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Sample GSM989792 Query DataSets for GSM989792
Status Public on Aug 23, 2012
Title PC 463T
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 463T2
Organism Homo sapiens
Characteristics ethnicity: Caucasian
age: 62
pre-operation treatment: None
individual: PC 457T
disease free survival: 38.67
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/2008-08/81198.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) [email protected]
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 GPL15971
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 12362 10220 62 119 12299 10100 14626 12038 65 126 14563 11919 0 0 5811 4777 18 49 100 100 100 100 22399 26482 1.218 .821 .818 .841 .821 7.191 80 448 .794 .96 100 1980 6800 27 37 21 31 0 10479 122 10356 .842 12343 12221 1.188 .839 -.248 -.253
2 14298 12035 73 127 14224 11907 15076 12086 75 138 15002 11958 0 0 3505 1668 20 56 100 100 100 100 26131 26960 1.195 .837 .797 .878 .796 4.131 52 249 .786 .96 90 2130 6810 28 37 36 45 0 12340 130 12209 .858 12393 12261 1.165 .817 -.22 -.291
3 12366 12453 69 131 12296 12321 14429 14464 72 139 14359 14332 0 0 4689 5575 18 59 100 98 100 97 24617 28691 .998 1.002 .998 .818 1.008 5.891 80 333 1.014 .97 100 2300 6800 27 37 53 63 0 12769 134 12634 1.027 14831 14696 .973 1.023 .039 .033
4 15487 12222 68 134 15419 12088 15356 12195 83 162 15288 12060 0 0 1604 1903 111 179 100 100 100 100 27507 27348 1.276 .784 .789 .778 .797 3.331 52 269 .781 .97 90 2440 6790 26 35 67 76 0 12532 137 12395 .804 12504 12366 1.244 .809 -.315 -.306
5 715 262 66 127 649 134 769 255 80 155 702 127 0 0 218 92 110 175 97 30 95 0 783 829 4.843 .206 .181 .177 .201 9.041 80 268 .155 .48 100 2590 6800 27 37 82 92 0 269 130 137 .212 261 130 4.723 .186 -2.24 -2.43
6 9908 12139 75 138 9832 12001 9720 11871 82 144 9644 11733 0 0 1604 2451 29 54 100 100 100 100 21833 21377 .819 1.221 1.217 1.206 1.247 3.487 80 280 1.226 .95 110 2740 6800 26 37 96 107 0 12447 142 12306 1.252 12172 12031 .799 1.247 .324 .319
7 187 204 62 114 124 90 185 192 66 126 123 78 0 0 75 105 22 52 89 59 80 31 214 201 1.378 .726 .634 .827 .727 10.341 120 342 3.414 .84 120 2910 6800 26 38 113 125 0 209 117 92 .744 197 80 1.344 .65 -.426 -.621
8 11301 13607 60 110 11240 13496 12692 14636 64 127 12631 14525 0 0 4064 5516 25 61 100 97 100 97 24736 27156 .833 1.201 1.15 1.001 1.16 9.221 80 229 1.177 .95 100 3040 6790 26 36 127 137 0 13952 113 13838 1.231 15007 14894 .812 1.179 .3 .238
9 137 199 62 117 74 81 138 185 65 129 76 68 0 0 48 81 22 57 82 54 70 30 155 144 .914 1.095 .895 1.04 1.053 10.209 120 331 .91 .41 120 3190 6790 25 37 141 153 -100 204 120 83 1.122 190 70 .891 .917 .167 -.124
10 172 240 66 117 106 122 179 233 68 126 113 115 0 0 70 93 17 51 83 74 79 53 228 228 .869 1.151 1.018 1.238 1.196 8.816 120 354 .976 .66 120 3340 6790 25 37 156 168 -100 246 120 125 1.18 239 118 .847 1.044 .239 .061
11 458 612 72 133 386 479 461 595 72 138 389 462 0 0 147 185 18 49 98 100 98 98 865 851 .806 1.241 1.188 1.336 1.209 6.029 80 279 1.136 .87 100 3500 6800 27 37 173 183 0 628 136 491 1.272 610 474 .786 1.218 .348 .284
12 419 866 73 127 346 738 418 875 73 134 344 747 0 0 88 226 18 49 100 100 100 100 1084 1091 .469 2.133 2.172 2.086 2.051 4.212 80 278 2.126 .9 110 3650 6800 26 37 187 198 0 888 130 757 2.187 897 766 .457 2.227 1.129 1.155
13 350 375 73 121 276 254 352 324 75 131 279 202 0 0 99 221 22 51 100 97 98 91 530 481 1.087 .92 .724 .806 .836 5.82 80 223 .862 .63 100 3800 6790 26 36 203 213 0 385 124 260 .944 332 207 1.06 .742 -.084 -.43
14 212 346 74 129 138 216 228 358 76 141 153 228 0 0 59 126 21 61 92 87 90 78 354 381 .639 1.565 1.49 1.593 1.65 6.423 120 299 1.508 .77 120 3950 6790 25 37 217 229 -100 355 132 221 1.605 367 234 .623 1.528 .683 .612
15 100 167 76 138 24 28 93 155 79 141 17 17 0 0 35 86 21 57 46 30 29 12 52 34 .857 1.167 1 2.174 1.847 10.631 120 315 1.94 .32 120 4100 6790 25 37 232 244 -100 171 142 29 1.196 159 17 .836 1.025 .259 .036
16 945 1096 82 146 863 950 976 1151 84 150 894 1004 0 0 258 351 21 56 100 100 100 98 1813 1898 .908 1.101 1.123 1.074 1.157 4.876 80 210 1.052 .91 100 4260 6790 26 36 249 259 0 1124 150 974 1.129 1180 1029 .886 1.152 .175 .204
17 175 317 79 139 96 177 181 308 82 146 102 168 0 0 51 92 21 52 90 93 83 74 273 270 .542 1.844 1.647 1.982 1.829 6.291 120 294 1.641 .68 120 4400 6790 25 37 262 274 -100 325 143 181 1.891 316 172 .529 1.689 .919 .756
18 99 168 89 143 9 25 94 155 92 153 5 11 0 0 34 78 28 61 28 26 13 12 34 16 .36 2.778 2.2 1.875 1.94 9.544 120 393 1.833 .28 120 4550 6790 25 37 277 289 -100 172 147 26 2.848 159 11 .351 2.256 1.51 1.174
19 483 416 100 163 382 252 494 395 102 172 394 231 0 0 111 104 27 68 100 100 98 90 634 625 1.516 .66 .586 .648 .628 4.83 80 319 .556 .74 110 4710 6800 26 37 293 304 0 427 167 258 .676 405 237 1.478 .601 -.564 -.734
20 1696 4027 100 180 1596 3846 2107 5007 103 185 2007 4827 0 0 938 2236 27 69 98 96 95 95 5442 6834 .415 2.41 2.405 2.294 2.487 6.886 120 412 2.387 .96 120 4860 6800 26 38 308 320 0 4129 185 3944 2.471 5134 4949 .405 2.466 1.305 1.302

Total number of rows: 44544

Table truncated, full table size 9659 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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