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Sample GSM46638 Query DataSets for GSM46638
Status Public on Apr 09, 2005
Title Tiling microarray analysis of rice indica chromosome 10(reverse strand, normal)
Sample type RNA
 
Source name Poly(A)+ RNA derived from rice seedling roots, seedling shoots, panicles, and suspension cultured cells.
Organism Oryza sativa
Extracted molecule total RNA
 
Description The four RNA population from seedling roots, seedling shoots, panicles, and suspension-cultured cells were pooled in equal amount and cDNAs were derived from the RNA mixture. 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).
 
Submission date Mar 31, 2005
Last update date Oct 28, 2005
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 GPL1938
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
1 366 420 300.23 512.56 30.70
2 614 216 922.08 1862.44 34.72
3 359 931 294.68 500.56 51.18
4 438 992 429.90 708.33 27.45
5 344 412 198.12 353.67 139.63
6 436 432 208.26 386.00 42.50
7 51 961 361.39 689.33 60.08
8 418 338 2558.31 6406.56 107.12
9 114 196 208.58 339.22 63.92
10 693 501 228.74 409.78 58.12
11 220 22 2604.92 4656.00 80.86
12 187 695 890.26 1498.78 83.18
13 574 1020 320.81 527.56 75.76
14 476 514 343.12 619.00 62.38
15 372 152 437.39 867.89 43.13
16 241 831 526.94 952.56 137.55
17 539 779 1129.08 1963.00 35.40
18 755 249 2042.82 3893.67 87.47
19 606 22 359.26 612.22 108.81
20 481 347 329.08 529.67 191.03

Total number of rows: 336307

Table truncated, full table size 11547 Kbytes.




Supplementary data files not provided

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