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Sample GSM989731 Query DataSets for GSM989731
Status Public on Aug 23, 2012
Title PC 166T
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 166T2
Organism Homo sapiens
Characteristics ethnicity: Caucasian
age: 65
pre-operation treatment: None
individual: PC 252T
disease free survival: 10.20
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/2008-08/81186.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 GPL9497
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 13557 15851 61 120 13496 15730 14990 17884 75 149 14929 17764 0 0 5627 5612 64 124 100 100 98 100 29226 32693 .858 1.166 1.19 1.365 1.17 2.998 52 358 1.13 .97 90 1620 6910 18 27 21 30 0 12782 97 12685 .94 14422 14325 1.064 .96 -.089 -.06
2 13934 15766 66 143 13868 15623 15815 17986 88 193 15749 17842 0 0 6062 6960 84 175 100 100 98 100 29491 33591 .888 1.127 1.133 1.277 1.142 3.19 52 245 1.119 .97 80 1770 6910 19 27 37 45 0 12714 115 12599 .908 14504 14388 1.101 .914 -.139 -.13
3 14682 42794 67 149 14614 42644 16534 48205 84 184 16466 48056 0 0 5893 15237 63 128 100 100 100 100 57258 64522 .343 2.918 2.918 3.19 2.949 2.448 52 244 2.905 .97 80 1920 6910 19 27 52 60 0 34509 120 34388 2.353 38873 38753 .425 2.354 1.235 1.235
4 15624 17791 66 131 15558 17660 17888 19680 84 172 17822 19549 0 0 6702 6105 57 180 100 100 100 100 33218 37371 .881 1.135 1.097 1.372 1.126 3.01 52 268 1.082 .98 80 2070 6910 19 27 67 75 0 14347 106 14241 .915 15870 15764 1.092 .885 -.128 -.177
5 732 434 68 139 663 295 736 422 88 203 667 282 0 0 106 113 66 215 100 78 100 12 958 949 2.247 .445 .423 .419 .441 2.274 32 216 .452 .63 70 2220 6900 18 25 82 89 0 350 112 238 .359 340 227 2.787 .341 -1.479 -1.552
6 9341 10382 122 216 9219 10165 9730 11199 152 258 9607 10983 0 0 1940 2739 99 198 100 100 100 100 19384 20590 .907 1.103 1.143 1.069 1.119 1.982 52 285 1.113 .97 90 2370 6900 17 26 96 105 0 8372 174 8197 .889 9031 8857 1.125 .922 -.169 -.117
7 266 253 79 148 186 105 264 248 106 209 185 100 0 0 100 95 88 210 84 11 61 0 291 285 1.771 .565 .541 .605 .673 4.414 52 233 2.197 .44 80 2520 6910 19 27 112 120 0 204 119 85 .455 200 81 2.197 .436 -1.135 -1.198
8 17934 48768 60 139 17874 48628 20405 57275 72 191 20345 57135 0 0 5972 20850 41 165 100 100 100 100 66502 77480 .368 2.721 2.808 2.243 2.84 2.722 52 326 2.876 .98 90 2680 6900 17 26 127 136 0 39327 112 39214 2.194 46187 46074 .456 2.265 1.134 1.179
9 156 205 60 129 96 75 155 198 74 164 94 68 0 0 31 74 42 122 100 25 65 0 171 162 1.28 .781 .723 .686 .922 4.891 32 211 2.98 .32 70 2830 6900 18 25 143 150 0 165 104 60 .63 160 55 1.587 .583 -.667 -.778
10 186 252 58 117 128 134 193 218 73 169 134 100 0 0 60 220 53 213 86 15 67 1 262 234 .955 1.047 .746 .85 .987 3.888 52 242 2.994 .59 80 2980 6900 18 26 158 166 0 203 94 108 .844 176 81 1.185 .602 -.244 -.733
11 369 1004 59 135 310 868 374 1024 70 166 315 888 0 0 93 251 42 194 100 100 98 94 1178 1203 .357 2.8 2.819 2.835 2.825 2.21 52 248 2.978 .9 80 3130 6900 18 26 173 181 0 810 109 700 2.258 826 716 .443 2.273 1.175 1.185
12 390 1754 59 111 330 1642 412 1801 65 139 352 1690 0 0 124 567 31 106 100 100 92 100 1972 2042 .201 4.976 4.801 5.111 5.094 2.17 52 257 5.249 .92 80 3280 6900 18 26 188 196 0 1414 90 1324 4.012 1452 1363 .249 3.872 2.004 1.953
13 271 281 57 129 213 151 288 273 67 160 231 143 0 0 88 100 35 124 94 53 88 15 364 374 1.411 .709 .619 .621 .647 3.482 52 257 .862 .59 80 3430 6900 18 26 203 211 0 227 104 122 .572 220 115 1.749 .499 -.807 -1.002
14 215 357 58 135 156 221 217 377 71 177 158 241 0 0 34 113 44 142 100 75 93 28 377 399 .706 1.417 1.525 1.248 1.37 2.748 32 213 2.036 .63 70 3580 6890 17 24 218 225 0 288 109 178 1.142 304 194 .875 1.23 .192 .299
15 68 100 55 118 13 -18 64 74 71 165 8 -44 0 0 19 80 53 151 2 3 0 1 -5 -36 null null null 5.121 6.002 7.205 80 394 6.389 .37 100 3730 6890 16 26 232 242 -50 81 95 -15 null 60 -35 null null null null
16 1289 2541 57 140 1231 2400 1437 2667 70 181 1379 2527 0 0 349 597 49 134 100 100 98 100 3631 3906 .513 1.95 1.832 2.022 1.914 2.218 52 292 1.968 .95 90 3890 6900 17 26 248 257 0 2049 113 1935 1.572 2151 2038 .636 1.478 .653 .563
17 122 225 61 123 61 101 120 211 71 169 58 88 0 0 22 69 39 148 87 31 21 0 162 146 .604 1.656 1.517 1.742 1.677 3.597 32 181 3.588 .47 70 4040 6900 18 25 264 271 0 181 99 81 1.335 170 71 .749 1.224 .417 .291
18 84 138 59 117 25 20 70 85 71 156 10 -31 0 0 74 192 45 151 10 8 5 6 45 -21 1.25 .8 null 4.305 4.265 6.038 80 323 4.741 .56 100 4190 6890 16 26 278 288 -50 111 94 16 .645 69 -25 1.55 null -.632 null
19 294 504 59 122 235 382 288 524 71 171 228 401 0 0 59 149 40 178 100 92 98 63 617 629 .615 1.626 1.759 1.55 1.755 2.657 52 272 2.599 .67 90 4340 6890 16 25 293 302 0 406 98 308 1.311 423 323 .763 1.418 .39 .504
20 1240 5491 59 123 1181 5367 1403 6179 77 175 1343 6056 0 0 454 1613 64 181 96 100 94 100 6548 7399 .22 4.544 4.509 5.355 4.496 3.073 52 224 4.543 .96 80 4490 6900 18 26 309 317 0 4428 99 4328 3.665 4983 4884 .273 3.636 1.874 1.862

Total number of rows: 44544

Table truncated, full table size 9506 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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