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Sample GSM989707 Query DataSets for GSM989707
Status Public on Aug 23, 2012
Title PC 625T
Sample type RNA
 
Channel 1
Source name reference RNA
Organism Homo sapiens
Characteristics reference: common reference mRNA (Stratagene-Agilent Technologies, Inc, Santa Clara, CA, USA), pooled from 11 established human cell lines
Extracted molecule total RNA
Extraction protocol not provided
Label Cy3
Label protocol not provided
 
Channel 2
Source name PC 625T2
Organism Homo sapiens
Characteristics ethnicity: Caucasian
age: 65
pre-operation treatment: None
individual: PC 336T
disease free survival: 22.20
tissue: prostate
Growth protocol All prostate samples used for this study were collected at the Stanford University Medical Center between 1999 and 2007 with patient's informed consent under an Institutional Review Board (IRB)-approved protocol. Multiple tissue samples were harvested from each prostate, flash-frozen and stored at 80oC. Frozen sections of each prostate sample were performed and evaluated by a genitourinary pathologist (JKM). The tumor and nontumor areas were marked and contaminating tissues were trimmed away from the block as described previously.48 Tumor samples in which at least 90% of the epithelial cells were cancerous were selected for extraction of DNA and RNA. In total, we selected 98 tumors from 86 patients that met these criteria. Associated clinical data were collected and included preoperative PSA levels, clinical stage, pathological stage, tumor Gleason grade and clinical follow-up. Recurrence was defined as a measurable serum PSA (>0.1ng/ml on two consecutive measurements) after surgery.
Gene-expression profiling was performed as reported. Briefly, Cy5-labeled cDNA was prepared by using 50ug of total RNA from prostate samples and Cy3-labeled cDNA was prepared by using common reference mRNA (Stratagene-Agilent Technologies, Inc, Santa Clara, CA, USA), pooled from 11 established human cell lines. For each experimental sample, Cy5- and Cy3-labeled samples were cohybridized to HEEBO spotted microarrays.49 HEEBO microarrays were manufactured in the Stanford Functional Genomics Facility at Stanford University and contained 44-544 70-mer probes.
Extracted molecule total RNA
Extraction protocol not provided
Label Cy5
Label protocol not provided
 
 
Hybridization protocol not provided
Scan protocol After hybridization, microarrays were imaged using an Axon GenePix 4000 scanner (Axon Instruments-Molecular Devices, LLC, Sunnyvale, CA, USA). Fluorescence ratios for array elements were extracted using GENEPIX software and uploaded into the Stanford Microarray Database for subsequent analysis.
Description Image: http://smd.stanford.edu/MicroArray/gifs/2008-08/81152.gif
Data processing VALUE is Log (base 2) of the ratio of the median of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm)
 
Submission date Aug 21, 2012
Last update date Aug 23, 2012
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 GPL15973
Series (1)
GSE40272 Gene-expression profiling of prostate tumors

