NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM989683 Query DataSets for GSM989683
Status Public on Aug 23, 2012
Title PC 47T
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 47T2
Organism Homo sapiens
Characteristics ethnicity: Caucasian
age: 64
pre-operation treatment: None
individual: PC 482T
disease free survival: 45.90
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/2008-08/81090.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 39426 62807 322 205 39103 62602 43436 69614 326 219 43113 69409 0 68 11344 15286 162 125 100 100 100 100 101705 112522 .625 1.601 1.61 1.633 1.582 1.504 32 224 1.622 .95 70 1720 6900 26 33 28 35 -100 57199 187 57012 1.458 63398 63211 .686 1.466 .544 .552
2 35500 60667 337 182 35163 60484 43831 69614 338 208 43494 69431 0 62 16587 15820 106 113 100 100 100 100 95647 112925 .581 1.72 1.596 2.093 1.574 2.176 32 176 1.605 .94 60 1870 6900 27 33 44 50 -100 55250 166 55083 1.567 63398 63231 .638 1.454 .648 .54
3 36377 57509 273 192 36104 57316 47332 69614 299 217 47059 69422 0 65 19396 20097 151 127 100 100 96 100 93420 116481 .63 1.588 1.475 2.327 1.476 2.896 32 222 1.469 .96 70 2020 6900 26 33 58 65 -100 52374 175 52198 1.446 63398 63223 .692 1.343 .532 .426
4 29107 35371 226 181 28880 35190 24377 29806 257 258 24150 29625 13 46 27388 33457 138 421 73 65 69 65 64070 53775 .821 1.218 1.227 1.156 1.175 2.224 52 324 1.285 .96 90 2160 6890 24 33 71 80 -50 32213 165 32048 1.11 27145 26980 .901 1.117 .15 .16
5 1142 515 193 169 948 345 614 395 235 235 420 225 0 0 973 389 197 410 55 34 50 13 1293 645 2.748 .364 .536 .519 .418 3.048 52 339 .362 .78 90 2310 6890 24 33 86 95 0 469 154 314 .331 360 205 3.017 .488 -1.593 -1.035
6 21792 50985 164 175 21627 50810 24779 55213 362 233 24614 55038 0 15 10133 19011 1911 267 90 100 88 100 72437 79652 .426 2.349 2.236 3.203 2.33 3.029 52 353 2.232 .96 90 2470 6900 25 34 102 111 -100 46432 159 46273 2.14 50283 50123 .467 2.036 1.097 1.026
7 620 570 138 197 481 372 675 524 175 256 537 327 0 0 230 214 213 299 81 53 71 18 853 864 1.293 .773 .609 .826 .795 3.102 32 176 1.504 .61 60 2620 6910 28 34 119 125 0 519 179 339 .704 477 298 1.42 .555 -.506 -.851
8 50086 64218 113 148 49972 64069 61694 69614 132 179 61580 69465 59 68 17997 10629 70 148 100 100 100 100 114041 131045 .78 1.282 1.128 1.431 1.128 1.779 32 236 1.194 .96 70 2770 6900 26 33 133 140 -100 58484 135 58348 1.168 63398 63262 .856 1.027 .224 .039
9 218 485 96 142 122 343 225 485 103 163 129 343 0 0 75 220 38 114 81 87 68 68 465 472 .356 2.811 2.659 2.861 2.555 3.906 32 168 4.018 .62 60 2930 6900 27 33 150 156 0 442 129 312 2.56 442 312 .391 2.421 1.356 1.276
10 243 445 96 141 146 303 249 438 110 173 152 297 0 0 70 147 52 124 93 90 75 65 449 449 .482 2.075 1.954 2.077 2.219 2.276 32 217 3.684 .47 70 3070 6890 25 32 163 170 0 405 128 276 1.89 399 270 .529 1.779 .918 .831
11 610 1166 96 132 513 1033 674 1270 109 163 577 1137 0 0 429 886 47 115 71 69 67 67 1546 1714 .497 2.014 1.971 1.853 2.11 3.685 52 327 2.249 .88 90 3220 6890 24 33 177 186 0 1062 120 941 1.834 1157 1035 .545 1.795 .875 .844
12 455 2107 99 140 355 1967 504 2348 109 168 404 2208 0 0 208 1113 44 121 94 92 82 88 2322 2612 .18 5.541 5.465 5.506 5.477 2.329 52 294 6.029 .9 80 3380 6890 25 33 194 202 0 1919 127 1791 5.046 2138 2011 .198 4.977 2.335 2.315
13 536 475 99 129 436 346 526 445 108 159 426 315 0 0 145 126 43 144 100 96 100 65 782 741 1.26 .794 .739 .797 .789 1.854 32 218 .776 .7 70 3520 6900 26 33 208 215 0 433 117 315 .723 405 287 1.384 .673 -.468 -.57
14 361 565 105 128 256 436 373 571 109 176 268 442 0 0 131 212 40 156 90 84 84 75 692 710 .587 1.703 1.649 1.812 1.727 2.604 32 171 1.87 .72 60 3670 6900 27 33 224 230 0 515 117 397 1.551 520 403 .645 1.502 .633 .587
15 143 120 99 137 43 -16 134 107 105 176 34 -29 0 0 48 81 41 143 40 3 19 1 27 5 null null null 1.188 1.329 2.812 52 342 -1 -1 90 3820 6890 24 33 237 246 -50 109 125 -15 null 97 -26 null null null null
16 5353 2728 108 138 5245 2590 5474 2731 112 182 5365 2592 0 0 910 734 40 173 100 100 100 100 7835 7957 2.025 .494 .483 .474 .495 1.734 32 168 .481 .92 60 3980 6890 26 32 255 261 0 2484 126 2359 .45 2487 2361 2.224 .44 -1.153 -1.184
17 192 371 100 149 92 222 191 318 111 181 90 168 0 0 63 189 48 122 75 62 46 40 314 258 .414 2.413 1.867 1.876 1.9 4.261 32 173 4.984 .46 60 4130 6880 25 31 270 276 0 338 136 202 2.198 290 153 .455 1.7 1.136 .766
18 105 140 100 151 4 -11 99 146 112 183 0 -5 0 0 34 72 49 132 11 3 1 0 -7 -5 null null null 2.223 2.565 3.842 52 350 11.371 .19 90 4280 6880 23 32 283 292 -50 127 138 -10 null 133 -5 null null null null
19 827 696 102 152 724 543 814 620 113 176 711 467 0 0 224 256 49 125 100 100 100 90 1267 1178 1.333 .75 .657 .713 .634 1.881 32 230 1.254 .65 70 4430 6880 24 31 299 306 0 634 138 495 .683 565 425 1.464 .598 -.55 -.741
20 3899 9693 105 172 3793 9520 4159 9762 115 203 4053 9590 0 0 825 1332 54 147 100 100 100 100 13313 13643 .398 2.51 2.366 2.552 2.386 1.518 32 171 2.554 .93 60 4580 6890 26 32 315 321 0 8827 157 8670 2.286 8890 8734 .437 2.155 1.193 1.108

Total number of rows: 44544

Table truncated, full table size 9755 Kbytes.




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