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Sample GSM825809 Query DataSets for GSM825809
Status Public on Nov 22, 2011
Title species: Corn - rep2
Sample type RNA
 
Source name 8##GRO:0005306## (species: Corn)
Organism Zea mays
Characteristics age: 7d
tissue: seedling
Growth protocol Growth Description: Seedlings were grown in the greenhouse for 7 days.
Extracted molecule total RNA
Extraction protocol Hot Phenol/Guanidine Thiocyanate and RNeasy Clean up
Label biotin
Label protocol Affy-Eukaryotic Target Preparation
 
Hybridization protocol Affy- Eukaryotic Target Hybridization
Scan protocol Affy- Array Scanning
Description gro: 0005118##GRO:0005306## (Organism Part); GRO:0007060 (Development Stage); 7 days (Age);
Data processing The MAS5.0 Normalization is performed using the justMAS function in the simpleaffy package of Bioconductor (www.bioconductor.org). The target value is 500 for all cases. The code was developed using R2.4.1, Bioconductor 1.9, and simpleaffy 2.8.0. The CDF files were downloaded from the Bioconductor website at http://www.bioconductor.org/packages/release/AffymetrixChip.html. The normalization scripts are available from the PLEXdb team by request.
 
Submission date Nov 02, 2011
Last update date Nov 22, 2011
Contact name PLEXdb Curator, Sudhansu Dash
Organization name Iowa State University
Department Virtual Reality Application Center
Lab PLEXdb
Street address 1023 Crop Genomes Informatics Lab (Iowa State University)
City Ames
State/province IA
ZIP/Postal code 50011
Country USA
 
Platform ID GPL1340
Series (1)
GSE33391 Cross-species Detection in Barley1 GeneChip Array

Data table header descriptions
ID_REF Affymetrix probe set id
VALUE MAS5-calculated Signal intensity
ABS_CALL the call in an absolute analysis that indicates if the transcript was present (P), absent (A), marginal (M), or no call (NC)
DETECTION P-VALUE 'detection p-value', p-value that indicates the significance level of the detection call

Data table
ID_REF VALUE ABS_CALL DETECTION P-VALUE
1200459_Reg_88-1740_at 1482.4 P 0
1289374_Reg_826-1545_at 207.74 A 0
149174_Reg_66-1115_at 168.17 A 0
150775_Reg_211-1236_at 223.65 A 0
23381122_R_1101-1898_at 977.93 A 0
2623978_R_1403-2212_at 1059.3 P 0
40321-46140.AF427791_x_at 51.916 A 0
48446_Reg_1231-2205_at 141.51 A 0
48446_Reg_137-1204_at 50.571 A 0
74797-75570.AF427791_x_at 109.84 A 0
8829-9073.AF427791_x_at 105.83 A 0
9507414_R_4264-4644_at 3148 A 0
A00196.1_at 628.67 A 0
A06498.1_s_at 135.72 A 0
AB011264_at 445.13 A 0
AB011266_at 706.66 A 0
AB019525_at 218.02 A 0
AB024007_at 407.81 A 0
AF016328_at 3329.8 A 0
AF026538_at 774.15 A 0

Total number of rows: 22840

Table truncated, full table size 582 Kbytes.




Supplementary file Size Download File type/resource
GSM825809_0315-3.CEL.gz 3.5 Mb (ftp)(http) CEL
Processed data included within Sample table

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