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Sample GSM205365 Query DataSets for GSM205365
Status Public on Sep 01, 2007
Title Mo17 13 DAP endosperm tissue biological replicate 1
Sample type RNA
 
Source name Zea mays 13 day after pollination endosperm tissue
Organism Zea mays
Characteristics Stage: 13 day after pollination endosperm; Genotype: Mo17
Growth protocol Endosperm tissues were isolated from kernels of inbreds Mo17 and B73, and hybrids Mo17xB73 and B73xMo17 for gene expression analysis. Samples were collected during August 2005 from field-grown maize plants grown on the St. Paul campus Agricultural Experiment Station. Inbred and hybrid crosses were performed at three different dates to produce biological replicates. The crosses for all genotypes within a biological replicate were performed within 30 minutes of each other. Six ears of each genotypes were harvested at 13 DAP. Six endosperms were collected from each of the six ears and pooled for a total of 36 endosperms from each genotype by biological replicate combination. All tissues were flash frozen in a dry-ice cooled ethanol bath, and subsequently stored at −80˚C.
Extracted molecule total RNA
Extraction protocol RNAs for 13 DAP endosperm tissues were isolated using the plant RNeasy kit, according to the manufacturer’s instructions (Qiagen Corp., Valencia, CA). All purified RNA samples were quantified and qualified using the Nanodrop spectrophotometer (Nanodrop Technologies, Montchanin, DE) and agarose gel electrophoresis.
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 No other relevant details
Data processing MAS5.0 values are reported; the .cel file is also available
 
Submission date Jun 25, 2007
Last update date Aug 14, 2011
Contact name Nathan M Springer
E-mail(s) springer@umn.edu
Phone 6126246241
Fax 6126251738
Organization name University of Minnesota
Department Plant Biology
Street address 1445 Gortner Ave
City Saint Paul
State/province MN
ZIP/Postal code 55108
Country USA
 
Platform ID GPL4032
Series (2)
GSE8275 Non-additive and imprinted gene expression in hybrid maize endosperm_13DAP
GSE8308 Non-additive and imprinted gene expression in hybrid maize endosperm_13DAP and 19DAP

Data table header descriptions
ID_REF
VALUE MAS5.0 processed signal value
ABS_CALL Present-Absent-Marginal Call
DETECTION P-VALUE P-value for ABS_Call

Data table
ID_REF VALUE ABS_CALL DETECTION P-VALUE
AFFX-BioB-5_at 324.956 P 0.000126798
AFFX-BioB-M_at 477.053 P 4.42873e-05
AFFX-BioB-3_at 383.711 P 4.42873e-05
AFFX-BioC-5_at 620.12 P 5.16732e-05
AFFX-BioC-3_at 630.955 P 5.16732e-05
AFFX-BioDn-5_at 963.171 P 4.42873e-05
AFFX-BioDn-3_at 3844.51 P 5.16732e-05
AFFX-CreX-5_at 7038.24 P 4.42873e-05
AFFX-CreX-3_at 9053.47 P 4.42873e-05
AFFX-DapX-5_at 534.532 P 4.42873e-05
AFFX-DapX-M_at 1064.2 P 7.00668e-05
AFFX-DapX-3_at 1131.15 P 5.16732e-05
AFFX-LysX-5_at 50.5549 P 4.42873e-05
AFFX-LysX-M_at 82.0449 P 0.00141043
AFFX-LysX-3_at 162.175 P 8.14279e-05
AFFX-PheX-5_at 80.0247 P 6.02111e-05
AFFX-PheX-M_at 95.791 P 0.000856509
AFFX-PheX-3_at 114.669 P 8.14279e-05
AFFX-ThrX-5_at 167.481 P 5.16732e-05
AFFX-ThrX-M_at 205.696 P 4.42873e-05

Total number of rows: 17734

Table truncated, full table size 651 Kbytes.




Supplementary file Size Download File type/resource
GSM205365.CEL.gz 3.5 Mb (ftp)(http) CEL
GSM205365.CHP.gz 5.9 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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