Data table header descriptions
ID_REF ID_REF
CH1I_MEAN Mean feature pixel intensity at wavelength 532 nm.; Type: integer; Scale: linear_scale
CH2I_MEAN Mean feature pixel intensity at wavelength 635 nm.; Type: integer; Scale: linear_scale
CH1B_MEDIAN The median feature background intensity at wavelength 532 nm.; Type: integer; Scale: linear_scale; Channel: Cy3 Channel; Background
CH2B_MEDIAN The median feature background intensity at wavelength 635 nm.; Type: integer; Scale: linear_scale; Channel: Cy5 channel; Background
CH1D_MEAN The mean feature pixel intensity at wavelength 532 nm with the median background subtracted.; Type: integer; Scale: linear_scale; Channel: Cy3 Channel
CH2D_MEAN .The mean feature pixel intensity at wavelength 635 nm with the median background subtracted.; Type: integer; Scale: linear_scale; Channel: Cy5 channel
CH1I_MEDIAN Median feature pixel intensity at wavelength 532 nm.; Type: integer; Scale: linear_scale
CH2I_MEDIAN Median feature pixel intensity at wavelength 635 nm.; Type: integer; Scale: linear_scale
CH1B_MEAN The mean feature background intensity at wavelength 532 nm.; Type: integer; Scale: linear_scale; Background
CH2B_MEAN The mean feature background intensity at wavelength 635 nm.; Type: integer; Scale: linear_scale; Background
CH1D_MEDIAN The median feature pixel intensity at wavelength 532 nm with the median background subtracted.; Type: integer; Scale: linear_scale
CH2D_MEDIAN The median feature pixel intensity at wavelength 635 nm with the median background subtracted.; Type: integer; Scale: linear_scale
CH1_PER_SAT The percentage of feature pixels at wavelength 532 nm that are saturated.; Type: integer; Scale: linear_scale
CH2_PER_SAT The percentage of feature pixels at wavelength 635 nm that are saturated.; Type: integer; Scale: linear_scale
CH1I_SD The standard deviation of the feature intensity at wavelength 532 nm.; Type: integer; Scale: linear_scale; Channel: Cy3 Channel
CH2I_SD The standard deviation of the feature pixel intensity at wavelength 635 nm.; Type: integer; Scale: linear_scale; Channel: Cy5 channel
CH1B_SD The standard deviation of the feature background intensity at wavelength 532 nm.; Type: float; Scale: linear_scale; Channel: Cy3 Channel; Background
CH2B_SD The standard deviation of the feature background intensity at wavelength 635 nm.; Type: integer; Scale: linear_scale; Channel: Cy5 channel; 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
PERGTBCH1I_2SD The percentage of feature pixels with intensities more than two standard deviations above the background pixel intensity, at wavelength 532 nm.; Type: integer; Scale: linear_scale
PERGTBCH2I_2SD The percentage of feature pixels with intensities more than two standard deviations above the background pixel intensity, at wavelength 532 nm.; Type: integer; Scale: linear_scale
SUM_MEAN The sum of the arithmetic mean intensities for each wavelength, with the median background subtracted.; Type: integer; Scale: linear_scale
SUM_MEDIAN The sum of the median intensities for each wavelength, with the median background subtracted.; Type: integer; Scale: linear_scale
RAT1_MEAN Ratio of the arithmetic mean intensities of each spot for each wavelength, with the median background subtracted. Channel 1/Channel 2 ratio, (CH1I_MEAN - CH1B_MEDIAN)/(CH2I_MEAN - CH2B_MEDIAN) or Green/Red ratio.; Type: float; Scale: linear_scale
RAT2_MEAN The ratio of the arithmetic mean intensities of each feature for each wavelength, with the median background subtracted.; Type: float; Scale: linear_scale
RAT2_MEDIAN The ratio of the median intensities of each feature for each wavelength, with the median background subtracted.; Type: float; Scale: linear_scale
PIX_RAT2_MEAN The geometric mean of the pixel-by-pixel ratios of pixel intensities, with the median background subtracted.; Type: float; Scale: linear_scale
PIX_RAT2_MEDIAN The median of pixel-by-pixel ratios of pixel intensities, with the median background subtracted.; Type: float; Scale: linear_scale
RAT2_SD The geometric standard deviation of the pixel intensity ratios.; Type: float; Scale: linear_scale
TOT_SPIX The total number of feature pixels.; Type: integer; Scale: linear_scale
TOT_BPIX The total 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
DIAMETER The diameter in um of the feature-indicator.; Type: integer; Scale: linear_scale
X_COORD X-coordinate of the center of the spot-indicator associated with the spot, where (0,0) is the top left of the image.; Type: integer; Scale: linear_scale
Y_COORD Y-coordinate of the center of the spot-indicator associated with the spot, where (0,0) is the top left of the image.; Type: integer; 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 The type of flag associated with a feature: -100 = user-flagged null spot; -50 = software-flagged null spot; 0 = spot valid.; 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
CH2IN_MEDIAN Normalized value of median Channel 2 (usually 635 nm) intensity (CH2I_MEDIAN/Normalization factor).; Type: integer; Scale: linear_scale
CH2DN_MEDIAN Normalized value of median Channel 2 (usually 635 nm) intensity with normalized background subtracted (CH2IN_MEDIAN - CH2BN_MEDIAN).; Type: integer; 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
RAT2N_MEDIAN Channel 2/Channel 1 ratio normalized, RAT2_MEDIAN/Normalization factor or Red/Green median ratio normalized.; Type: float; Scale: linear_scale
LOG_RAT2N_MEAN 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
VALUE Log (base 2) of the ratio of the median of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm) [log (base 2) (RAT2N_MEDIAN)].; Type: float; Scale: log_base_2

