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Sample GSM989780 Query DataSets for GSM989780
Status Public on Aug 23, 2012
Title PC 551N
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 551N2
Organism Homo sapiens
Characteristics individual: PC 551N
disease state: Normal
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/2008-08/81124.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 57032 72661 193 279 56839 72381 58126 73887 209 303 57932 73608 90 90 3891 4701 102 158 100 100 100 100 129220 131540 .785 1.273 1.271 1.274 1.271 1.407 32 228 1.239 .96 70 2500 6480 16 23 38 45 -100 67494 259 67234 1.183 68633 68374 .845 1.18 .242 .239
2 46236 57117 218 337 46018 56779 58126 73887 263 411 57908 73550 65 65 20508 26410 219 373 100 96 90 96 102797 131458 .81 1.234 1.27 1.383 1.27 4.023 32 176 1.214 .97 60 2640 6480 17 23 53 59 -100 53056 313 52742 1.146 68633 68320 .873 1.18 .197 .239
3 53507 68735 208 321 53298 68414 58126 73887 242 358 57917 73566 78 84 11737 15025 146 235 100 100 100 100 121712 131483 .779 1.284 1.27 1.318 1.27 2.025 32 232 1.285 .98 70 2800 6480 16 23 68 75 -100 63848 298 63549 1.192 68633 68335 .839 1.18 .254 .239
4 56278 71849 179 285 56099 71564 58126 73887 281 337 57947 73602 90 87 7856 5798 1125 250 100 100 100 100 127663 131549 .784 1.276 1.27 1.297 1.27 1.559 32 223 1.216 .93 70 2950 6470 15 22 83 90 -100 66740 265 66475 1.185 68633 68369 .844 1.18 .245 .239
5 3300 987 624 603 2675 384 3648 1015 630 637 3024 412 0 0 1223 377 407 372 90 56 84 9 3059 3436 6.966 .144 .136 .193 .139 5.264 32 169 .092 .28 60 3100 6470 16 22 99 105 0 917 560 357 .133 943 383 7.499 .127 -2.907 -2.982
6 56676 73199 1153 942 55522 72256 58126 73887 1220 1050 56972 72945 87 71 5327 2000 594 490 100 100 100 100 127778 129917 .768 1.301 1.28 1.309 1.28 1.397 32 218 1.265 .99 70 3250 6470 15 22 113 120 -100 67994 875 67118 1.209 68633 67758 .827 1.189 .274 .25
7 2633 878 439 337 2193 541 2211 853 517 445 1771 516 0 0 1375 277 360 338 96 78 93 21 2734 2287 4.054 .247 .291 .258 .273 2.543 32 218 .203 .64 70 3410 6470 15 22 129 136 0 816 313 503 .229 792 479 4.364 .271 -2.126 -1.886
8 38695 51186 200 268 38495 50918 58126 73887 273 302 57925 73619 53 55 24768 30302 220 182 90 96 84 90 89413 131544 .756 1.323 1.271 1.588 1.271 3.236 52 310 1.296 .98 90 3560 6470 14 23 143 152 -100 47546 249 47297 1.229 68633 68384 .814 1.181 .297 .239
9 873 824 128 225 745 598 915 800 141 243 786 575 0 0 227 270 76 138 100 100 100 91 1343 1361 1.246 .803 .732 .766 .747 2.206 12 104 .746 .72 50 3710 6470 16 21 160 165 0 765 209 555 .746 743 534 1.341 .68 -.424 -.557
10 963 1313 120 240 842 1073 919 1278 144 285 799 1038 0 0 240 301 94 219 100 100 100 100 1915 1837 .785 1.274 1.299 1.276 1.305 1.974 32 210 1.252 .84 70 3860 6470 15 22 174 181 0 1220 223 997 1.184 1187 964 .845 1.207 .243 .271
11 4226 7513 127 237 4098 7275 5054 8335 155 296 4927 8097 0 0 1883 2610 137 361 96 96 93 93 11373 13024 .563 1.775 1.643 2.022 1.804 2.044 32 219 1.684 .96 70 4000 6470 15 22 188 195 0 6979 220 6758 1.649 7742 7521 .606 1.527 .722 .61
12 3573 10310 136 230 3436 10080 3475 9963 157 282 3338 9733 0 0 655 2364 91 222 100 100 100 100 13516 13071 .341 2.934 2.916 2.897 2.977 1.535 32 217 3.088 .97 70 4160 6480 16 23 204 211 0 9577 214 9363 2.725 9255 9041 .367 2.708 1.446 1.437
13 1750 1520 136 240 1614 1280 1858 1600 162 289 1721 1360 0 0 555 484 98 208 98 100 98 94 2894 3081 1.261 .793 .79 .835 .825 2.844 52 264 .774 .89 80 4310 6480 16 24 219 227 0 1412 223 1189 .737 1486 1263 1.357 .734 -.441 -.446
14 1156 1236 141 249 1015 987 1161 1223 155 292 1020 974 0 0 376 462 78 191 93 96 93 87 2002 1994 1.028 .972 .955 1.083 .957 4.033 32 175 1.036 .85 60 4460 6470 16 22 235 241 0 1148 231 917 .903 1136 905 1.107 .887 -.147 -.173
15 325 287 129 218 196 68 160 216 153 255 31 -2 0 0 322 248 85 190 37 28 34 9 264 29 2.882 .347 null 1.831 2.225 4.88 32 171 .626 .53 60 4620 6460 15 21 251 257 0 267 202 63 .322 201 -2 3.103 null -1.634 null
16 10524 9262 136 227 10387 9034 12293 9971 155 275 12156 9743 0 0 4653 2908 79 175 98 100 94 100 19421 21899 1.15 .87 .801 1.096 .859 2.733 52 271 .811 .97 80 4760 6470 15 23 264 272 0 8603 211 8392 .808 9262 9050 1.238 .745 -.308 -.426
17 413 702 115 206 298 496 423 637 141 251 307 430 0 0 158 299 86 175 87 87 78 56 794 737 .601 1.664 1.401 1.586 1.643 2.188 32 212 2.501 .63 70 4920 6470 15 22 280 287 0 652 191 461 1.546 592 399 .647 1.301 .629 .38
18 154 198 124 214 30 -15 96 126 153 250 -27 -87 0 0 327 262 100 182 5 9 1 1 15 -114 null null null 2.221 2.136 3.837 52 308 1.008 .56 90 5070 6470 14 23 294 303 -50 184 199 -14 null 117 -81 null null null null
19 3446 2120 133 214 3312 1906 3476 2056 154 242 3342 1842 0 0 811 518 86 149 100 100 100 100 5218 5184 1.738 .575 .551 .578 .535 1.779 52 265 .545 .92 80 5220 6470 15 23 310 318 0 1969 199 1770 .535 1910 1711 1.871 .512 -.904 -.966
20 14126 38960 140 237 13986 38722 15711 41670 167 270 15571 41432 0 0 4499 8232 188 188 96 100 96 100 52708 57003 .361 2.769 2.661 3.347 2.664 2.87 32 211 2.614 .97 70 5360 6470 15 22 324 331 0 36190 220 35969 2.572 38707 38486 .389 2.472 1.363 1.305

Total number of rows: 44544

Table truncated, full table size 10078 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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