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Sample GSM989751 Query DataSets for GSM989751
Status Public on Aug 23, 2012
Title PC 540T
Sample type RNA
 
Channel 1
Source name Human 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 hoaa 012 RNA
Organism Homo sapiens
Characteristics ethnicity: Caucasian
age: 48
pre-operation treatment: None
individual: PC 579T
disease free survival: 22.60
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/2008-08/80822.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 4002 2747 79 103 3923 2644 3588 2503 84 121 3509 2400 0 0 2959 2230 25 83 93 90 90 87 6567 5909 1.484 .674 .684 .786 .734 4.409 32 176 .695 .94 60 1700 7150 40 46 43 49 0 3158 118 3040 .775 2878 2759 1.291 .786 -.368 -.347
2 3499 2212 87 112 3412 2100 2316 2003 97 131 2229 1891 0 0 3226 1996 45 89 87 84 78 68 5512 4120 1.625 .615 .848 .672 .608 2.836 32 176 .601 .94 60 1850 7150 40 46 58 64 0 2543 129 2414 .708 2303 2174 1.413 .975 -.499 -.036
3 8057 11143 95 128 7962 11015 5855 6503 98 150 5760 6375 0 0 7547 10176 33 111 100 87 90 84 18977 12135 .723 1.383 1.107 1.508 1.388 3.819 32 236 1.38 .96 70 2000 7150 39 46 72 79 0 12811 147 12663 1.59 7476 7329 .629 1.272 .669 .348
4 5177 3447 94 129 5083 3318 5402 3696 102 156 5308 3567 0 0 3871 2472 55 125 93 87 87 84 8401 8875 1.532 .653 .672 .795 .663 2.837 32 236 .635 .96 70 2160 7150 39 46 88 95 0 3963 148 3815 .75 4249 4101 1.333 .773 -.414 -.372
5 484 120 90 116 394 4 493 107 97 159 403 -9 0 0 76 60 33 128 100 8 100 0 398 394 98.5 .01 null .102 .111 2.043 12 68 .047 .14 40 2300 7150 41 45 104 108 0 138 133 5 .012 123 -10 85.678 null -6.421 null
6 2821 3387 96 127 2725 3260 3289 3611 113 173 3193 3484 0 0 1234 1039 58 150 96 100 96 96 5985 6677 .836 1.196 1.091 1.481 1.174 1.86 32 211 1.117 .95 70 2460 7150 39 46 118 125 0 3894 146 3748 1.375 4151 4005 .727 1.254 .46 .327
7 148 117 85 109 63 8 113 100 94 134 28 -9 0 0 76 91 39 92 44 3 34 1 71 19 7.875 .127 null 1.456 2 6.242 52 364 5.815 .23 90 2600 7140 37 46 131 140 -50 135 125 9 .146 115 -10 6.85 null -2.776 null
8 18005 23734 99 139 17906 23595 19274 26254 107 160 19175 26115 0 0 3457 5719 57 115 100 100 100 100 41501 45290 .759 1.318 1.362 1.301 1.358 1.181 12 104 1.383 .96 50 2750 7140 39 44 148 153 0 27286 160 27126 1.515 30183 30023 .66 1.566 .599 .647
9 125 136 84 117 41 19 114 111 93 140 30 -6 0 0 56 84 37 89 46 21 32 5 60 24 2.158 .463 null 1.485 1.407 3.478 52 361 7.47 .25 90 2910 7140 37 46 162 171 -50 156 135 22 .533 128 -7 1.877 null -.908 null
10 218 189 80 107 138 82 233 181 91 160 153 74 0 0 91 79 46 248 78 3 68 0 220 227 1.683 .594 .484 .722 .92 3.095 32 218 2.921 .42 70 3070 7140 38 45 179 186 0 217 123 94 .683 208 85 1.464 .556 -.55 -.847
11 352 396 91 103 261 293 328 389 98 143 237 286 0 0 73 104 34 167 100 91 100 33 554 523 .891 1.123 1.207 1.085 1.227 1.647 12 104 1.397 .67 50 3210 7140 39 44 194 199 0 455 118 337 1.291 447 329 .775 1.387 .368 .472
12 547 763 97 126 450 637 560 762 101 149 463 636 0 0 113 169 34 92 100 100 100 100 1087 1099 .706 1.416 1.374 1.407 1.237 1.384 12 104 1.532 .87 50 3360 7140 39 44 209 214 0 877 145 732 1.627 876 731 .614 1.579 .703 .659
13 296 186 90 117 206 69 314 182 108 164 224 65 0 0 124 80 116 183 75 12 46 0 275 289 2.986 .335 .29 .348 .354 4.065 32 227 .995 .5 70 3510 7140 38 45 223 230 0 214 135 79 .385 209 75 2.597 .334 -1.377 -1.584
14 307 227 87 124 220 103 300 228 95 149 213 104 0 0 57 65 44 91 100 58 100 16 323 317 2.136 .468 .488 .378 .552 2.533 12 68 .652 .71 40 3660 7150 41 45 240 244 0 261 143 118 .538 262 120 1.858 .561 -.894 -.833
15 126 209 87 113 39 96 111 130 98 153 24 17 0 0 67 233 60 184 15 19 7 11 135 41 .406 2.462 .708 4.336 3.755 4.671 52 350 4.026 .72 90 3810 7140 37 46 252 261 -50 240 130 110 2.83 149 20 .353 .814 1.501 -.296
16 1187 1433 87 119 1100 1314 1216 1385 100 152 1129 1266 0 0 768 884 49 125 96 84 96 81 2414 2395 .837 1.195 1.121 1.161 1.186 2.232 32 223 1.187 .96 70 3970 7140 38 45 269 276 0 1647 137 1511 1.373 1592 1455 .728 1.289 .458 .366
17 338 358 86 123 252 235 326 380 96 140 240 257 0 0 71 123 38 86 100 83 100 75 487 497 1.072 .933 1.071 .737 1.039 2.977 12 104 1.86 .49 50 4120 7140 39 44 285 290 0 412 141 270 1.072 437 295 .933 1.231 .1 .3
18 88 104 86 126 2 -22 83 92 103 197 -3 -34 0 0 29 56 99 432 1 0 0 0 -20 -37 null null null 3.101 2.429 3.523 52 328 9.305 .43 90 4260 7130 36 45 297 306 -50 120 145 -25 null 106 -39 null null null null
19 322 237 83 115 239 122 327 230 91 131 244 115 0 0 84 86 29 85 100 58 100 33 361 359 1.959 .51 .471 .475 .638 1.623 12 104 .635 .57 50 4410 7130 38 43 314 319 0 272 132 140 .587 264 132 1.704 .542 -.769 -.884
20 2370 6767 88 125 2282 6642 2529 7552 94 139 2441 7427 0 0 555 2252 37 88 100 100 100 100 8924 9868 .344 2.911 3.043 2.769 2.981 1.367 12 104 3.138 .97 50 4570 7130 38 43 330 335 0 7780 144 7636 3.346 8682 8538 .299 3.498 1.743 1.807

Total number of rows: 44544

Table truncated, full table size 9613 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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