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Sample GSM202281 Query DataSets for GSM202281
Status Public on Jun 21, 2007
Title Mo17 11-day seedling aerial tissue biological replicate 2
Sample type RNA
Source name Zea mays 11-day seedling aerial tissue genotype Mo17
Organism Zea mays
Characteristics Genotype: Mo17 Stage: 11-day old seedling, all aerial tissue
Extracted molecule total RNA
Extraction protocol Seeds for inbreds Mo17 and B73 and hybrids Mo17 x B73 and B73 x Mo17 were sown and grown under greenhouse conditions for 11 days and then sampled for gene expression analysis. Three biological replicates were planted and grown sequentially over an 5-week period during May 2005. Seeds were planted such that one seed of each genotype was present in every pot. Twelve pots were selected for tissue collection; thus 12 plants were sampled per genotype. All plants were sampled between 9 am and 10 am and plants were cut immediately above the highest root; thus all aboveground tissues and meristems were sampled. The sampled tissues were flash frozen in liquid nitrogen and stored at -80 C prior to RNA isolation.
Label biotin
Label protocol For seedling RNA isolation, tissues from 12 seedlings/genotype/biological replicate were pooled and ground in liquid nitrogen. RNAs were extracted using Trizol reagent according to the manufacturer’s instructions (Invitrogen, Carlsbad, CA). All RNAs were subsequently subjected to DNAse treatment and phenol:chloroform extraction. RNAs were precipitated with 0.13 volume sodium acetate (pH 5.5) and 2.53 volume ethanol. Resuspended RNAs were purified further using the RNeasy system, according to the manufacturer’s instructions (QIAGEN, Valencia, 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)
GSE8174 Cis-transcriptional variation in maize inbred lines B73 and Mo17 leads to additive expression - Seedling 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 182.749 P 0.000389797
AFFX-BioB-M_at 209.868 P 8.14279e-05
AFFX-BioB-3_at 169.18 P 4.42873e-05
AFFX-BioC-5_at 290.066 P 7.00668e-05
AFFX-BioC-3_at 299.381 P 5.16732e-05
AFFX-BioDn-5_at 405.877 P 4.42873e-05
AFFX-BioDn-3_at 1999.26 P 5.16732e-05
AFFX-CreX-5_at 3336.58 P 5.16732e-05
AFFX-CreX-3_at 5199.53 P 4.42873e-05
AFFX-DapX-5_at 170.596 P 4.42873e-05
AFFX-DapX-M_at 346.801 P 0.000169227
AFFX-DapX-3_at 419.674 P 5.16732e-05
AFFX-LysX-5_at 30.649 P 0.000146581
AFFX-LysX-M_at 45.0567 P 0.00762003
AFFX-LysX-3_at 105.382 P 8.14279e-05
AFFX-PheX-5_at 31.1713 P 0.000224668
AFFX-PheX-M_at 44.6565 P 0.0020226
AFFX-PheX-3_at 39.6815 P 0.000389797
AFFX-ThrX-5_at 50.914 P 0.000445901
AFFX-ThrX-M_at 67.2142 P 4.42873e-05

Total number of rows: 17734

Table truncated, full table size 652 Kbytes.

Supplementary file Size Download File type/resource
GSM202281.CEL.gz 3.4 Mb (ftp)(http) CEL
GSM202281.CHP.gz 5.7 Mb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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