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Sample GSM202311 Query DataSets for GSM202311
Status Public on Jun 21, 2007
Title Mo17xB73 19 day after pollination embryo tissue, biological replicate 1
Sample type RNA
 
Source name Zea mays 19 day after pollination embryo tissue, genotype Mo17xB73
Organism Zea mays
Characteristics Stage: 19 day after pollination embryo; Genotype: Mo17xB73
Growth protocol Embryos were collected 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 time intervals within the same week. Embryos were collected at 19 days after pollination (DAP) for the three bioreplicates. All tissues were flash frozen in a dry ice-cooled ethanol bath and subsequently stored at -80C. We collected the plant materials for each biological replicate on the same date between 9 am and 10 am. The three biological replicates represent collections performed on three different dates.
Extracted molecule total RNA
Extraction protocol Embryo RNAs were isolated using the plant RNeasy kit, according to the manufacturer’s instructions (QIAGEN).
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 Jun 19, 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)
GSE8179 Cis-transcriptional variation in maize inbred lines B73 and Mo17 leads to additive expression - Embryo data
GSE8194 Cis-transcriptional variation in maize inbred lines B73 and Mo17 leads to additive expression

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 231.811 P 0.000169227
AFFX-BioB-M_at 286.527 P 4.42873e-05
AFFX-BioB-3_at 268.403 P 4.42873e-05
AFFX-BioC-5_at 466.625 P 5.16732e-05
AFFX-BioC-3_at 451.152 P 5.16732e-05
AFFX-BioDn-5_at 703.845 P 4.42873e-05
AFFX-BioDn-3_at 2848.65 P 6.02111e-05
AFFX-CreX-5_at 5272.46 P 5.16732e-05
AFFX-CreX-3_at 7340.81 P 4.42873e-05
AFFX-DapX-5_at 459.329 P 4.42873e-05
AFFX-DapX-M_at 920.547 P 6.02111e-05
AFFX-DapX-3_at 1096.91 P 4.42873e-05
AFFX-LysX-5_at 49.1477 P 7.00668e-05
AFFX-LysX-M_at 79.5436 P 0.000972149
AFFX-LysX-3_at 203.583 P 7.00668e-05
AFFX-PheX-5_at 93.0513 P 9.4506e-05
AFFX-PheX-M_at 110.518 P 4.42873e-05
AFFX-PheX-3_at 108.28 P 6.02111e-05
AFFX-ThrX-5_at 137.706 P 0.00010954
AFFX-ThrX-M_at 187.066 P 4.42873e-05

Total number of rows: 17734

Table truncated, full table size 654 Kbytes.




Supplementary file Size Download File type/resource
GSM202311.CEL.gz 3.5 Mb (ftp)(http) CEL
GSM202311.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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