Data table
ID_REF CH1I_MEAN CH2I_MEAN CH1B_MEDIAN CH2B_MEDIAN CH1D_MEAN CH2D_MEAN CH1I_MEDIAN CH2I_MEDIAN CH1B_MEAN CH2B_MEAN CH1D_MEDIAN CH2D_MEDIAN CH1_PER_SAT CH2_PER_SAT CH1I_SD CH2I_SD CH1B_SD CH2B_SD PERGTBCH1I_1SD PERGTBCH2I_1SD PERGTBCH1I_2SD PERGTBCH2I_2SD SUM_MEAN SUM_MEDIAN RAT1_MEAN RAT2_MEAN RAT2_MEDIAN PIX_RAT2_MEAN PIX_RAT2_MEDIAN RAT2_SD TOT_SPIX TOT_BPIX REGR CORR DIAMETER X_COORD Y_COORD TOP BOT LEFT RIGHT FLAG CH2IN_MEAN CH2BN_MEDIAN CH2DN_MEAN RAT2N_MEAN CH2IN_MEDIAN CH2DN_MEDIAN RAT1N_MEAN RAT2N_MEDIAN LOG_RAT2N_MEAN VALUE
1 1568 1456 128 105 1439 1350 1223 1343 143 131 1094 1238 0 0 987 526 160 243 100 98 100 94 2789 2332 1.066 .938 1.132 1.038 1.106 1.433 52 305 .791 .88 80 2120 6800 12 20 68 76 0 1384 100 1283 .892 1277 1177 1.121 1.076 -.165 .105
2 1946 2067 139 123 1806 1944 1341 1551 145 130 1202 1427 0 0 2077 2533 47 58 100 100 100 100 3750 2629 .929 1.076 1.187 1.121 1.064 1.224 32 225 1.111 .95 70 2270 6790 11 18 83 90 0 1965 117 1848 1.023 1474 1356 .977 1.128 .033 .174
3 1297 2620 142 121 1154 2499 1221 2688 165 147 1079 2567 0 0 502 925 106 162 100 100 98 98 3653 3646 .462 2.166 2.379 2.171 2.339 1.397 52 234 2.243 .91 80 2430 6810 13 21 99 107 0 2490 115 2375 2.058 2555 2440 .486 2.261 1.042 1.177
4 2142 1788 153 128 1988 1659 1413 1439 359 411 1259 1310 0 0 2076 1374 2381 2704 19 11 3 1 3647 2569 1.198 .835 1.041 .933 .961 1.318 52 244 .71 .94 90 2580 6810 12 21 113 122 0 1700 122 1577 .793 1368 1245 1.261 .989 -.334 -.016
5 4263 4777 153 134 4109 4642 505 740 223 223 351 605 0 0 10083 11165 695 856 34 34 23 25 8751 956 .885 1.13 1.724 1.649 1.657 1.816 52 281 1.12 .97 90 2720 6790 10 19 127 136 0 4541 127 4413 1.074 703 575 .931 1.638 .103 .712
6 11395 12294 177 159 11218 12135 2069 2964 245 242 1892 2805 3 5 18187 18105 681 835 96 96 78 94 23353 4697 .924 1.082 1.483 1.333 1.379 1.514 52 292 1.027 .94 90 2870 6800 11 20 142 151 0 11686 151 11535 1.028 2817 2666 .973 1.409 .04 .495
7 6221 6414 168 171 6052 6242 652 765 220 258 484 593 3 6 15758 15568 336 617 56 46 40 37 12294 1077 .97 1.031 1.225 1.504 1.666 2.259 32 231 .989 .99 70 3020 6780 10 17 158 165 0 6097 163 5933 .98 727 564 1.02 1.165 -.029 .22
8 6361 7849 172 155 6188 7694 1308 2978 193 209 1136 2823 1 3 15234 14714 112 346 100 98 100 92 13882 3959 .804 1.243 2.485 1.95 2.204 1.426 52 263 1.002 .95 80 3180 6800 12 20 174 182 0 7461 147 7314 1.182 2831 2683 .846 2.362 .241 1.24
9 261 455 148 139 112 315 262 448 172 172 113 309 0 0 61 138 157 187 23 82 0 30 427 422 .356 2.813 2.735 2.793 2.459 1.617 52 251 1.839 .58 80 3330 6800 12 20 189 197 0 433 132 299 2.673 426 294 .374 2.599 1.419 1.378
