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Sample GSM202278 Query DataSets for GSM202278
Status Public on Jun 21, 2007
Title B73 11-day seedling aerial tissue biological replicate 1
Sample type RNA
 
Source name Zea mays 11-day seedling aerial tissue genotype B73
Organism Zea mays
Characteristics Genotype: B73 Stage: 11-day old seedling, all aerial tissue
Growth 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.
Extracted molecule total RNA
Extraction 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).
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 Apr 23, 2013
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 (3)
GSE8174 Cis-transcriptional variation in maize inbred lines B73 and Mo17 leads to additive expression - Seedling data
GSE8188 Expression profiling of zmet2-m1 mutants relative to wild-type
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 203.998 P 0.000224668
AFFX-BioB-M_at 301.734 P 7.00668e-05
AFFX-BioB-3_at 244.317 P 4.42873e-05
AFFX-BioC-5_at 439.396 P 6.02111e-05
AFFX-BioC-3_at 408.138 P 5.16732e-05
AFFX-BioDn-5_at 571.079 P 4.42873e-05
AFFX-BioDn-3_at 2412.06 P 5.16732e-05
AFFX-CreX-5_at 4700.42 P 5.16732e-05
AFFX-CreX-3_at 5906.06 P 4.42873e-05
AFFX-DapX-5_at 218.689 P 8.14279e-05
AFFX-DapX-M_at 376.422 P 0.000195116
AFFX-DapX-3_at 522.841 P 4.42873e-05
AFFX-LysX-5_at 27.0873 P 0.000972149
AFFX-LysX-M_at 49.8037 P 0.00762003
AFFX-LysX-3_at 137.223 P 0.000258358
AFFX-PheX-5_at 35.4572 P 0.000224668
AFFX-PheX-M_at 41.397 P 0.0012475
AFFX-PheX-3_at 46.9164 P 0.000389797
AFFX-ThrX-5_at 50.9568 P 0.00141043
AFFX-ThrX-M_at 85.9289 P 4.42873e-05

Total number of rows: 17734

Table truncated, full table size 654 Kbytes.




Supplementary file Size Download File type/resource
GSM202278.CEL.gz 3.4 Mb (ftp)(http) CEL
GSM202278.CHP.gz 5.8 Mb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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