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Sample GSM96018 Query DataSets for GSM96018
Status Public on Feb 25, 2006
Title Ovarian Cell Line OVCAR-5
Sample type RNA
 
Channel 1
Source name CRD Reference
Organism Homo sapiens
Characteristics CRD Reference
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name Ovarian Ca OVCAR-5
Organism Homo sapiens
Characteristics Ovarian Ca OVCAR-5
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Cell-line, Ovarian
Image: http://smd.stanford.edu/MicroArray/gifs/2000-04/4679.gif
Data processing VALUE is Log (base 2) of the ratio of the mean of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm)
 
Submission date Feb 07, 2006
Last update date Sep 22, 2006
Organization Stanford Microarray Database (SMD)
E-mail(s) array@genome.stanford.edu
Phone 650-498-6012
URL http://genome-www5.stanford.edu/
Department Stanford University, School of Medicine
Street address 300 Pasteur Drive
City Stanford
State/province CA
ZIP/Postal code 94305
Country USA
 
Platform ID GPL178
Series (1)
GSE4197 Ovarian cell lines

Data table header descriptions
ID_REF ID_REF
CH1I_MEAN Uncorrected Cy3 mean pixel intensity.; Type: integer; Scale: linear_scale; Channel: Cy3 Channel
CH2I_MEAN Uncorrected Cy3 mean pixel intensity.; Type: integer; Scale: linear_scale; Channel: Cy5 channel
CH1B_MEDIAN Median intensities of background pixels of Cy3.; Type: integer; Scale: linear_scale; Channel: Cy3 Channel
CH2B_MEDIAN Median intensities of background pixels of Cy3.; Type: integer; Scale: linear_scale; Channel: Cy5 channel
CH1D_MEAN The mean feature pixel intensity with the median background subtracted (channel 1).; Type: integer; Scale: linear_scale; Channel: Cy3 Channel
CH2D_MEAN The mean feature pixel intensity with the median background subtracted (channel 2).; Type: integer; Scale: linear_scale; Channel: Cy5 channel
CH1B_MEAN Mean intensities of background pixels of Cy3.; Type: integer; Scale: linear_scale; Background
CH2B_MEAN Mean intensities of background pixels of Cy5.; Type: integer; Scale: linear_scale; Background
PERGTBCH1I_1SD The percentage of feature pixels with intensities more than one standard deviation above the background pixel intensity, at wavelength 532 nm.; Type: integer; Scale: linear_scale
PERGTBCH2I_1SD The percentage of feature pixels with intensities more than one standard deviation above the background pixel intensity, at wavelength 635 nm.; Type: integer; Scale: linear_scale
PIX_RAT2_MEDIAN Contains median of Ch2PI-CH2B/Ch1PI-CH1B where Ch1PI & Ch2PI represent single pixel intensities.; Type: float; Scale: linear_scale
TOT_SPIX Count of the number of pixels in the spot.; Type: integer; Scale: linear_scale
TOT_BPIX Number of background pixels.; Type: integer; Scale: linear_scale
REGR The regression ratio of every pixel in a 2-feature-diameter circle around the center of the feature.; Type: float; Scale: linear_scale
CORR The correlation between channel1 (Cy3) & Channel 2 (Cy5) pixels within the spot, and is a useful quality control parameter. Generally, high values imply better fit & good spot quality.; Type: float; Scale: linear_scale
TOP Box top: int(((centerX - radius) - Xoffset) / pixelSize).; Type: integer; Scale: linear_scale
BOT Box bottom: int(((centerX + radius) - Xoffset) / pixelSize).; Type: integer; Scale: linear_scale
LEFT Box left: int(((centerY - radius) - yoffset) / pixelSize).; Type: integer; Scale: linear_scale
RIGHT Box right: int(((centerY + radius) - yoffset) / pixelSize); Type: integer; Scale: linear_scale
FLAG User defined spot flag (default 0).; Type: integer; Scale: linear_scale
CH2IN_MEAN Normalized value of mean Channel 2 (usually 635 nm) intensity (CH2I_MEAN/Normalization factor).; Type: integer; Scale: linear_scale; Channel: Cy5 channel
CH2BN_MEDIAN Normalized value of median Channel 2 (usually 635 nm) background (CH2B_MEDIAN/Normalization factor).; Type: integer; Scale: linear_scale; Channel: Cy5 channel; Background
CH2DN_MEAN Normalized value of mean Channel 2 (usually 635 nm) intensity with normalized background subtracted (CH2IN_MEAN - CH2BN_MEDIAN).; Type: integer; Scale: linear_scale; Channel: Cy5 channel
RAT2N_MEAN Type: float; Scale: linear_scale
RAT1N_MEAN Ratio of the means of Channel 1 (usually 532 nm) intensity to normalized Channel 2 (usually 635 nm) intensity with median background subtracted (CH1D_MEAN/CH2DN_MEAN). Channel 1/Channel 2 ratio normalized or Green/Red ratio normalized.; Type: float; Scale: linear_scale
VALUE Log (base 2) of the ratio of the mean of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm) [log (base 2) (RAT2N_MEAN)].; Type: float; Scale: log_base_2

