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Sample GSM989753 Query DataSets for GSM989753
Status Public on Aug 23, 2012
Title PC 488T
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 488T2
Organism Homo sapiens
Characteristics ethnicity: Caucasian
age: 61
pre-operation treatment: None
individual: PC 501T
disease free survival: 41.37
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/2008-09/81284.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 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 7093 8311 44 129 7049 8181 8156 9176 91 169 8111 9047 0 0 2823 3095 100 140 97 98 97 98 15230 17158 .862 1.161 1.115 1.244 1.152 4.109 80 398 1.131 .97 100 1770 6860 29 39 32 42 0 7546 117 7428 1.054 8331 8214 .949 1.013 .076 .018
2 5743 5610 52 167 5691 5442 7658 6714 102 191 7606 6546 0 0 3233 3066 104 139 96 96 91 91 11133 14152 1.046 .956 .861 1.013 .968 6.096 80 284 .936 .97 100 1920 6860 29 39 47 57 0 5093 152 4941 .868 6096 5943 1.152 .781 -.204 -.356
3 10145 12640 45 126 10100 12514 10351 12824 85 203 10305 12698 0 0 1351 1547 345 387 100 100 100 100 22614 23003 .807 1.239 1.232 1.25 1.243 3.256 52 248 1.193 .96 80 2060 6850 29 37 62 70 0 11476 114 11362 1.125 11643 11529 .889 1.119 .17 .162
4 7051 7028 40 129 7011 6898 7191 6946 65 175 7151 6817 0 0 1190 1300 269 305 100 100 100 100 13909 13968 1.016 .984 .953 .982 .968 3.061 80 412 .963 .97 110 2210 6860 28 39 75 86 0 6381 117 6263 .893 6306 6189 1.119 .866 -.163 -.208
5 435 223 39 118 395 105 441 190 46 135 402 71 0 0 83 132 24 92 100 41 98 22 500 473 3.762 .266 .177 .222 .25 8.099 80 386 .257 .35 110 2370 6860 28 39 91 102 0 202 107 95 .241 173 64 4.143 .16 -2.051 -2.641
6 3617 5455 45 121 3572 5334 3589 5445 52 148 3544 5324 0 0 429 918 26 102 100 100 100 100 8906 8868 .67 1.493 1.502 1.481 1.472 3.05 80 410 1.503 .96 110 2510 6850 27 38 105 116 0 4953 110 4843 1.356 4944 4834 .738 1.364 .439 .448
7 127 164 40 108 87 55 132 142 46 140 92 33 0 0 49 87 20 113 86 26 82 3 142 125 1.582 .632 .359 .903 1.009 12.072 52 272 .824 .23 80 2680 6840 28 36 124 132 0 149 98 50 .574 129 30 1.742 .326 -.801 -1.619
8 7966 9170 36 118 7930 9052 9300 10520 41 167 9263 10402 0 0 3260 3910 17 566 100 93 100 90 16982 19665 .876 1.141 1.123 1.11 1.139 4.368 80 326 1.171 .98 100 2830 6850 28 38 138 148 0 8326 107 8219 1.036 9551 9444 .965 1.02 .052 .028
9 110 113 35 102 74 11 108 108 48 180 72 6 0 0 26 63 144 718 1 0 0 0 85 78 6.727 .149 .083 .595 .692 7.234 52 213 13.207 .28 90 2960 6870 30 39 151 160 0 103 93 10 .135 98 5 7.409 .076 -2.889 -3.724
10 136 159 34 87 101 71 135 132 36 108 100 44 0 0 22 99 9 71 100 36 100 25 172 144 1.423 .703 .44 .807 .833 6.136 52 239 1.169 .35 80 3120 6850 29 37 168 176 0 144 79 64 .638 120 40 1.567 .399 -.648 -1.324
11 388 692 32 97 355 595 375 649 33 116 342 551 0 0 96 243 8 78 100 100 100 98 950 893 .597 1.676 1.611 1.589 1.557 4.168 80 287 1.682 .83 100 3270 6860 29 39 182 192 0 628 88 540 1.522 589 500 .657 1.463 .606 .549
12 275 409 32 95 243 313 266 369 33 121 233 273 0 0 66 203 8 86 100 88 100 72 556 506 .776 1.288 1.172 1.141 1.21 5.274 80 332 1.438 .74 110 3420 6850 27 38 196 207 0 371 86 284 1.169 335 248 .855 1.064 .226 .089
13 216 190 34 99 181 91 220 169 35 126 185 70 0 0 49 102 8 92 98 40 98 18 272 255 1.989 .503 .378 .494 .513 8.691 80 296 .469 .34 100 3570 6860 29 39 212 222 0 173 90 83 .456 153 64 2.191 .344 -1.131 -1.541
14 130 217 34 108 95 108 123 187 36 131 89 78 0 0 30 119 10 92 100 47 100 27 203 167 .88 1.137 .876 1.06 1.333 7.757 80 242 1.894 .4 100 3720 6860 29 39 227 237 0 197 98 98 1.032 170 71 .969 .796 .046 -.33
15 43 100 32 115 10 -14 41 71 35 134 9 -43 0 0 10 79 10 89 46 7 15 5 -4 -34 null null null 6.731 6.637 12.385 120 334 -72.327 -.09 120 3870 6850 27 39 241 253 -100 91 104 -13 null 64 -39 null null null null
16 630 839 33 100 596 739 662 830 35 115 628 729 0 0 203 340 8 70 97 98 96 95 1335 1357 .806 1.24 1.161 1.307 1.265 4.86 80 280 1.27 .89 100 4030 6850 28 38 258 268 0 762 91 671 1.126 754 662 .888 1.054 .171 .076
17 93 151 35 99 58 52 95 132 36 126 60 33 0 0 27 84 11 171 92 10 88 1 110 93 1.115 .897 .55 1.225 1.083 9.332 80 346 2.373 .15 100 4180 6840 27 37 273 283 0 137 90 47 .814 120 30 1.228 .499 -.297 -1.002
18 38 91 34 94 3 -3 36 60 37 119 2 -33 0 0 9 71 14 147 13 5 2 0 0 -31 null null null 12.228 11.038 10.95 120 508 39.984 .36 120 4330 6840 26 38 287 299 -100 83 85 -3 null 54 -30 null null null null
19 275 372 34 111 240 260 266 340 38 124 232 228 0 0 76 193 15 79 100 82 100 62 500 460 .923 1.083 .983 .886 .955 5.811 80 309 1.093 .64 100 4480 6850 28 38 303 313 0 338 101 236 .984 309 207 1.017 .892 -.024 -.164
20 1228 4623 35 115 1193 4508 1301 4858 36 127 1266 4743 0 0 401 1524 10 87 100 96 97 93 5701 6009 .265 3.779 3.746 3.52 3.652 5.923 80 292 3.831 .97 100 4630 6840 27 37 318 328 0 4197 104 4093 3.431 4411 4306 .291 3.402 1.779 1.766

Total number of rows: 44544

Table truncated, full table size 9620 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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