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Sample GSM26046 Query DataSets for GSM26046
Status Public on Aug 13, 2009
Title 2102_1_C0001_T0002
Sample type RNA
 
Channel 1
Source name Control (CH1) source: Seedling (leaf) grown hydrponically for 11 days without treatment
Organism Oryza sativa
Extracted molecule total RNA
 
Channel 2
Source name Target (CH2) source: 11-days grown leaves treated with 0.1M mannitol for 2days
Organism Oryza sativa
Extracted molecule total RNA
 
 
Description Control (CH1): The japonica rice variety Nipponbare were grown hydrponically for 11-days without treatment. Leaves of plants used for totall RNA extraction by phenol-SDS method. Messenger RNA was purified by oligo(dT) cellulose, labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Target (CH2): The japonica rice variety Nipponbare were grown hydrponically for 11-days that treated with 0.1M mannitol for 2days. Leaves of plants used for total RNA extraction by phenol-SDS method. Messenger RNA was purified by oligo(dT) cellulose, labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Keyword: Rice microarray project, Rice 8987 EST array, Osmotic, ,
 
Submission date Jun 25, 2004
Last update date Aug 13, 2008
Contact name Shoshi Kikuchi
E-mail(s) skikuchi@nias.affrc.go.jp
Phone 81-298-38-7007
Fax 81-298-38-7007
URL http://cdna01.dna.affrc.go.jp/cDNA/
Organization name National Institute of Agrobiological Sciences
Department Molecular Genetics
Lab Gene Expression
Street address 2-1-2 Kan-nondai
City Tsukuba
State/province Ibaraki
ZIP/Postal code 305-8602
Country Japan
 
Platform ID GPL1245
Series (1)
GSE1532 NIAS Rice Project

Data table header descriptions
ID_REF
VALUE Normalized log2 ratio of means defined by CH2_RAW/CH1_RAW
Ratio of Means Unnormalized ratio of means defined by CH1_RAW/CH2_RAW
CH1_RAW_spot1 Signal intensity at control spot 1 (Left side of the glass. Background-noise-processed value quantified by ArrayGauge)
CH1_RAW_spot2 Signal intensity at control spot 2 (Right side of the glass)
CH1_RAW Mean signal intensity of control spots 1 and 2
CH2_RAW_spot1 Signal intensity at target spot 1 (Left side of the glass)
CH2_RAW_spot2 Signal intensity at target spot 2 (Right side of the glass)
CH2_RAW Mean signal intensity of control spots 1 and 2
Flags Has a value of 1 if any spot was determined to be unsatisfactory through PRIM filtering (Kadota, K. 2001 Physiol. Genomics, 4, 183); otherwise has a value of 0

Data table
ID_REF VALUE Ratio of Means CH1_RAW_spot1 CH1_RAW_spot2 CH1_RAW CH2_RAW_spot1 CH2_RAW_spot2 CH2_RAW Flags
1 -0.492055996761 0.685555122629 244.52 705.09 474.805 317.7 333.31 325.505 0
2 -0.337851876368 0.76289092021 1907.15 1837.54 1872.345 1568.45 1288.34 1428.395 0
3 -0.801964714295 0.553032380621 937.59 557.44 747.515 516.25 310.55 413.4 0
4 -0.968244700889 0.492827912079 536.22 411.9 474.06 291.76 175.5 233.63 0
5 -1.08560385928 0.454325036195 591.55 555.03 573.29 316.33 204.59 260.46 0
6 -0.28957162754 0.788853304496 619.48 582.67 601.075 435.19 513.13 474.16 0
7 -1.40841565752 0.363237464598 380.5 371.57 376.035 153.69 119.49 136.59 0
8 0.373322420835 1.24895629602 1018.78 919.03 968.905 1491.93 928.31 1210.12 0
9 -0.544366342953 0.66114298926 1552.01 826.84 1189.425 925.37 647.39 786.38 0
10 0.216999744782 1.12070014246 512.11 737.35 624.73 649.61 750.66 700.135 0
11 -1.21007912282 0.416769454775 447.47 630.8 539.135 238.06 211.33 224.695 0
12 -0.527577272559 0.668881848824 1060.1 717.03 888.565 698.83 489.86 594.345 0
13 0.828736184527 51.02 53.03 52.025 57.02 29.21 43.115 1
14 0.0102288671867 0.971058045258 448.14 543.5 495.82 499.82 463.12 481.47 0
15 0.184350353506 1.09562259729 788.3 611.16 699.73 687.09 846.19 766.64 0
16 -0.311654244714 0.776870658525 1194.11 472.95 833.53 697.42 597.67 647.545 0
17 -0.119924385201 0.887289123166 537.85 380.34 459.095 399.64 415.06 407.35 0
18 -0.606458929041 0.633291510408 700.78 741.81 721.295 501.74 411.84 456.79 0
19 0.6797085226 1.54446705398 879.7 1154.84 1017.27 1423.2 1719.08 1571.14 0
20 -0.453252333351 0.704244472503 659.76 393.61 526.685 453.56 288.27 370.915 0

Total number of rows: 8987

Table truncated, full table size 713 Kbytes.




Supplementary data files not provided
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