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Sample GSM989821 Query DataSets for GSM989821
Status Public on Aug 23, 2012
Title PC 362T
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 362T2
Organism Homo sapiens
Characteristics ethnicity: Caucasian
age: 57
pre-operation treatment: None
individual: PC 111T
disease free survival: 61.37
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/2008-08/81249.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 8765 9510 85 182 8680 9327 6909 8566 89 204 6823 8383 0 0 8639 9038 35 120 75 67 64 63 18007 15206 .931 1.075 1.229 1.427 1.069 9.427 120 563 .994 .94 120 1770 6690 7 19 11 23 0 9430 180 9249 1.066 8494 8313 .939 1.218 .092 .285
2 20630 20623 92 194 20537 20428 21531 22134 101 218 21439 21939 0 0 4548 5615 48 127 100 100 100 100 40965 43378 1.005 .995 1.023 .951 .997 2.747 52 229 .962 .92 90 1930 6690 8 17 28 37 0 20450 192 20257 .986 21948 21755 1.014 1.015 -.02 .021
3 11961 12735 96 203 11864 12532 14803 14552 102 225 14706 14349 0 0 9861 10406 33 120 91 85 84 80 24396 29055 .947 1.056 .976 1.392 1.05 7.807 120 297 1.023 .94 120 2080 6690 7 19 42 54 0 12628 201 12427 1.047 14430 14229 .955 .968 .067 -.048
4 14518 15047 96 198 14421 14848 18628 19396 102 214 18531 19197 0 0 9051 9355 35 113 99 97 97 94 29269 37728 .971 1.03 1.036 1.108 1.045 6.621 120 277 .996 .94 120 2240 6700 8 20 58 70 0 14921 196 14723 1.021 19233 19036 .979 1.027 .03 .039
5 1136 385 95 209 1041 175 1107 389 302 330 1012 179 0 0 188 190 1116 672 30 1 0 0 1216 1191 5.949 .168 .177 .16 .193 5.058 52 187 .131 .33 90 2400 6690 8 17 75 84 0 382 207 174 .167 386 177 5.999 .175 -2.585 -2.511
6 7952 7499 109 236 7843 7263 8502 8055 268 323 8392 7819 0 0 3215 2648 874 520 92 96 91 95 15106 16211 1.08 .926 .932 .985 .923 3.659 120 335 .868 .94 130 2540 6700 7 20 87 100 0 7436 234 7202 .918 7987 7753 1.089 .924 -.123 -.114
7 298 252 118 258 179 -5 302 252 141 268 183 -5 0 0 77 123 100 142 86 7 42 1 174 178 null null null .463 .328 9.377 52 173 -.139 -.03 80 2690 6710 11 19 105 113 0 250 256 -5 null 250 -5 null null null null
8 13078 13376 95 216 12982 13159 18245 18543 109 247 18149 18326 0 0 9773 10129 53 222 90 78 83 75 26141 36475 .987 1.014 1.01 1.205 1.037 5.485 120 383 .997 .95 120 2850 6700 8 20 119 131 0 13264 214 13049 1.005 18387 18172 .995 1.001 .007 .002
9 279 245 99 200 179 45 273 215 120 268 174 15 0 0 60 156 60 319 100 6 87 0 224 189 3.978 .251 .086 .539 .658 6.051 32 153 -1 -1 70 3010 6700 10 17 137 144 0 243 198 45 .249 213 15 4.011 .085 -2.004 -3.548
10 282 426 83 189 199 237 286 311 89 205 203 122 0 0 80 800 39 118 95 52 91 30 436 325 .84 1.191 .601 .814 .717 5.356 80 288 14.719 .24 110 3150 6690 7 18 149 160 0 422 187 235 1.181 308 121 .847 .596 .24 -.747
11 1215 1788 78 181 1136 1607 1171 1808 91 197 1093 1627 0 0 269 612 59 124 100 100 100 100 2743 2720 .707 1.415 1.489 1.326 1.401 2.874 52 252 1.553 .87 90 3290 6680 7 16 164 173 0 1773 179 1594 1.403 1793 1613 .713 1.476 .488 .562
12 985 1922 79 172 905 1749 1026 1994 86 192 947 1821 0 0 244 813 48 118 98 97 98 92 2654 2768 .517 1.933 1.923 1.717 1.921 3.865 80 309 2.134 .89 110 3450 6680 6 17 179 190 0 1906 171 1734 1.916 1977 1806 .522 1.907 .938 .931
13 585 397 80 171 504 226 590 373 83 188 510 201 0 0 140 159 24 109 98 75 98 45 730 711 2.23 .448 .394 .375 .443 3.877 80 223 .394 .52 100 3600 6690 8 18 195 205 0 394 170 224 .445 370 199 2.249 .391 -1.169 -1.355
14 267 392 85 182 182 209 266 359 86 211 181 177 0 0 54 189 24 122 100 63 100 37 391 358 .871 1.148 .978 1 1.228 4.989 80 181 1.713 .38 100 3750 6690 8 18 210 220 0 389 180 207 1.139 356 176 .878 .97 .187 -.044
15 287 358 86 205 200 152 85 164 91 229 -1 -41 0 0 1270 1627 27 135 20 14 7 7 352 -42 1.316 .76 null 4.362 4.372 11.727 120 236 1.089 .69 120 3900 6680 6 18 224 236 -50 355 203 151 .754 163 -41 1.327 null -.408 null
16 1329 1174 95 231 1234 942 1458 1217 107 256 1362 985 0 0 478 480 128 155 93 91 93 86 2176 2347 1.31 .763 .723 .775 .782 4.398 80 218 .74 .83 100 4050 6680 7 17 240 250 0 1164 229 934 .757 1207 977 1.321 .717 -.402 -.48
17 229 477 98 251 131 226 219 477 110 281 120 226 0 0 61 178 133 156 40 67 3 28 357 346 .58 1.725 1.883 1.93 2.047 4.674 80 198 3.879 .41 110 4210 6690 7 18 255 266 0 473 249 224 1.711 473 224 .585 1.868 .775 .901
18 89 183 113 226 -24 -42 78 146 123 245 -34 -79 0 0 56 134 47 129 2 8 0 2 -66 -113 null null null 2.918 2.864 4.922 120 306 13.76 .14 120 4350 6680 6 18 269 281 -50 181 224 -42 null 145 -78 null null null null
19 898 735 115 225 782 510 866 714 123 242 750 489 0 0 190 318 46 144 100 82 100 75 1292 1239 1.533 .652 .652 .514 .615 4.234 80 318 .671 .74 110 4500 6680 6 17 284 295 0 729 223 506 .647 708 485 1.546 .647 -.629 -.629
20 3907 10471 93 222 3813 10248 4192 11236 100 256 4098 11014 0 0 1111 3900 35 175 100 96 100 95 14061 15112 .372 2.688 2.688 2.294 2.682 5.13 80 257 2.853 .92 110 4650 6680 6 17 299 310 0 10383 220 10162 2.665 11142 10922 .375 2.665 1.414 1.414

Total number of rows: 44544

Table truncated, full table size 9723 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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