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Sample GSM205423 Query DataSets for GSM205423
Status Public on Sep 01, 2007
Title B73xMo17 19 DAP endosperm tissue biological replicate 1
Sample type RNA
 
Source name Zea mays 19 day after pollination endosperm tissue
Organism Zea mays
Characteristics Stage: 19 day after pollination endosperm; Genotype: B73xMo17
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 19 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 Initial isolation of 19 DAP endosperm RNAs involved a combination of phenol/chloroform extraction and the TRIzol procedure, and essentially followed published methods (Leiva-Neto et al. 2004). Briefly, powders for 19 DAP endosperm were homogenized in extraction buffer (50mM TRIS pH 8.0, 150mM LiCl, 5mM EDTA pH 8.0, 1% SDS), extracted twice with an equal volume of 1:1 phenol chloroform, extracted with an equal volume of chloroform, and then extracted with TRIzol according to the manufacturer’s instructions (Invitrogen, Carlsbad, CA). The 19 DAP endosperm RNAs were further purified using the RNeasy protocol (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)
GSE8278 Non-additive and imprinted gene expression in hybrid maize endosperm_19DAP
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 270.009 P 7.00668e-05
AFFX-BioB-M_at 331.632 P 4.42873e-05
AFFX-BioB-3_at 388.127 P 4.42873e-05
AFFX-BioC-5_at 638.078 P 6.02111e-05
AFFX-BioC-3_at 668.299 P 4.42873e-05
AFFX-BioDn-5_at 727.714 P 4.42873e-05
AFFX-BioDn-3_at 3597.72 P 6.02111e-05
AFFX-CreX-5_at 6254.7 P 5.16732e-05
AFFX-CreX-3_at 8731.21 P 4.42873e-05
AFFX-DapX-5_at 557.023 P 5.16732e-05
AFFX-DapX-M_at 1019.71 P 9.4506e-05
AFFX-DapX-3_at 1344.22 P 5.16732e-05
AFFX-LysX-5_at 64.5557 P 7.00668e-05
AFFX-LysX-M_at 92.5798 P 0.0113844
AFFX-LysX-3_at 238.701 P 5.16732e-05
AFFX-PheX-5_at 104.795 P 6.02111e-05
AFFX-PheX-M_at 97.2685 P 0.000258358
AFFX-PheX-3_at 124.513 P 0.000296708
AFFX-ThrX-5_at 217.25 P 0.000126798
AFFX-ThrX-M_at 203.202 P 7.00668e-05

Total number of rows: 17734

Table truncated, full table size 648 Kbytes.




Supplementary file Size Download File type/resource
GSM205423.CEL.gz 3.4 Mb (ftp)(http) CEL
GSM205423.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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