10 273 598 138 125 135 473 254 584 148 143 116 459 0 0 133 171 60 95 73 100 48 98 608 575 .285 3.504 3.957 4.019 3.983 1.87 52 286 2.013 .74 90 3470 6800 11 20 202 211 0 568 119 450 3.33 555 436 .3 3.761 1.736 1.911
11 2569 3462 141 121 2428 3340 688 1354 164 157 547 1233 0 0 6983 8260 202 237 92 98 73 94 5768 1780 .727 1.376 2.254 2.149 2.142 1.51 52 227 1.262 .84 80 3630 6800 12 20 219 227 0 3291 115 3175 1.308 1287 1172 .765 2.143 .387 1.099
12 2015 2247 150 138 1864 2109 498 989 182 185 348 851 0 0 6325 4557 198 245 73 78 46 69 3973 1199 .884 1.131 2.445 1.9 2.348 2.812 52 280 .939 .89 90 3770 6790 10 19 232 241 -50 2136 131 2005 1.076 940 809 .93 2.325 .105 1.217
13 220 348 148 130 71 218 228 410 290 327 80 279 0 0 90 213 1196 1607 0 0 0 0 289 359 .326 3.07 3.488 2.287 2.824 2.714 52 316 1.615 .98 90 3920 6790 10 19 247 256 -50 331 124 207 2.919 390 265 .343 3.315 1.545 1.729
14 1827 1892 146 127 1681 1765 377 669 249 219 230 542 0 0 4677 3621 1015 1040 15 18 12 12 3446 772 .952 1.05 2.357 2.073 2.183 1.621 32 222 .796 .91 70 4080 6790 11 18 264 271 0 1798 121 1678 .998 636 515 1.002 2.24 -.003 1.164
15 272 553 137 125 135 428 263 538 155 146 126 413 0 0 83 117 72 97 76 98 34 96 563 539 .315 3.17 3.278 3.809 3.39 2.078 52 261 2.868 .63 90 4230 6800 11 20 278 287 0 526 119 407 3.014 511 393 .332 3.116 1.592 1.64
16 426 946 138 123 287 822 285 621 151 156 147 498 0 0 1030 2516 72 239 70 73 50 52 1109 645 .349 2.864 3.388 2.922 2.878 2.113 80 315 2.603 .92 100 4370 6800 11 21 292 302 0 899 117 781 2.723 590 473 .367 3.22 1.445 1.687
17 311 469 140 127 170 342 317 478 153 164 177 351 0 0 95 145 78 272 82 78 57 7 512 528 .497 2.012 1.983 2.317 1.934 2.194 52 226 1.487 .81 80 4530 6810 13 21 309 317 0 446 121 325 1.912 454 334 .523 1.885 .935 .915
18 302 383 145 140 157 242 227 321 246 292 82 181 0 0 292 296 828 1342 5 2 1 0 399 263 .649 1.541 2.207 2.305 1.892 2.935 80 355 1.137 .94 100 4680 6800 11 21 323 333 0 364 133 230 1.465 305 172 .683 2.098 .551 1.069
19 1432 1630 157 144 1275 1486 552 714 313 305 395 570 0 0 3373 3291 1279 1160 17 20 10 12 2761 965 .858 1.165 1.443 1.387 1.44 2.062 80 337 .969 .83 100 4830 6810 12 22 338 348 0 1549 137 1413 1.108 679 542 .903 1.372 .148 .456
20 602 844 158 146 444 697 368 502 334 328 209 355 0 0 983 1419 1396 1267 5 7 1 5 1141 564 .637 1.57 1.699 1.684 1.65 1.594 52 283 1.116 .94 90 4980 6800 11 20 353 362 0 802 139 663 1.492 477 337 .67 1.615 .577 .691

Total number of rows: 44544

Table truncated, full table size 9788 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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