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Sample GSM258534 Query DataSets for GSM258534
Status Public on Jan 24, 2008
Title DpDf siblings in family segregating for T5-6b DpDf plants; Biological replicate 2
Sample type RNA
 
Source name Zea mays 11-day seedling aerial tissue; DpDf siblings in family segregating for T5-6b DpDf plants
Organism Zea mays
Characteristics Genotype: DpDf siblings (B73 background); Stage: 11-day seedling, all aerial tissue; Seed Source:49646-1self
Growth protocol The T5-6b translocation, backcrossed into B73 maize genetic background for over 10 generations, was available from the University of Minnesota collection. The interchange T5-6b possesses a break at 5S.1 (ca. 300 cM on IBM2 2004 Neighbors genetic map) and between the middle and distal chromomere of the satellite of 6S (break occurs prior to 50 cM on IBM2 2004 Neighbors genetic map). Duplicate-Deficient (DpDf) heterozygous plants were identified among progeny derived from crossing a female B73/T5-6b translocation heterozygote by a male B73 plant. The chromosome constitution of DpDf heterozygous plants is normal for all chromosomes except 5 and 6. The DpDf plants contain one normal chromosome 6 and one 65 chromosome that is lacking the terminal chromomere of the chromosome 6 satellite and contains ~90% of the short arm of chromosome 5. Four biological replicates were grown using standard greenhouse conditions (1:1 mix of autoclaved field soil and MetroMix; 16 hours light and 8 hours dark; daytime temperature of 300C and night temperature of 220C) and sampled for gene expression on the 11th day after planting between 8:00 and 9:00 am. The plants were cut immediately above the highest brace root, thus all above-ground tissues and meristems were collected. For each biological replicate, sibling seeds produced by self pollination of a DpDf plant that segregate for wild-type and DpDf plants were planted individually and thirty plants were collected and genotyped using an SSR marker (bnlg161) that is tightly linked to the translocation breakpoint on chromosome 5. A pool of twelve wild-type plants and a separate pool of twelve DpDf plants were generated from each of the biological replicates. The sampled tissues were flash frozen in liquid nitrogen and stored at -80 0C 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). 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 No other relevant details
Data processing MAS5.0 values are reported; the .cel file is also available
 
Submission date Jan 23, 2008
Last update date Jan 23, 2008
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 (1)
GSE10243 Profiling expression changes caused by a segmental aneuploid in maize

Data table header descriptions
ID_REF
VALUE GC-RMA signal

Data table
ID_REF VALUE
AFFX-BioB-3_at 189.7
AFFX-BioB-5_at 172.1
AFFX-BioB-M_at 213.5
AFFX-BioC-3_at 337.7
AFFX-BioC-5_at 295.8
AFFX-BioDn-3_at 2737
AFFX-BioDn-5_at 497.6
AFFX-CreX-3_at 12712
AFFX-CreX-5_at 7613
AFFX-DapX-3_at 887.8
AFFX-DapX-5_at 139.2
AFFX-DapX-M_at 407.5
AFFX-LysX-3_at 156.3
AFFX-LysX-5_at 27.69
AFFX-LysX-M_at 33.96
AFFX-PheX-3_at 68.6
AFFX-PheX-5_at 34.33
AFFX-PheX-M_at 48.85
AFFX-r2-Bs-dap-3_at 1442
AFFX-r2-Bs-dap-5_at 153

Total number of rows: 17734

Table truncated, full table size 393 Kbytes.




Supplementary file Size Download File type/resource
GSM258534.CEL.gz 3.3 Mb (ftp)(http) CEL
GSM258534.CHP.gz 5.6 Mb (ftp)(http) CHP
Raw data provided as supplementary file
Processed data included within Sample table
Processed data provided as supplementary file

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