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Sample GSM258194 Query DataSets for GSM258194
Status Public on Jan 26, 2008
Title Oh43 11-day seedling aerial tissue biological replicate 3
Sample type RNA
Source name Zea mays 11-day seedling aerial tissue genotype Oh43
Organism Zea mays
Characteristics Genotype: Oh43; 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 (2)
GSE10236 Similar patterns of additive and non-additive gene expression in maize hybrids with varying levels of heterosis
GSE10237 Gene expression variation among eight maize inbreds

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

Data table
AFFX-BioB-5_at 167.968 P 0.00159257
AFFX-BioB-M_at 226.845 P 9.4506e-05
AFFX-BioB-3_at 166.61 P 5.16732e-05
AFFX-BioC-5_at 327.817 P 5.16732e-05
AFFX-BioC-3_at 346.132 P 4.42873e-05
AFFX-BioDn-5_at 400.427 P 4.42873e-05
AFFX-BioDn-3_at 2390.5 P 5.16732e-05
AFFX-CreX-5_at 3289.58 P 5.16732e-05
AFFX-CreX-3_at 5425.04 P 4.42873e-05
AFFX-DapX-5_at 228.985 P 4.42873e-05
AFFX-DapX-M_at 447.151 P 9.4506e-05
AFFX-DapX-3_at 497.559 P 5.16732e-05
AFFX-LysX-5_at 16.5847 P 0.000662269
AFFX-LysX-M_at 44.4491 P 0.00762003
AFFX-LysX-3_at 83.0397 P 0.000126798
AFFX-PheX-5_at 30.2622 P 0.00159257
AFFX-PheX-M_at 31.6694 P 0.0032123
AFFX-PheX-3_at 47.9278 P 0.026111
AFFX-ThrX-5_at 75.413 P 0.000126798
AFFX-ThrX-M_at 118.272 P 4.42873e-05

Total number of rows: 17734

Table truncated, full table size 652 Kbytes.

Supplementary file Size Download File type/resource
GSM258194.CEL.gz 3.4 Mb (ftp)(http) CEL
GSM258194.CHP.gz 5.8 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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