NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM989727 Query DataSets for GSM989727
Status Public on Aug 23, 2012
Title PC 99T
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 99T2
Organism Homo sapiens
Characteristics ethnicity: Caucasian
age: 47
pre-operation treatment: None
individual: PC 85T
disease free survival: 70.00
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/2008-08/81077.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 10753 7715 66 194 10686 7521 13096 9687 71 248 13029 9493 0 0 6927 4452 29 200 100 96 100 90 18207 22522 1.421 .704 .729 .739 .631 3.428 32 176 .631 .89 60 1750 6870 36 42 64 70 0 5580 140 5440 .509 7006 6866 1.964 .527 -.974 -.924
2 14344 8967 75 204 14269 8763 15151 8442 87 292 15075 8238 0 0 2909 2992 62 325 100 100 100 100 23032 23313 1.628 .614 .546 .59 .619 1.563 12 104 .656 .89 50 1900 6860 35 40 79 84 0 6485 148 6338 .444 6106 5958 2.251 .395 -1.171 -1.339
3 5263 8101 71 196 5192 7905 4219 8272 78 253 4148 8076 0 0 4395 6189 29 209 93 90 87 90 13097 12224 .657 1.523 1.947 1.969 1.419 9.782 32 176 1.484 .92 60 2060 6860 35 41 95 101 0 5859 142 5717 1.101 5983 5841 .908 1.408 .139 .494
4 10989 7406 76 207 10912 7198 11963 8049 82 261 11887 7842 0 0 7594 4084 32 201 100 100 100 96 18110 19729 1.516 .66 .66 .897 .593 5.805 32 169 .583 .92 60 2210 6860 35 41 110 116 0 5356 150 5206 .477 5821 5672 2.096 .477 -1.068 -1.068
5 757 395 74 191 683 204 726 282 76 214 652 90 0 0 145 264 25 130 100 41 100 41 887 742 3.348 .299 .138 .291 .35 3.305 12 68 .483 .46 40 2360 6860 36 40 126 130 0 286 138 148 .216 204 65 4.629 .1 -2.211 -3.324
6 5758 5988 100 205 5657 5783 5688 5350 115 276 5587 5145 0 0 1506 2686 54 374 100 100 100 100 11440 10732 .978 1.022 .921 .971 .95 1.946 32 195 1.108 .87 70 2510 6860 34 41 139 146 0 4331 148 4183 .739 3869 3721 1.353 .666 -.436 -.586
7 142 217 74 216 68 1 130 189 89 300 56 -26 0 0 81 148 67 453 42 1 21 0 69 30 68 .015 null 2.217 2.611 6.305 52 277 43.49 .15 90 2660 6860 33 42 153 162 -50 157 156 1 .011 137 -19 94.02 null -6.555 null
8 6570 10416 73 161 6497 10254 7512 13147 78 261 7439 12986 0 0 3780 5685 32 437 100 90 100 84 16751 20425 .634 1.578 1.746 1.252 1.373 3.47 32 190 1.573 .93 70 2810 6860 34 41 169 176 0 7533 116 7416 1.141 9509 9392 .876 1.263 .191 .336
9 115 228 61 169 54 59 92 160 68 223 31 -8 0 0 62 180 25 189 55 21 40 9 113 23 .915 1.093 null 7.154 6.058 4.063 52 285 21.969 .2 90 2960 6850 32 41 183 192 -50 165 122 43 .79 116 -6 1.265 null -.34 null
10 127 197 62 214 65 -16 116 158 70 268 54 -56 0 0 56 153 33 214 67 13 38 0 49 -2 null null null 2.231 3.426 6.03 52 285 19.123 .22 90 3110 6850 32 41 198 207 -50 142 155 -12 null 114 -41 null null null null
11 341 601 61 224 279 376 347 568 67 278 286 344 0 0 142 309 25 237 93 62 90 40 655 630 .742 1.348 1.203 1.192 1.306 3.606 32 158 2.427 .59 60 3260 6860 35 41 215 221 0 435 162 272 .975 411 249 1.026 .87 -.037 -.201
12 450 722 63 223 386 499 462 691 70 333 399 468 0 0 46 186 24 322 100 91 100 16 885 867 .774 1.293 1.173 1.223 1.224 1.725 12 104 2.341 .59 50 3410 6850 34 39 230 235 0 522 161 361 .935 500 338 1.07 .848 -.097 -.237
13 194 251 64 210 130 40 166 213 71 264 102 2 0 0 130 179 31 244 65 11 57 1 170 104 3.25 .308 .02 1.708 1.574 7.766 52 294 15.781 .1 90 3560 6850 32 41 243 252 -50 182 152 29 .223 154 1 4.494 .014 -2.168 -6.14
14 110 241 64 188 46 52 104 199 69 256 40 11 0 0 46 162 27 261 57 11 34 1 98 51 .885 1.13 .275 2.731 2.762 6.503 52 272 34.628 .14 90 3710 6850 32 41 258 267 -50 174 136 38 .818 144 8 1.223 .199 -.291 -2.33
15 79 201 62 199 16 2 73 158 69 280 10 -41 0 0 36 149 28 283 15 3 11 0 18 -31 8 .125 null 5.081 4.793 6.541 52 299 34.007 .42 90 3860 6850 32 41 273 282 -50 145 144 1 .09 114 -30 11.061 null -3.467 null
16 651 851 63 213 588 638 769 842 72 278 706 629 0 0 292 251 41 269 93 96 90 62 1226 1335 .922 1.085 .891 1.19 .903 3.372 32 163 1.141 .68 60 4020 6850 34 40 291 297 0 615 154 461 .785 609 455 1.274 .644 -.35 -.634
17 115 292 61 178 53 114 98 174 75 239 37 -3 0 0 56 317 69 289 40 15 7 7 167 34 .465 2.151 null 4.598 2.975 8.524 52 278 8.984 .45 90 4160 6850 32 41 303 312 -50 211 129 82 1.556 126 -2 .643 null .638 null
18 74 234 61 174 12 59 69 185 68 202 8 10 0 0 25 227 52 150 3 21 1 11 71 18 .203 4.917 1.25 5.958 6.288 4.796 52 274 26.387 .1 90 4310 6850 32 41 318 327 -50 169 126 43 3.556 134 7 .281 .904 1.83 -.146
19 304 1007 64 198 240 808 234 283 69 245 170 85 0 0 543 3650 24 199 75 26 65 19 1048 255 .297 3.367 .5 1.393 1.559 7.346 52 320 7.033 .87 90 4460 6850 32 41 333 342 -50 728 143 584 2.435 205 61 .411 .362 1.284 -1.467
20 1286 3209 64 182 1222 3026 1392 3270 73 245 1328 3087 0 0 760 1959 32 234 90 93 87 81 4248 4415 .404 2.476 2.325 2.906 2.546 4.173 32 165 2.603 .94 60 4630 6850 34 40 352 358 0 2321 132 2189 1.791 2365 2233 .558 1.681 .841 .75

Total number of rows: 44544

Table truncated, full table size 9582 Kbytes.




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