NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM989801 Query DataSets for GSM989801
Status Public on Aug 23, 2012
Title PC 15T
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 15T2
Organism Homo sapiens
Characteristics ethnicity: Caucasian
age: 53
pre-operation treatment: None
individual: PC 97T
disease free survival: 61.13
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/2008-08/81097.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 13856 21878 224 203 13631 21675 16186 25320 245 238 15961 25117 0 0 4832 7221 98 129 100 100 100 100 35306 41078 .629 1.59 1.574 1.576 1.573 1.447 32 235 1.613 .96 70 1800 6800 8 15 32 39 0 19745 183 19561 1.435 22851 22668 .697 1.42 .521 .506
2 10300 17197 251 216 10048 16981 13229 19305 268 237 12977 19089 0 0 5687 9195 114 126 100 100 96 100 27029 32066 .592 1.69 1.471 1.847 1.661 1.963 32 175 1.701 .97 60 1970 6800 9 15 50 56 0 15520 195 15325 1.525 17422 17227 .656 1.328 .609 .409
3 12281 30462 247 230 12033 30232 15203 35239 263 245 14955 35009 0 0 6351 14536 106 127 100 100 96 100 42265 49964 .398 2.512 2.341 3.179 2.463 2.428 32 176 2.52 .97 60 2110 6800 9 15 64 70 0 27491 208 27284 2.267 31803 31595 .441 2.113 1.181 1.079
4 13015 19734 207 176 12807 19558 14789 21098 291 223 14581 20922 0 0 4949 4445 905 244 96 100 93 100 32365 35503 .655 1.527 1.435 1.765 1.441 1.776 32 234 1.458 .96 70 2260 6800 8 15 78 85 0 17810 159 17651 1.378 19041 18882 .726 1.295 .463 .373
5 887 333 179 147 707 186 922 298 188 157 742 151 0 0 119 150 66 76 100 66 100 50 893 893 3.801 .263 .204 .208 .227 2.809 12 104 .309 .62 50 2400 6800 9 14 93 98 0 301 133 168 .237 269 136 4.212 .184 -2.074 -2.445
6 3254 7285 203 182 3050 7103 833 1825 222 229 629 1643 0 0 3380 7681 98 152 93 98 88 96 10153 2272 .429 2.329 2.612 2.497 2.271 1.843 120 405 2.332 .98 130 2570 6790 4 17 106 119 0 6575 164 6410 2.102 1647 1483 .476 2.357 1.072 1.237
7 324 316 224 219 99 97 334 254 244 262 109 35 0 0 122 196 101 167 51 26 13 15 196 144 1.021 .98 .321 .985 1.154 3.607 52 246 2.75 .48 90 2710 6790 6 15 122 131 -50 285 198 88 .884 229 32 1.131 .29 -.177 -1.787
8 17137 34634 208 183 16928 34451 18203 38293 218 206 17994 38110 0 0 4327 11919 83 121 100 100 100 100 51379 56104 .491 2.035 2.118 1.895 2.045 1.376 32 214 2.144 .98 70 2860 6790 7 14 138 145 0 31257 165 31091 1.837 34559 34394 .544 1.911 .877 .935
9 218 186 184 160 33 26 203 179 211 184 18 19 0 0 75 81 193 118 3 11 0 1 59 37 1.269 .788 1.056 1.315 1.318 3.592 52 312 .066 .13 90 3010 6790 6 15 152 161 -50 168 144 23 .711 162 17 1.406 .953 -.492 -.07
10 418 259 196 167 221 92 433 269 221 203 236 102 0 0 89 62 102 115 83 33 66 0 313 338 2.402 .416 .432 .434 .464 3.243 12 68 .243 .22 40 3170 6790 9 13 171 175 0 234 151 83 .376 243 92 2.662 .39 -1.412 -1.358
11 594 1190 188 162 405 1028 553 1188 212 183 364 1026 0 0 180 419 91 108 100 96 87 96 1433 1390 .394 2.538 2.819 2.458 2.72 1.61 32 176 2.792 .84 60 3310 6790 8 14 184 190 0 1074 146 928 2.291 1072 926 .437 2.544 1.196 1.347
12 609 1139 179 160 429 979 649 1095 193 185 469 935 0 0 185 232 79 108 100 100 87 100 1408 1404 .438 2.282 1.994 2.53 2.349 1.702 32 173 2.253 .87 60 3460 6790 8 14 199 205 0 1028 144 884 2.06 988 844 .486 1.799 1.042 .847
13 497 363 170 144 326 219 481 334 186 168 310 190 0 0 111 128 80 102 100 81 96 46 545 500 1.489 .672 .613 .583 .585 2.022 32 218 .786 .65 70 3610 6790 7 14 213 220 0 328 130 198 .606 301 171 1.649 .553 -.722 -.854
14 411 295 190 135 220 160 418 318 208 159 227 183 0 0 119 89 84 98 87 71 68 46 380 410 1.375 .727 .806 .685 .754 1.954 32 168 .745 .54 60 3760 6790 8 14 229 235 0 266 122 144 .656 287 165 1.524 .728 -.607 -.459
15 206 112 188 148 17 -36 196 97 203 167 7 -51 0 0 56 59 80 106 15 1 1 0 -19 -44 null null null 1.755 1.636 3.191 52 278 2.116 .13 90 3910 6790 6 15 242 251 -50 101 134 -32 null 88 -46 null null null null
16 1818 3422 190 152 1627 3270 1847 3456 202 178 1656 3304 0 0 358 522 80 119 100 100 100 100 4897 4960 .498 2.01 1.995 2.036 2.024 1.279 32 208 2.058 .95 70 4060 6790 7 14 258 265 0 3088 137 2951 1.814 3119 2982 .551 1.801 .859 .848
17 494 255 173 146 320 109 470 260 184 170 296 114 0 0 123 95 68 104 100 58 91 16 429 410 2.936 .341 .385 .312 .323 2.011 12 104 .507 .46 50 4220 6780 7 12 275 280 0 230 132 98 .307 235 103 3.253 .348 -1.702 -1.525
18 180 109 177 141 2 -32 180 106 194 165 2 -35 0 0 63 46 107 104 3 0 0 0 -30 -33 null null null 1.392 1.17 4.696 52 293 2.477 .36 90 4370 6780 5 14 288 297 -50 98 127 -29 null 96 -32 null null null null
19 472 551 181 141 290 410 473 568 190 172 291 427 0 0 118 181 71 123 96 90 84 81 700 718 .707 1.414 1.467 1.357 1.715 2.298 32 223 1.822 .69 70 4520 6790 7 14 304 311 0 497 127 370 1.276 513 385 .784 1.324 .352 .405
20 1933 9184 179 144 1753 9040 2167 10089 192 177 1987 9945 0 0 710 2468 101 137 100 100 96 100 10793 11932 .194 5.157 5.005 5.686 5.058 1.566 32 171 5.097 .96 60 4660 6790 8 14 319 325 0 8288 130 8158 4.654 9105 8975 .215 4.517 2.218 2.175

Total number of rows: 44544

Table truncated, full table size 9916 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap