated, full table size 653 Kbytes.

Supplementary file Size Download File type/resource
GSM258187.CEL.gz 3.4 Mb (ftp)(http) CEL
GSM258187.CHP.gz 5.7 Mb (ftp)(http) CHP
Processed data included within Sample table
Raw data provided as supplementary file
Processed data provided as supplementary file

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