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Sample GSM46497 Query DataSets for GSM46497
Status Public on Apr 09, 2005
Title Tiling microarray analysis of rice japonica chromosome 10 forward strand ,stressed
Sample type RNA
 
Source name Poly(A)+ RNA derived from rice seedlings undergone mineral/nutrient disturbances.
Organism Oryza sativa
Extracted molecule total RNA
 
Description The cDNA target was derived from pooled poly(A)+ RNA isolated from leaves of stress-treated japonica seedlings. For stress treatment, japonica seedlings were grown for seven days on MS medium under four different conditions: (i) MS medium deprived of nitrogen, (ii) MS medium deprived of phosphorus, or (iii) supplemented with 150 mM NaCl or (iv) 100 M CdSO4. For RNA isolation, plant materials were frozen in liquid nitrogen and homogenized. Total RNA and mRNA were isolated using the RNeasy Plant Mini kit (Qiagen, Valencia, CA) and the Oligotex mRNA kit (Qiagen), respectively. First-strand cDNA was generated from 4 µg poly(A)+ RNA with SuperScript II reverse transcriptase (Invitrogen, Carlsbad, CA). The cDNAs were precipitated in ethanol:isopropanol (1:1 v/v) and resuspended in 0.1 M NaHCO3 to facilitate coupling of Alexa Fluor 555 NHS esters (Molecular Probes, Eugene, OR) to the reactive groups of the amino-allyl dUTPs and were purified with CyScribe GFX glass fiber spin columns (Amersham Bioscience, Piscataway, NJ). Microarrays were hybridized with 4 µg labeled cDNA in 300 µL hybridization buffer (50 mM MES, 0.5 M NaCl, 10 mM EDTA, and 0.005% (v/v) Tween-20) for 16 hours at 50°C in disposable adhesive chambers (Grace BioLabs, Bend, OR) in a hybridization oven with constant agitation. Hybridized arrays were washed on an orbital platform in non-stringent buffer (6× SSPE, 0.01% [v/v] Tween-20) for 10 minutes at room temperature, then in stringent buffer (100 mM MES, 0.1 M NaCl, 0.01% Tween-20) for 30 minutes at 45°C. This was followed by a 5-minute wash in non-stringent buffer and a 2-minute wash in 0.1X SSC. The arrays were dried with compressed nitrogen and scanned with an Axon 4000B laser scanner at 5 µm resolution. The fluorescence intensity data were extracted with the NimbleScan software (NimbleGen Systems, Madison, WI).
Keywords = Rice
Keywords = poly(A)+ RNA
Keywords = stress
 
Submission date Mar 29, 2005
Last update date Sep 08, 2006
Contact name Xing-Wang Deng
E-mail(s) xingwang.deng@yale.edu
Phone 203-432-8908
Organization name Yale University
Department MCD Biology
Street address 165 Prospect
City New Haven
State/province CT
ZIP/Postal code 06520
Country USA
 
Platform ID GPL1933
Series (1)
GSE2500 Tiling microarray analysis of japonica and indica rice chromosome 10

Data table header descriptions
ID_REF
X X coordinate of the array feature
Y Y coordinate of the array feature
VALUE Median fluorescence signal intensity of the array feature
SIGNAL_MEAN Mean fluorescence signal intensity of the array feature
SIGNAL_STD Standard deviation of the fluorescence signal for the array feature

Data table
ID_REF X Y VALUE SIGNAL_MEAN SIGNAL_STD
1 603 389 828.25 950.22 220.77
2 215 327 567.18 678.11 97.42
3 705 129 1337.89 1984.44 353.87
4 548 400 1676.79 1973.67 342.13
5 412 980 427.70 550.78 120.89
6 659 573 4404.91 12347.67 7103.70
7 364 698 601.29 712.67 118.99
8 12 284 676.49 875.67 228.94
9 255 959 648.64 780.22 93.64
10 650 622 660.13 877.00 133.21
11 704 770 762.58 795.44 81.40
12 175 181 890.32 1071.11 162.03
13 608 706 384.03 473.89 133.24
14 57 593 363.95 433.56 86.02
15 142 710 469.08 538.56 103.85
16 655 597 402.75 464.22 69.47
17 642 240 468.64 618.33 220.03
18 715 323 1271.88 2502.00 1152.41
19 178 964 644.21 746.22 167.11
20 577 631 449.51 505.67 66.11

Total number of rows: 375140

Table truncated, full table size 13177 Kbytes.




Supplementary data files not provided

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