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Sample GSM202309 Query DataSets for GSM202309
Status Public on Jun 21, 2007
Title Mo17 19 day after pollination embryo tissue, biological replicate 1
Sample type RNA
Source name Zea mays 19 day after pollination embryo tissue, genotype Mo17
Organism Zea mays
Characteristics Stage: 19 day after pollination embryo; Genotype: Mo17
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
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
VALUE MAS5.0 processed signal value
ABS_CALL Present-Absent-Marginal Call

Data table
AFFX-BioB-5_at 199.677 P 0.000340305
AFFX-BioB-M_at 282.713 P 5.16732e-05
AFFX-BioB-3_at 229.568 P 4.42873e-05
AFFX-BioC-5_at 456.059 P 5.16732e-05
AFFX-BioC-3_at 415.092 P 4.42873e-05
AFFX-BioDn-5_at 592.522 P 4.42873e-05
AFFX-BioDn-3_at 2671.1 P 6.02111e-05
AFFX-CreX-5_at 5032.4 P 5.16732e-05
AFFX-CreX-3_at 7493.77 P 4.42873e-05
AFFX-DapX-5_at 599.112 P 4.42873e-05
AFFX-DapX-M_at 1076.81 P 6.02111e-05
AFFX-DapX-3_at 1228.2 P 4.42873e-05
AFFX-LysX-5_at 49.519 P 4.42873e-05
AFFX-LysX-M_at 89.1825 P 0.00556451
AFFX-LysX-3_at 201.551 P 8.14279e-05
AFFX-PheX-5_at 74.5409 P 9.4506e-05
AFFX-PheX-M_at 115.925 P 0.000169227
AFFX-PheX-3_at 124.935 P 5.16732e-05
AFFX-ThrX-5_at 133.99 P 0.00010954
AFFX-ThrX-M_at 205.303 P 5.16732e-05

Total number of rows: 17734

Table truncated, full table size 652 Kbytes.

Supplementary file Size Download File type/resource
GSM202309.CEL.gz 3.5 Mb (ftp)(http) CEL
GSM202309.CHP.gz 5.9 Mb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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