NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM989742 Query DataSets for GSM989742
Status Public on Aug 23, 2012
Title PC 223T
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 223T2
Organism Homo sapiens
Characteristics ethnicity: Caucasian
age: 69
pre-operation treatment: None
individual: PC 538T
disease free survival: 24.87
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/2008-08/81199.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 5505 4379 76 147 5428 4232 5507 4587 79 154 5430 4440 0 0 547 834 17 58 100 100 100 100 9660 9870 1.283 .78 .818 .762 .813 3.803 52 191 .777 .95 90 1760 6770 24 33 0 8 0 4545 153 4392 .809 4761 4608 1.236 .849 -.305 -.237
2 5348 4803 81 145 5267 4658 5726 4812 83 154 5645 4667 0 0 1358 593 19 58 100 100 100 100 9925 10312 1.131 .884 .827 .943 .857 4.8 52 246 .799 .94 90 1910 6770 24 33 14 23 0 4985 150 4834 .918 4994 4844 1.089 .858 -.124 -.221
3 5236 5714 83 143 5152 5570 5980 6548 87 154 5896 6405 0 0 1782 2103 23 62 100 100 100 100 10722 12301 .925 1.081 1.086 1.041 1.081 5.397 80 338 1.05 .94 110 2070 6770 23 34 29 40 0 5930 148 5781 1.122 6796 6648 .891 1.127 .166 .173
4 5000 4329 85 157 4914 4172 5558 4731 90 167 5473 4573 0 0 1604 1357 31 77 100 100 100 100 9086 10046 1.178 .849 .836 .864 .839 5.134 80 309 .798 .94 110 2220 6770 23 34 44 55 0 4493 163 4330 .881 4910 4746 1.135 .867 -.183 -.206
5 269 230 89 155 179 74 264 221 93 167 175 65 0 0 60 91 31 76 98 42 97 15 253 240 2.419 .413 .371 .457 .509 8.298 80 271 .274 .27 110 2370 6760 22 33 59 70 0 239 161 77 .429 229 67 2.331 .385 -1.221 -1.375
6 4370 5489 99 162 4271 5326 4369 5646 104 173 4270 5484 0 0 795 1249 36 65 100 100 100 100 9597 9754 .802 1.247 1.284 1.226 1.276 4.079 80 261 1.204 .94 110 2510 6760 22 33 73 84 0 5697 168 5528 1.294 5860 5692 .773 1.333 .372 .415
7 146 225 103 173 42 51 144 214 113 183 40 41 0 0 34 83 38 67 52 37 14 12 93 81 .824 1.214 1.025 1.454 1.664 9.711 120 385 .888 .18 120 2660 6760 22 34 88 100 -100 234 180 53 1.26 222 43 .793 1.064 .334 .089
8 5753 6723 106 173 5646 6550 6261 7156 109 181 6154 6983 0 0 1679 1755 25 67 100 100 100 100 12196 13137 .862 1.16 1.135 1.187 1.128 4.764 80 223 1.074 .94 110 2820 6770 23 34 104 115 0 6978 180 6798 1.204 7427 7247 .831 1.178 .268 .236
9 150 242 104 166 46 76 144 221 107 171 40 55 0 0 39 90 25 64 69 47 38 29 122 95 .605 1.652 1.375 1.845 2.021 12.656 120 303 .924 .23 120 2970 6760 22 34 119 131 -100 251 172 79 1.715 229 57 .583 1.427 .778 .513
10 165 247 98 160 66 86 166 237 100 164 67 76 0 0 34 84 23 55 85 60 70 38 152 143 .767 1.303 1.134 1.287 1.472 9.812 120 310 1.169 .39 120 3120 6760 22 34 134 146 -100 256 166 89 1.352 246 79 .739 1.177 .436 .235
11 293 446 105 171 188 275 300 437 107 176 195 266 0 0 58 122 26 57 98 95 98 92 463 461 .684 1.463 1.364 1.371 1.457 5.219 80 238 1.384 .77 110 3280 6760 22 33 150 161 0 463 177 285 1.518 454 276 .659 1.416 .602 .502
12 235 408 113 185 122 223 237 382 115 190 124 197 0 0 55 143 25 62 93 88 91 75 345 321 .547 1.828 1.589 1.675 1.685 7.765 120 301 1.686 .61 120 3420 6760 22 34 164 176 -100 423 192 231 1.897 396 204 .527 1.649 .924 .721
13 207 299 108 181 99 117 210 296 110 186 102 114 0 0 54 90 24 65 90 70 81 42 216 216 .846 1.182 1.118 1.175 1.22 6.758 120 289 .906 .48 120 3570 6760 22 34 179 191 -100 310 188 121 1.227 307 118 .815 1.16 .295 .214
14 174 280 113 190 60 90 173 280 120 199 59 90 0 0 36 84 34 70 74 56 36 26 150 149 .667 1.5 1.525 1.638 1.778 9.362 120 380 1.127 .35 120 3730 6760 22 34 195 207 -100 291 197 93 1.557 291 93 .642 1.583 .639 .663
15 146 230 123 202 22 27 135 214 129 206 12 12 0 0 56 95 35 70 37 28 20 13 49 24 .815 1.227 1 2.063 2.173 10.25 120 436 .827 .28 120 3880 6750 21 33 210 222 -100 239 210 28 1.274 222 12 .785 1.038 .349 .054
16 639 877 128 197 511 680 685 929 129 197 556 732 0 0 157 266 26 65 100 98 98 98 1191 1288 .751 1.331 1.317 1.279 1.35 4.571 80 221 1.329 .89 110 4040 6760 22 33 226 237 0 910 204 706 1.381 964 760 .724 1.366 .466 .45
17 166 294 124 190 42 103 156 294 126 193 32 103 0 0 39 84 27 62 56 64 30 36 145 135 .408 2.452 3.219 2.684 2.445 7.97 120 298 1.522 .35 120 4180 6750 21 33 240 252 -100 305 197 107 2.545 305 107 .393 3.341 1.348 1.74
18 151 254 126 206 25 48 149 237 128 214 23 31 0 0 39 84 29 69 40 35 15 15 73 54 .521 1.92 1.348 2.285 2.21 13.388 120 317 .838 .16 120 4330 6750 21 33 255 267 -100 264 214 50 1.993 246 32 .502 1.399 .995 .484
19 384 482 128 223 255 259 387 477 130 225 258 254 0 0 73 117 28 70 100 96 100 81 514 512 .985 1.016 .984 .936 1.005 5.407 80 284 .911 .72 110 4490 6760 22 33 271 282 0 500 231 269 1.054 495 264 .949 1.022 .076 .031
20 954 2290 134 207 820 2082 977 2307 132 209 843 2099 0 0 160 443 25 67 100 100 100 100 2902 2942 .394 2.539 2.49 2.521 2.598 3.988 80 279 2.492 .94 110 4640 6760 22 33 286 297 0 2377 215 2161 2.635 2394 2179 .379 2.584 1.398 1.37

Total number of rows: 44544

Table truncated, full table size 9596 Kbytes.




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