NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM989717 Query DataSets for GSM989717
Status Public on Aug 23, 2012
Title PC 19T
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 19T2
Organism Homo sapiens
Characteristics ethnicity: Caucasian
age: 63
pre-operation treatment: None
individual: PC 448T
disease free survival: 35.63
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/2008-08/81103.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 18461 20380 638 479 17823 19901 20156 24642 663 561 19517 24162 0 0 4915 8664 190 453 100 100 100 100 37724 43679 .896 1.117 1.238 .97 1.218 3.262 32 236 1.186 .96 70 1860 6780 22 29 26 33 0 17168 404 16765 .941 20759 20354 1.063 1.043 -.088 .061
2 15164 17744 696 535 14467 17208 16553 20104 665 641 15856 19568 0 0 4630 7561 270 401 100 100 100 100 31675 35424 .841 1.189 1.234 1.089 1.259 3.287 32 176 1.224 .96 60 2010 6780 23 29 42 48 0 14948 451 14496 1.002 16936 16484 .998 1.04 .003 .056
3 16931 21676 534 589 16397 21086 18497 26990 575 717 17962 26401 0 0 5877 11026 265 469 100 100 100 96 37483 44363 .778 1.286 1.47 1.062 1.394 3.877 32 176 1.362 .94 60 2160 6780 23 29 57 63 0 18260 496 17763 1.083 22737 22240 .923 1.238 .115 .308
4 15031 17259 717 465 14313 16794 16002 18198 731 544 15285 17733 0 0 3157 4512 261 386 100 100 100 100 31107 33018 .852 1.173 1.16 1.155 1.183 2.677 32 223 1.182 .96 70 2310 6780 22 29 71 78 0 14539 392 14147 .988 15330 14938 1.012 .977 -.017 -.033
5 1758 727 480 336 1278 390 1754 741 456 446 1273 404 0 0 315 188 272 449 100 41 91 0 1668 1677 3.277 .305 .317 .255 .344 5.189 12 68 .239 .5 40 2450 6770 23 27 87 91 0 612 283 329 .257 624 340 3.89 .267 -1.96 -1.903
6 8342 12698 259 432 8083 12266 9333 14091 277 541 9074 13658 0 0 2965 5080 141 482 100 100 100 92 20349 22732 .659 1.518 1.505 1.395 1.537 3.025 52 276 1.527 .96 80 2610 6780 22 30 101 109 0 10697 364 10333 1.278 11870 11506 .782 1.268 .354 .343
7 422 413 159 322 262 90 427 379 198 415 267 56 0 0 173 155 126 360 69 7 53 0 352 323 2.911 .344 .21 .585 .641 7.025 52 315 .998 .25 90 2760 6780 21 30 115 124 -50 348 271 76 .289 319 47 3.456 .177 -1.789 -2.501
8 29212 40014 131 300 29081 39713 31322 42120 148 393 31190 41819 0 0 7164 8416 85 458 100 100 100 100 68794 73009 .732 1.366 1.341 1.389 1.377 2.469 32 212 1.33 .98 70 2910 6780 22 29 131 138 0 33708 253 33454 1.15 35482 35229 .869 1.129 .202 .176
9 176 297 98 243 78 53 153 262 117 322 55 18 0 0 76 143 72 429 44 1 19 0 131 73 1.472 .679 .327 1.129 1.305 9.829 52 304 14.631 .42 90 3060 6770 20 29 145 154 -50 250 205 45 .572 221 15 1.747 .276 -.805 -1.859
10 168 365 80 232 87 132 167 318 94 307 86 85 0 0 57 197 53 310 67 15 32 1 219 171 .659 1.517 .988 1.795 2.289 6.002 52 291 7.633 .41 90 3210 6770 20 29 160 169 -50 307 195 111 1.278 268 72 .782 .833 .354 -.264
11 456 992 81 217 374 775 488 983 91 288 406 766 0 0 292 635 48 321 73 65 71 55 1149 1172 .483 2.072 1.887 2.298 2 5.674 52 273 2.318 .8 80 3360 6770 21 29 176 184 0 836 183 653 1.746 828 645 .573 1.589 .804 .668
12 525 931 80 228 444 703 527 919 89 276 446 690 0 0 109 281 36 180 100 96 100 93 1147 1136 .632 1.583 1.547 1.494 1.529 3.612 32 230 1.642 .8 70 3510 6770 21 28 191 198 0 784 192 592 1.334 774 581 .75 1.303 .416 .382
13 536 397 76 217 460 180 532 376 91 296 455 159 0 0 108 163 69 465 100 3 100 0 640 614 2.556 .391 .349 .303 .379 6.163 32 230 .513 .44 70 3670 6770 21 28 207 214 0 334 183 152 .33 317 134 3.034 .294 -1.601 -1.764
14 307 418 75 214 232 204 283 418 91 253 207 204 0 0 80 135 53 221 100 50 100 0 436 411 1.137 .879 .986 .856 .962 3.855 12 104 1.886 .41 50 3810 6770 22 27 222 227 0 352 180 172 .741 352 172 1.35 .83 -.433 -.268
15 94 188 74 231 19 -42 87 149 86 273 12 -81 0 0 34 112 48 249 19 1 1 0 -23 -69 null null null 3.851 4.351 10.262 52 351 8.36 .52 90 3960 6770 20 29 235 244 -50 158 195 -35 null 126 -68 null null null null
16 3983 2677 81 194 3901 2482 4006 2701 94 281 3924 2506 0 0 636 773 73 397 100 96 100 96 6383 6430 1.572 .636 .639 .595 .675 3.267 32 230 .64 .89 70 4120 6770 21 28 252 259 0 2255 163 2091 .536 2275 2111 1.866 .538 -.9 -.894
17 163 408 73 200 90 208 168 414 82 242 94 214 0 0 35 131 34 174 91 58 75 25 298 308 .433 2.311 2.277 2.353 2.424 4.877 12 104 5.299 .6 50 4270 6770 22 27 268 273 0 344 168 175 1.947 349 180 .514 1.918 .961 .939
18 95 190 75 207 19 -16 88 166 86 262 13 -40 0 0 31 139 48 253 23 3 1 1 3 -27 null null null 4.95 6.381 13.464 52 343 13.446 .48 90 4420 6770 20 29 281 290 -50 160 174 -13 null 140 -34 null null null null
19 638 769 68 187 569 582 616 779 77 218 547 592 0 0 129 249 31 166 100 100 100 84 1151 1139 .978 1.023 1.082 .94 .971 3.409 32 230 1.065 .76 70 4570 6770 21 28 297 304 0 648 158 490 .862 656 499 1.161 .912 -.215 -.133
20 3674 10723 80 208 3593 10515 3977 11242 90 245 3896 11034 0 0 1121 3443 36 181 100 100 100 100 14108 14930 .342 2.927 2.832 2.921 2.973 2.591 32 227 2.965 .97 70 4720 6770 21 28 312 319 0 9033 175 8858 2.465 9470 9295 .406 2.386 1.302 1.254

Total number of rows: 44544

Table truncated, full table size 9676 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap