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Sample GSM202401 Query DataSets for GSM202401
Status Public on Dec 01, 2007
Title Zmet2 study 11-day seedling aerial tissue genotype B73 zmet2-m1 Rep4
Sample type RNA
Source name B73 zmet2-m1 seedling
Organism Zea mays
Characteristics Stage: 11-day seedling all aerial tissue; Genotype: B73 zmet2-m1
Growth protocol The zmet2-m1 allele was generated by Mu transposon mutagenesis and contains a Mu insertion in exon 18 that results in a loss-of-function mutation. This allele was backcrossed into the Mo17 and B73 maize inbred lines for six generations and then self-pollinated for two generations to produce homozygous near-isogenic lines of Mo17 and B73 that are homozygous for the zmet2-m1 allele. Three biological replicates of the B73 and B73 zmet2-m1 genotypes were grown sequentially over a 5 week period during May and June 2005. Three additional biological replicates involving the B73, B73 zmet2-m1, Mo17 and Mo17 zmet2-m1 genotypes were grown during January and February 2006. The plants were grown using standard greenhouse conditions (1:1 mix of autocalaved field soil and MetroMix; 16 hours light and 8 hours dark; daytime temperature of 30 C and night temperature of 22 C) and were sampled for gene expression on the 11th day after planting between 8 am and 9 am. The plants were cut immediately above the highest root, thus all above-ground tissues and meristems were collected. For each biological replicate, the seeds were planted such that one seed of each genotype was present in every pot. Eight pots were selected for tissue collection resulting in sampling of eight plants per genotype in each replicate. The sampled tissues were flash frozen in liquid nitrogen and stored at -80C prior to RNA isolation.
Extracted molecule total RNA
Extraction protocol For RNA isolation tissues from 8 seedlings per genotype per biological replicate were pooled and ground in liquid nitrogen. RNAs were extracted using Trizol reagent according to the manufacturer’s instructions (Invitrogen Corp., Carlsbad CA) and purified using the RNeasy kit, according to the manufactures instructions (Qiagen Corp., Valencia, CA). The quality and quantity of all purified RNA samples were assessed using agarose gel electrophoresis and the Nanodrop spectrophotometer (Nanodrop Technologies, Montchanin, DE).
Label biotin
Label protocol Eight μg 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 No other relevant details
Data processing The MAS5.0 values are available in the submitted file; RMA processing of the .cel files was also used.
Submission date Jun 20, 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 (1)
GSE8188 Expression profiling of zmet2-m1 mutants relative to wild-type

Data table header descriptions
VALUE MAS5.0 processed signal value
ABS_CALL Present-Absent-Marginal Call

Data table
AFFX-BioB-5_at 223.45 P 9.4506e-05
AFFX-BioB-M_at 288.303 P 4.42873e-05
AFFX-BioB-3_at 232.131 P 4.42873e-05
AFFX-BioC-5_at 518.105 P 4.42873e-05
AFFX-BioC-3_at 467.698 P 5.16732e-05
AFFX-BioDn-5_at 725.087 P 4.42873e-05
AFFX-BioDn-3_at 2441.19 P 5.16732e-05
AFFX-CreX-5_at 4304 P 5.16732e-05
AFFX-CreX-3_at 6313.92 P 4.42873e-05
AFFX-DapX-5_at 196.676 P 4.42873e-05
AFFX-DapX-M_at 433.351 P 7.00668e-05
AFFX-DapX-3_at 675.404 P 4.42873e-05
AFFX-LysX-5_at 29.1257 P 7.00668e-05
AFFX-LysX-M_at 41.8584 P 0.00401721
AFFX-LysX-3_at 112.733 P 6.02111e-05
AFFX-PheX-5_at 54.6384 P 9.4506e-05
AFFX-PheX-M_at 47.3934 P 0.000296708
AFFX-PheX-3_at 45.8308 P 5.16732e-05
AFFX-ThrX-5_at 72.7268 P 0.000169227
AFFX-ThrX-M_at 107.215 P 4.42873e-05

Total number of rows: 17734

Table truncated, full table size 655 Kbytes.

Supplementary file Size Download File type/resource
GSM202401.CEL.gz 3.3 Mb (ftp)(http) CEL
GSM202401.CHP.gz 5.6 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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