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Sample GSM989692 Query DataSets for GSM989692
Status Public on Aug 23, 2012
Title PC 159T
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 159T2
Organism Homo sapiens
Characteristics ethnicity: Caucasian
age: 51
pre-operation treatment: None
individual: PC 47T
disease free survival: 37.60
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/2008-08/81168.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) [email protected]
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 19126 8777 89 186 19036 8590 20884 9720 104 217 20795 9533 0 0 5919 2709 52 131 100 100 100 100 27626 30328 2.216 .451 .458 .449 .442 1.99 32 235 .438 .97 70 1740 6730 29 36 34 41 0 6377 135 6241 .328 7062 6927 3.05 .333 -1.609 -1.586
2 16550 7288 124 211 16425 7076 17523 8155 142 223 17399 7943 0 0 3990 2982 72 125 100 100 100 100 23501 25342 2.321 .431 .457 .369 .457 2.842 32 236 .446 .96 70 1890 6720 28 35 49 56 0 5295 153 5141 .313 5925 5771 3.195 .332 -1.676 -1.592
3 9832 4931 132 204 9700 4727 12123 4975 161 230 11991 4770 0 0 5841 3090 92 140 96 100 96 96 14427 16761 2.052 .487 .398 .492 .518 3.446 32 170 .477 .94 60 2040 6730 30 36 65 71 0 3583 148 3435 .354 3615 3466 2.824 .289 -1.498 -1.791
4 18138 7475 125 223 18012 7251 17744 7687 160 244 17619 7463 0 0 2485 1660 100 138 100 100 100 100 25263 25082 2.484 .403 .424 .391 .42 2.2 32 226 .395 .95 70 2200 6730 29 36 80 87 0 5431 162 5269 .292 5585 5423 3.419 .308 -1.773 -1.7
5 1130 286 113 181 1017 105 1133 269 128 204 1020 87 0 0 169 162 66 133 100 40 100 15 1122 1107 9.686 .103 .085 .117 .138 5.258 32 220 .087 .3 70 2340 6720 28 35 94 101 0 208 132 76 .075 195 63 13.33 .062 -3.737 -4.012
6 6121 3148 161 215 5959 2933 5953 2972 170 246 5792 2756 0 0 1596 923 77 172 100 100 100 100 8892 8548 2.032 .492 .476 .487 .485 2.101 52 255 .465 .93 80 2510 6730 29 37 111 119 0 2287 156 2131 .358 2159 2002 2.796 .346 -1.483 -1.532
7 408 241 117 197 291 43 413 218 132 222 296 20 0 0 86 121 57 135 100 16 100 8 334 316 6.767 .148 .068 .305 .247 5.938 12 102 -.109 -.09 50 2660 6730 30 35 127 132 0 175 143 31 .107 158 15 9.314 .049 -3.219 -4.348
8 13462 6404 100 184 13361 6220 14413 6621 117 229 14312 6437 0 0 3339 1865 102 161 100 100 100 100 19581 20749 2.148 .466 .45 .446 .464 2.074 32 190 .461 .97 70 2790 6730 29 36 139 146 0 4653 134 4519 .338 4811 4677 2.956 .327 -1.564 -1.614
9 166 205 90 194 75 11 168 182 102 229 78 -11 0 0 73 112 88 161 44 9 9 0 86 67 6.818 .147 null 1.426 1.908 11.338 52 279 -1 -1 90 2940 6720 27 36 153 162 -50 149 141 8 .107 132 -8 9.384 null -3.23 null
10 252 211 80 175 172 36 256 175 85 217 175 0 0 0 70 120 30 149 96 12 93 9 208 175 4.778 .209 null .401 .406 6.964 32 158 .363 .11 60 3090 6720 29 35 170 176 0 153 127 26 .152 127 0 6.576 null -2.717 null
11 392 313 78 180 314 133 386 307 85 213 308 126 0 0 167 137 43 192 94 38 90 0 447 434 2.361 .424 .409 .472 .495 4.32 52 257 .351 .35 80 3260 6730 29 37 186 194 0 227 131 97 .308 223 92 3.249 .297 -1.7 -1.75
12 455 475 81 180 374 295 465 436 86 213 384 256 0 0 135 220 43 197 100 61 98 30 669 640 1.268 .789 .667 .66 .732 4.14 52 249 1.153 .44 80 3410 6730 29 37 201 209 0 345 131 214 .573 317 186 1.745 .484 -.803 -1.046
13 390 304 88 190 302 114 390 248 103 294 301 58 0 0 82 276 120 795 96 3 75 0 416 359 2.649 .377 .193 .348 .385 5.016 32 208 .739 .22 70 3550 6720 28 35 215 222 0 221 138 83 .274 180 42 3.646 .14 -1.866 -2.836
14 289 215 102 192 186 22 271 191 122 239 169 -1 0 0 78 91 93 234 91 0 41 0 208 168 8.455 .118 null .324 .495 6.394 12 104 -1 -1 50 3700 6700 27 32 231 236 0 156 140 16 .086 139 -1 11.636 null -3.541 null
15 151 153 95 161 55 -7 145 128 101 190 50 -32 0 0 37 111 38 121 59 13 28 3 48 18 null null null 1.507 1.487 7.282 52 340 26.319 .07 90 3860 6700 25 34 245 254 -50 111 117 -5 null 93 -23 null null null null
16 1242 741 97 197 1144 543 1265 692 104 223 1167 494 0 0 232 324 33 130 100 93 100 78 1687 1661 2.107 .475 .423 .42 .439 2.754 32 202 .49 .79 70 4020 6710 27 34 262 269 0 538 143 395 .345 503 359 2.9 .308 -1.536 -1.701
17 215 209 99 196 115 12 225 192 105 208 126 -3 0 0 66 118 33 126 84 21 71 3 127 123 9.583 .104 null 1.002 .828 8.106 52 267 35.663 .03 90 4160 6710 26 35 275 284 -50 152 142 9 .076 140 -2 13.189 null -3.721 null
18 128 149 98 190 29 -40 126 116 101 210 28 -73 0 0 38 111 34 135 38 9 19 1 -11 -45 null null null 2.892 4.306 6.989 52 273 -72.174 -.04 90 4310 6710 26 35 290 299 -50 108 138 -29 null 84 -53 null null null null
19 411 277 82 175 328 102 404 241 89 204 321 65 0 0 78 134 35 152 100 31 100 9 430 386 3.216 .311 .202 .241 .325 6.519 32 208 .391 .18 70 4470 6710 27 34 307 314 0 201 127 74 .226 175 47 4.426 .147 -2.146 -2.765
20 2300 2365 75 166 2225 2199 2226 2350 85 194 2151 2184 0 0 314 648 37 118 100 100 100 100 4424 4335 1.012 .988 1.015 .933 .97 2.592 32 216 1.008 .93 70 4620 6720 28 35 322 329 0 1718 121 1598 .718 1707 1587 1.393 .738 -.478 -.439

Total number of rows: 44544

Table truncated, full table size 9563 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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