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Sample GSM989702 Query DataSets for GSM989702
Status Public on Aug 23, 2012
Title PC 85T
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 85T2
Organism Homo sapiens
Characteristics ethnicity: Caucasian
age: 64
pre-operation treatment: None
individual: PC 610T
disease free survival: 0.03
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/2008-08/81129.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 12340 13340 103 81 12237 13258 13591 15008 110 108 13487 14927 0 0 3708 5326 42 104 100 100 100 98 25495 28414 .923 1.083 1.107 .989 1.141 2.01 52 368 1.139 .95 90 1780 7070 22 31 25 34 0 11341 69 11271 .921 12759 12690 1.086 .941 -.119 -.088
2 12297 7800 75 59 12222 7741 15380 8940 83 78 15305 8881 0 0 6028 3930 32 59 100 100 100 100 19963 24186 1.579 .633 .58 .718 .664 2.279 52 267 .626 .96 80 1940 7040 20 28 42 50 0 6631 50 6581 .538 7600 7550 1.857 .493 -.893 -1.019
3 17128 21877 75 53 17053 21824 24241 28257 101 87 24166 28204 0 0 10414 13701 162 171 94 86 90 82 38877 52370 .781 1.28 1.167 1.004 1.244 3.241 52 276 1.369 .96 90 2090 7040 19 28 56 65 0 18599 45 18554 1.088 24023 23978 .919 .992 .122 -.011
4 11841 7256 71 59 11769 7197 15271 8422 95 89 15200 8363 0 0 6726 4351 151 161 98 95 95 91 18966 23563 1.635 .612 .55 .606 .623 2.377 80 317 .612 .96 100 2240 7050 20 30 71 81 0 6169 50 6119 .52 7160 7110 1.923 .468 -.944 -1.096
5 750 154 70 53 680 101 853 149 76 65 783 96 0 0 405 78 22 44 94 78 92 61 781 879 6.733 .149 .123 .157 .136 2.729 52 217 .114 .53 80 2390 7040 20 28 87 95 0 131 45 86 .126 127 82 7.919 .104 -2.985 -3.262
6 9594 14916 113 57 9481 14859 10886 16676 134 68 10772 16619 0 0 4457 7052 69 47 100 100 100 100 24340 27391 .638 1.567 1.543 1.562 1.585 1.944 80 301 1.615 .96 100 2540 7060 21 31 101 111 0 12681 48 12632 1.332 14177 14129 .751 1.312 .414 .391
7 260 100 109 59 150 41 268 91 132 70 158 32 0 0 52 47 62 37 90 43 68 12 191 190 3.659 .273 .203 .283 .221 2.586 32 221 .474 .31 70 2690 7030 19 26 117 124 0 85 50 35 .232 77 27 4.303 .172 -2.105 -2.538
8 19573 25721 82 52 19491 25669 24566 29108 87 65 24484 29056 0 0 7861 10290 26 51 100 100 100 100 45160 53540 .759 1.317 1.187 1.273 1.259 1.629 52 266 1.331 .96 80 2850 7050 21 29 133 141 0 21867 44 21823 1.12 24746 24702 .893 1.009 .163 .013
9 113 100 74 50 39 50 115 102 75 61 41 52 0 0 27 26 16 37 83 75 58 16 89 93 .78 1.282 1.268 1.297 1.018 2.221 12 68 10.344 .12 40 2990 7040 22 26 149 153 0 85 43 43 1.09 87 44 .917 1.078 .124 .109
10 118 87 70 62 48 24 120 81 75 74 50 18 0 0 27 30 21 49 80 17 63 0 72 68 2 .5 .36 .731 .859 2.614 52 325 2.655 .37 90 3140 7030 18 27 161 170 -50 74 53 20 .425 69 15 2.353 .306 -1.234 -1.708
11 605 953 72 56 533 897 615 904 78 66 543 848 0 0 144 256 24 48 100 100 100 100 1430 1391 .594 1.683 1.562 1.727 1.64 1.543 32 224 1.717 .92 70 3290 7030 19 26 177 184 0 810 48 763 1.431 769 721 .699 1.328 .517 .409
12 284 645 71 58 213 587 309 652 76 67 238 594 0 0 91 237 23 47 94 98 94 98 800 832 .363 2.756 2.496 3.017 2.589 2.756 52 283 3.026 .87 80 3450 7030 19 27 193 201 0 548 49 499 2.343 554 505 .427 2.122 1.228 1.085
13 271 126 66 57 205 69 275 129 72 71 209 72 0 0 80 39 22 57 100 61 94 15 274 281 2.971 .337 .344 .326 .362 2.288 52 253 .337 .49 80 3600 7030 19 27 208 216 0 107 48 59 .286 110 61 3.495 .293 -1.805 -1.772
14 220 219 66 54 154 165 215 220 73 70 149 166 0 0 42 70 26 62 100 96 100 62 319 315 .933 1.071 1.114 1.002 1.089 1.61 32 172 1.296 .76 60 3750 7030 20 26 224 230 0 186 46 140 .911 187 141 1.098 .947 -.135 -.078
15 62 42 68 50 -5 -7 60 38 114 75 -7 -11 0 0 11 21 475 118 0 0 0 0 -12 -18 null null null 1.524 1.211 3.663 52 288 5.751 .28 90 3900 7030 18 27 237 246 -50 36 43 -6 null 32 -9 null null null null
16 2642 1071 67 52 2575 1019 2730 1038 114 72 2663 986 0 0 479 354 487 114 100 100 100 98 3594 3649 2.527 .396 .37 .374 .374 1.479 52 274 .365 .9 90 4050 7030 18 27 252 261 0 911 44 866 .336 882 838 2.972 .315 -1.572 -1.668
17 85 132 70 54 15 78 84 131 75 66 14 77 0 0 17 61 22 44 30 69 5 44 93 91 .192 5.2 5.5 4.83 4.757 2.269 52 227 6.605 .38 80 4210 7040 20 28 269 277 0 112 46 66 4.421 111 65 .226 4.676 2.144 2.225
18 62 50 72 58 -9 -7 62 42 75 72 -9 -15 0 0 12 23 22 50 1 1 0 0 -16 -24 null null null 1.268 1.238 2.759 52 288 7.046 .28 90 4360 7030 18 27 283 292 -50 43 49 -6 null 36 -13 null null null null
19 485 272 71 58 414 214 469 253 76 73 398 195 0 0 99 103 32 95 100 88 100 51 628 593 1.935 .517 .49 .487 .539 1.602 52 324 .569 .83 90 4510 7020 17 26 298 307 0 231 49 182 .439 215 166 2.276 .417 -1.186 -1.263
20 2670 4683 67 50 2603 4633 2619 4305 73 61 2552 4255 0 0 266 1146 24 45 100 100 100 100 7236 6807 .562 1.78 1.667 1.74 1.667 1.189 32 219 1.977 .95 70 4660 7020 18 25 314 321 0 3981 43 3939 1.513 3660 3617 .661 1.417 .598 .503

Total number of rows: 44544

Table truncated, full table size 9344 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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