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Sample GSM258183 Query DataSets for GSM258183
Status Public on Jan 26, 2008
Title B84 11-day seedling aerial tissue biological replicate 2
Sample type RNA
Source name Zea mays 11-day seedling aerial tissue genotype B84
Organism Zea mays
Characteristics Genotype: B84; 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 202.312 P 0.000224668
AFFX-BioB-M_at 298.226 P 5.16732e-05
AFFX-BioB-3_at 244.124 P 6.02111e-05
AFFX-BioC-5_at 383.309 P 5.16732e-05
AFFX-BioC-3_at 373.038 P 5.16732e-05
AFFX-BioDn-5_at 500.84 P 4.42873e-05
AFFX-BioDn-3_at 2348.35 P 5.16732e-05
AFFX-CreX-5_at 3718.38 P 4.42873e-05
AFFX-CreX-3_at 5441.15 P 4.42873e-05
AFFX-DapX-5_at 240.742 P 5.16732e-05
AFFX-DapX-M_at 420.916 P 8.14279e-05
AFFX-DapX-3_at 656.234 P 4.42873e-05
AFFX-LysX-5_at 27.1078 P 0.000195116
AFFX-LysX-M_at 41.4697 P 0.00499819
AFFX-LysX-3_at 91.5962 P 4.42873e-05
AFFX-PheX-5_at 41.2336 P 0.000169227
AFFX-PheX-M_at 35.2852 P 0.000258358
AFFX-PheX-3_at 71.5111 P 0.0012475
AFFX-ThrX-5_at 81.85 P 7.00668e-05
AFFX-ThrX-M_at 149.429 P 4.42873e-05

Total number of rows: 17734

Table truncated, full table size 653 Kbytes.

Supplementary file Size Download File type/resource
GSM258183.CEL.gz 3.3 Mb (ftp)(http) CEL
GSM258183.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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