Data table
ID_REF CH1I_MEAN CH2I_MEAN CH1B_MEDIAN CH2B_MEDIAN CH1D_MEAN CH2D_MEAN CH1B_MEAN CH2B_MEAN PERGTBCH1I_1SD PERGTBCH2I_1SD PIX_RAT2_MEDIAN TOT_SPIX TOT_BPIX REGR CORR TOP BOT LEFT RIGHT FLAG CH2IN_MEAN CH2BN_MEDIAN CH2DN_MEAN RAT2N_MEAN RAT1N_MEAN VALUE
1 1997 4122 260 140 1737 3982 280 156 89 94 2.269 112 1245 2.01 .875 72 84 51 63 0 3945 134 3811 2.194 .456 1.134
2 2095 2397 257 141 1838 2256 302 178 83 92 1.213 112 1025 .992 .839 72 84 66 78 0 2294 135 2159 1.175 .851 .232
3 1637 2230 252 132 1385 2098 288 163 80 91 1.467 112 1037 1.213 .839 72 84 81 93 0 2134 126 2008 1.45 .69 .536
4 1031 699 258 129 773 570 283 138 72 81 .691 112 1035 .515 .734 73 85 98 110 0 669 123 546 .706 1.417 -.503
5 2783 793 271 131 2512 662 308 149 80 83 .246 112 1017 .199 .749 73 85 113 125 0 759 125 634 .252 3.965 -1.987
6 2162 2577 268 129 1894 2448 305 150 76 85 1.198 112 1017 1.078 .836 73 85 128 140 0 2466 123 2343 1.237 .808 .307
7 1009 705 266 125 743 580 298 147 60 76 .71 112 1017 .664 .848 73 85 143 155 0 675 120 555 .747 1.338 -.421
8 1014 1252 266 125 748 1127 290 149 71 84 1.329 112 1017 1.173 .809 73 85 158 170 0 1198 120 1079 1.442 .693 .528
9 13245 6820 263 128 12982 6692 293 156 84 89 .468 112 1017 .439 .861 73 85 173 185 0 6528 123 6405 .493 2.027 -1.019
10 1697 672 257 132 1440 540 283 150 73 77 .311 112 1017 .302 .773 73 85 188 200 0 643 126 517 .359 2.786 -1.478
11 1151 1440 260 133 891 1307 295 171 78 83 1.349 112 1017 1.161 .812 73 85 203 215 0 1378 127 1251 1.404 .712 .49
12 2523 10176 261 135 2262 10041 296 171 75 94 3.965 112 1013 3.491 .842 73 85 217 229 0 9740 129 9610 4.249 .235 2.087
13 1640 2030 266 138 1374 1892 322 191 71 78 1.231 112 1017 .982 .782 73 85 232 244 0 1943 132 1811 1.318 .759 .398
14 9303 12261 264 138 9039 12123 312 170 83 95 1.305 112 1017 1.132 .87 73 85 247 259 0 11735 132 11603 1.284 .779 .36
15 1093 1064 264 141 829 923 309 162 72 87 1.006 112 1017 .778 .76 73 85 262 274 0 1018 135 883 1.066 .938 .092
16 1793 2086 268 144 1525 1942 295 166 72 84 1.058 112 1017 .977 .776 73 85 277 289 0 1997 138 1859 1.219 .82 .285
17 7685 15906 278 146 7407 15760 303 168 84 93 2.148 112 1013 1.82 .871 73 85 292 304 0 15224 140 15084 2.036 .491 1.026
18 777 527 280 144 497 383 308 158 66 73 .614 112 1013 .532 .77 73 85 307 319 0 504 138 367 .738 1.356 -.439
19 4583 4029 278 143 4305 3886 303 163 81 91 .759 112 1017 .707 .824 73 85 322 334 0 3856 137 3719 .864 1.157 -.211
20 1491 1565 276 141 1215 1424 300 163 74 81 .985 112 1017 .877 .765 73 85 337 349 0 1498 135 1363 1.122 .891 .166

Total number of rows: 24192

Table truncated, full table size 2758 Kbytes.




Supplementary data files not provided

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