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Sample GSM202292 Query DataSets for GSM202292
Status Public on Jun 21, 2007
Title B73 immature ear tissue, biological replicate 1
Sample type RNA
 
Source name Zea mays immature ear tissue, genotype B73
Organism Zea mays
Characteristics Stage: immature ear (3.7-5.4mm); Genotype: B73
Growth protocol Immature ears from inbreds Mo17 and B73
and hybrids Mo17xB73 and B73xMo17 were collected from
field-grown maize plants during July 2005 for gene expression
analysis. The maize plants were grown on the St. Paul campus
Agricultural Experiment Station. Ears were collected for each
genotype between 9 am and 11 am on each of three consecutive
days from various positions in the field. Ears ranging
from 3.7 to 5.4 mm in length were sampled. Ears were flash
frozen in liquid nitrogen following the manual removal of
husks and silks.
Extracted molecule total RNA
Extraction protocol For immature ear RNA isolation, tissues from 6 ears/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 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)
GSE8176 Cis-transcriptional variation in maize inbred lines B73 and Mo17 leads to additive expression - Immature ear 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 246.712 P 0.000146581
AFFX-BioB-M_at 267.86 P 4.42873e-05
AFFX-BioB-3_at 194.304 P 4.42873e-05
AFFX-BioC-5_at 415.62 P 4.42873e-05
AFFX-BioC-3_at 379.906 P 4.42873e-05
AFFX-BioDn-5_at 516.286 P 4.42873e-05
AFFX-BioDn-3_at 2107.28 P 5.16732e-05
AFFX-CreX-5_at 4264.71 P 5.16732e-05
AFFX-CreX-3_at 5670.68 P 4.42873e-05
AFFX-DapX-5_at 47.8686 P 0.000126798
AFFX-DapX-M_at 83.1963 P 0.000752926
AFFX-DapX-3_at 112.08 P 0.000389797
AFFX-LysX-5_at 3.89201 A 0.313723
AFFX-LysX-M_at 7.77566 A 0.354453
AFFX-LysX-3_at 21.0943 P 0.0151826
AFFX-PheX-5_at 5.21125 A 0.368438
AFFX-PheX-M_at 12.8786 A 0.275146
AFFX-PheX-3_at 24.4194 A 0.139482
AFFX-ThrX-5_at 13.1231 A 0.275146
AFFX-ThrX-M_at 22.8184 P 0.0219019

Total number of rows: 17734

Table truncated, full table size 654 Kbytes.




Supplementary file Size Download File type/resource
GSM202292.CEL.gz 3.4 Mb (ftp)(http) CEL
GSM202292.CHP.gz 5.7 Mb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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