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Sample GSM96011 Query DataSets for GSM96011
Status Public on Feb 25, 2006
Title Ovarian Cell Line OVCA_420
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 MES-OV
Organism Homo sapiens
Characteristics Ovarian Ca MES-OV
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Cell-line, Ovarian
Image: http://smd.stanford.edu/MicroArray/gifs/2000-04/4680.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 1296 1298 130 90 1166 1208 231 176 86 87 1 112 1245 .63 .806 63 75 54 66 0 1908 132 1776 1.523 .657 .607
2 1230 1179 130 93 1100 1086 257 198 88 91 .938 112 1025 .6 .799 63 75 69 81 0 1733 136 1597 1.452 .689 .538
3 758 666 128 94 630 572 146 104 75 80 .857 112 1037 .765 .874 63 75 84 96 0 979 138 841 1.335 .749 .417
4 439 234 130 98 309 136 150 119 76 77 .441 112 1035 .387 .534 63 75 101 113 0 344 144 200 .647 1.545 -.628
5 1274 3517 133 99 1141 3418 146 119 83 97 2.957 112 1017 2.592 .902 63 75 116 128 0 5172 145 5027 4.406 .227 2.139
6 1195 1218 131 96 1064 1122 143 106 86 92 1.073 112 1017 .944 .909 63 75 131 143 0 1791 141 1650 1.551 .645 .633
7 524 420 131 93 393 327 143 101 71 69 .852 112 1017 .685 .841 63 75 146 158 0 617 136 481 1.224 .817 .292
8 471 567 131 93 340 474 146 101 70 82 1.33 112 1017 1.011 .803 63 75 161 173 0 833 136 697 2.05 .488 1.036
9 8622 4024 132 94 8490 3930 154 107 91 91 .48 112 1017 .405 .863 63 75 176 188 0 5917 138 5779 .681 1.469 -.555
10 1064 365 132 97 932 268 158 110 75 74 .278 112 1017 .242 .786 63 75 191 203 0 536 142 394 .423 2.365 -1.242
11 574 368 133 100 441 268 174 119 72 75 .625 112 1017 .529 .838 63 75 206 218 0 541 147 394 .893 1.119 -.163
12 1677 2287 134 100 1543 2187 189 135 77 79 1.308 112 1017 1.202 .894 63 75 221 233 0 3363 147 3216 2.084 .48 1.06
13 1176 863 135 99 1041 764 213 157 74 76 .729 112 1017 .592 .841 63 75 236 248 0 1269 145 1124 1.08 .926 .111
14 6832 5674 135 96 6697 5578 209 147 84 94 .804 112 1017 .726 .906 63 75 251 263 0 8344 141 8203 1.225 .816 .293
15 625 495 134 98 491 397 227 144 76 78 .777 112 1021 .253 .465 63 75 266 278 0 727 144 583 1.187 .842 .248
16 1260 672 135 98 1125 574 232 133 74 78 .497 112 1021 .31 .686 63 75 281 293 0 988 144 844 .75 1.333 -.415
17 5436 3035 136 99 5300 2936 207 123 81 85 .541 112 1017 .477 .908 63 75 296 308 0 4463 145 4318 .815 1.227 -.296
18 492 319 136 99 356 220 234 144 72 66 .623 112 1017 .45 .869 63 75 311 323 0 469 145 324 .91 1.099 -.136
19 3904 3508 136 100 3768 3408 210 151 76 82 .893 112 1017 .787 .897 63 75 326 338 0 5158 147 5011 1.33 .752 .411
20 1103 1219 136 99 967 1120 224 155 71 81 1.178 112 1017 .914 .869 63 75 341 353 0 1792 145 1647 1.703 .587 .768

Total number of rows: 24192

Table truncated, full table size 2686 Kbytes.




Supplementary data files not provided
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