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Sample GSM258199 Query DataSets for GSM258199
Status Public on Jan 26, 2008
Title B14a 11-day seedling aerial tissue biological replicate 1
Sample type RNA
Source name Zea mays 11-day seedling aerial tissue genotype B14a
Organism Zea mays
Characteristics Genotype: B14a; 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)
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 177.287 P 0.0012475
AFFX-BioB-M_at 242.785 P 9.4506e-05
AFFX-BioB-3_at 244.219 P 9.4506e-05
AFFX-BioC-5_at 359.759 P 6.02111e-05
AFFX-BioC-3_at 344.032 P 5.16732e-05
AFFX-BioDn-5_at 473.088 P 4.42873e-05
AFFX-BioDn-3_at 2470.5 P 5.16732e-05
AFFX-CreX-5_at 3820.21 P 5.16732e-05
AFFX-CreX-3_at 5943.14 P 4.42873e-05
AFFX-DapX-5_at 270.832 P 6.02111e-05
AFFX-DapX-M_at 489.556 P 8.14279e-05
AFFX-DapX-3_at 595.962 P 4.42873e-05
AFFX-LysX-5_at 23.388 P 0.000296708
AFFX-LysX-M_at 37.6312 P 0.0138105
AFFX-LysX-3_at 104.384 P 6.02111e-05
AFFX-PheX-5_at 40.6029 P 7.00668e-05
AFFX-PheX-M_at 50.0794 P 0.00141043
AFFX-PheX-3_at 69.1227 P 0.00110099
AFFX-ThrX-5_at 109.915 P 7.00668e-05
AFFX-ThrX-M_at 163.384 P 4.42873e-05

Total number of rows: 17734

Table truncated, full table size 652 Kbytes.

Supplementary file Size Download File type/resource
GSM258199.CEL.gz 3.4 Mb (ftp)(http) CEL
GSM258199.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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