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Sample GSM989713 Query DataSets for GSM989713
Status Public on Aug 23, 2012
Title S 07 8980T
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 S 07 8980T2
Organism Homo sapiens
Characteristics age: 71
individual: TB 1872T
disease free survival: ?-?-M1
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/2008-08/81189.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 9790 8388 87 121 9702 8267 11087 9511 115 151 10999 9390 0 0 4033 3716 182 137 98 94 98 92 17969 20389 1.174 .852 .854 .716 .861 4.258 52 306 .828 .94 80 1630 7090 33 41 19 27 0 6455 93 6362 .656 7319 7226 1.525 .657 -.609 -.606
2 10969 9092 115 125 10854 8966 12969 10682 146 155 12853 10556 0 0 4227 3322 197 141 98 100 98 100 19820 23409 1.211 .826 .821 .893 .829 3.8 52 253 .791 .95 80 1780 7100 34 42 34 42 0 6997 96 6900 .636 8220 8124 1.573 .632 -.654 -.662
3 17266 24705 168 145 17097 24560 21263 30902 195 176 21094 30757 0 0 8444 12381 154 191 92 92 92 90 41657 51851 .696 1.437 1.458 1.412 1.443 4.154 52 313 1.423 .95 90 1930 7090 32 41 48 57 0 19012 112 18900 1.105 23781 23669 .905 1.122 .145 .166
4 10151 8929 159 147 9992 8781 13616 11331 476 327 13457 11183 0 0 5716 4425 1605 1024 81 90 75 87 18773 24640 1.138 .879 .831 .998 .853 2.707 32 212 .789 .95 70 2070 7090 33 40 63 70 0 6871 113 6758 .676 8720 8606 1.479 .64 -.564 -.645
5 673 319 104 138 569 180 765 315 345 267 660 176 0 0 321 129 1456 824 0 0 0 0 749 836 3.161 .316 .267 .341 .336 4.516 52 250 .328 .68 80 2230 7090 33 41 79 87 0 245 106 139 .243 242 135 4.108 .205 -2.038 -2.285
6 5162 8321 140 200 5022 8120 6208 9862 157 226 6068 9662 0 0 2570 3672 73 133 98 98 92 96 13142 15730 .618 1.617 1.592 1.695 1.575 3.629 52 310 1.512 .95 90 2380 7090 32 41 93 102 0 6404 154 6249 1.244 7589 7436 .804 1.225 .315 .293
7 316 190 107 139 209 50 328 174 134 157 220 34 0 0 75 68 109 91 93 25 50 3 259 254 4.18 .239 .155 .221 .352 6.205 32 226 .307 .29 70 2530 7090 33 40 109 116 0 146 107 38 .184 134 26 5.432 .119 -2.441 -3.072
8 19042 26678 87 117 18954 26561 24393 34183 93 138 24306 34065 0 0 9707 13260 36 80 100 98 98 98 45515 58371 .714 1.401 1.402 1.481 1.4 3.835 52 273 1.358 .96 80 2690 7090 33 41 125 133 0 20530 90 20440 1.078 26306 26215 .927 1.079 .109 .109
9 175 150 87 118 88 31 168 133 94 133 81 14 0 0 53 72 37 83 84 25 53 6 119 95 2.839 .352 .173 .527 .621 5.619 32 159 .256 .14 60 2830 7090 34 40 140 146 0 115 91 24 .271 102 11 3.689 .133 -1.883 -2.91
10 218 178 84 112 134 65 220 171 96 131 136 59 0 0 110 89 59 80 66 36 55 12 199 195 2.062 .485 .434 .712 .534 8.891 80 335 .539 .39 100 2980 7090 32 42 153 163 -50 137 86 50 .373 132 45 2.679 .334 -1.422 -1.583
11 364 882 84 104 280 778 387 942 105 137 303 837 0 0 129 337 137 196 80 90 57 84 1058 1140 .36 2.779 2.762 2.828 3.029 2.981 52 232 .578 .98 80 3140 7090 33 41 170 178 0 679 80 599 2.138 725 644 .468 2.126 1.096 1.088
12 436 1580 87 124 349 1456 486 1852 106 171 399 1728 0 0 168 658 106 234 84 92 78 84 1805 2127 .24 4.172 4.331 4.047 4.307 3.637 52 232 4.171 .9 80 3290 7090 33 41 185 193 0 1216 95 1120 3.211 1425 1330 .311 3.333 1.683 1.737
13 313 223 95 126 218 96 327 213 113 166 231 87 0 0 123 87 101 213 78 11 63 0 314 318 2.271 .44 .377 .556 .578 6.22 52 250 .435 .35 80 3440 7090 33 41 200 208 0 172 97 74 .339 164 67 2.951 .29 -1.561 -1.787
14 318 285 108 124 209 160 322 269 133 172 213 145 0 0 55 80 111 224 93 25 40 0 369 358 1.306 .766 .681 .684 .602 3.525 32 211 3.172 .23 70 3600 7090 33 40 216 223 0 219 95 123 .589 207 112 1.697 .524 -.763 -.933
15 265 446 150 219 115 226 193 258 203 358 43 39 0 0 214 675 196 434 20 17 7 6 341 82 .509 1.965 .907 2.322 2.002 6.859 80 424 3.35 .58 100 3740 7080 31 41 229 239 -50 343 169 174 1.512 199 30 .661 .698 .597 -.519
16 1481 2603 134 256 1346 2347 1589 2668 185 423 1454 2412 0 0 389 704 182 497 98 98 96 94 3693 3866 .573 1.744 1.659 1.676 1.749 2.857 52 237 1.759 .92 80 3900 7090 33 41 246 254 0 2003 197 1806 1.342 2053 1856 .745 1.277 .424 .352
17 214 224 78 129 136 95 207 223 90 184 129 93 0 0 56 68 55 225 94 1 69 0 231 222 1.432 .699 .721 .789 .725 3.535 52 211 3.579 .55 80 4050 7090 33 41 261 269 0 172 99 73 .538 172 72 1.86 .555 -.895 -.85
18 100 134 82 139 17 -5 91 88 100 199 9 -51 0 0 50 133 80 219 7 6 3 2 12 -42 null null null 2.496 2.736 5.94 80 340 5.775 .43 100 4190 7080 31 41 274 284 -50 103 107 -4 null 68 -39 null null null null
19 259 339 75 131 184 207 276 310 94 168 200 178 0 0 122 204 71 151 78 61 65 18 391 378 .889 1.125 .89 1.125 1.047 5.163 80 364 1.519 .64 100 4350 7090 32 42 290 300 0 261 101 159 .866 239 137 1.155 .685 -.208 -.546
20 1373 5504 81 126 1292 5377 1488 5950 94 151 1407 5823 0 0 466 1517 81 129 96 100 96 100 6669 7230 .24 4.162 4.139 4.558 4.11 2.835 52 223 4.118 .95 80 4500 7090 33 41 306 314 0 4236 97 4138 3.203 4579 4481 .312 3.185 1.679 1.671

Total number of rows: 44544

Table truncated, full table size 9460 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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