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Sample GSM989787 Query DataSets for GSM989787
Status Public on Aug 23, 2012
Title PC 526T
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 526T2
Organism Homo sapiens
Characteristics individual: PC 526T
disease state: Tumor
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/2008-09/81296.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 15981 22489 80 90 15900 22398 17059 23878 87 120 16978 23787 0 0 6782 11355 47 413 98 95 97 93 38298 40765 .71 1.409 1.401 1.216 1.401 2.695 80 470 1.475 .97 110 1840 6780 16 27 26 37 0 20950 84 20865 1.312 22244 22159 .762 1.305 .392 .384
2 12408 17428 80 87 12328 17341 14590 20305 83 103 14510 20217 0 0 6830 9486 26 87 100 100 98 98 29669 34727 .711 1.407 1.393 1.588 1.389 3.243 80 276 1.401 .98 100 1980 6790 18 28 41 51 0 16235 81 16154 1.31 18915 18833 .763 1.298 .39 .376
3 15280 15598 80 97 15200 15500 16685 17619 83 109 16605 17521 0 0 5181 5872 25 86 100 100 100 98 30700 34126 .981 1.02 1.055 .975 1.032 2.199 80 357 1.037 .97 110 2140 6780 16 27 56 67 0 14530 90 14439 .95 16413 16322 1.053 .983 -.074 -.025
4 14784 20715 76 99 14707 20615 14737 20328 88 132 14660 20228 0 0 4751 6821 89 251 100 100 100 100 35322 34888 .713 1.402 1.38 1.426 1.394 1.958 80 317 1.412 .97 110 2270 6780 16 27 69 80 0 19297 92 19204 1.306 18937 18844 .766 1.285 .385 .362
5 906 412 76 93 829 319 944 408 94 136 868 315 0 0 294 167 102 281 95 55 92 8 1148 1183 2.599 .385 .363 .365 .35 2.843 80 249 .356 .77 100 2430 6780 17 27 86 96 0 384 87 297 .358 380 293 2.79 .338 -1.48 -1.565
6 7239 8761 82 99 7156 8661 8180 10045 97 118 8097 9945 0 0 3303 3831 54 83 100 98 99 98 15817 18042 .826 1.21 1.228 1.306 1.23 3.029 120 337 1.195 .97 120 2580 6790 17 29 100 112 0 8161 92 8068 1.127 9358 9264 .887 1.144 .173 .194
7 319 298 82 95 236 203 311 286 93 106 228 190 0 0 101 144 43 71 98 80 97 60 439 418 1.163 .86 .833 .753 .881 3.192 80 253 .921 .62 100 2730 6790 18 28 116 126 0 278 88 189 .801 266 177 1.248 .776 -.32 -.365
8 16419 16627 76 96 16342 16530 16149 16175 84 117 16072 16079 0 0 2480 2659 42 128 100 100 100 100 32872 32151 .989 1.012 1 1.01 1.019 1.562 80 327 1.002 .97 110 2880 6780 16 27 130 141 0 15489 89 15399 .942 15068 14979 1.061 .932 -.086 -.102
9 259 512 67 83 191 428 257 519 76 113 189 435 0 0 64 192 43 135 100 95 98 76 619 624 .446 2.241 2.302 2.07 2.396 2.457 80 288 2.795 .76 100 3030 6790 18 28 146 156 0 477 77 399 2.087 483 405 .479 2.144 1.062 1.1
10 275 433 64 81 210 351 272 399 67 94 208 318 0 0 60 166 19 58 100 96 100 93 561 526 .598 1.671 1.529 1.516 1.566 2.46 80 282 1.992 .79 100 3190 6790 18 28 162 172 0 403 75 327 1.557 372 296 .642 1.424 .639 .51
11 754 905 64 80 690 824 769 960 67 90 705 879 0 0 269 404 18 55 93 96 93 92 1514 1584 .837 1.194 1.247 1.141 1.27 2.251 80 295 1.297 .92 100 3340 6770 16 26 177 187 0 843 75 768 1.112 894 819 .899 1.161 .154 .216
12 617 1436 64 86 552 1350 619 1385 67 96 555 1299 0 0 121 426 19 57 100 100 100 100 1902 1854 .409 2.446 2.341 2.386 2.508 1.779 80 331 2.739 .91 110 3480 6780 16 27 190 201 0 1338 80 1258 2.278 1290 1210 .439 2.18 1.188 1.125
13 434 454 62 88 371 366 429 422 66 98 366 334 0 0 107 211 20 59 100 93 100 91 737 700 1.014 .987 .913 .821 .95 2.623 80 339 1.126 .84 110 3630 6780 16 27 205 216 0 423 82 341 .919 393 311 1.088 .85 -.122 -.234
14 306 495 59 88 247 406 305 467 60 89 246 379 0 0 61 184 17 51 100 100 100 96 653 625 .608 1.644 1.541 1.514 1.602 2.2 80 234 1.915 .83 100 3780 6790 18 28 221 231 0 461 82 378 1.531 435 353 .653 1.435 .615 .521
15 70 114 56 81 13 33 68 99 59 93 12 18 0 0 20 66 15 57 37 31 17 9 46 30 .394 2.538 1.5 3.274 3.546 5.163 120 371 10.996 .21 120 3930 6780 16 28 235 247 -100 106 75 31 2.365 92 17 .423 1.397 1.242 .483
16 1537 2266 53 76 1484 2189 1473 2312 55 87 1419 2235 0 0 362 673 14 55 100 100 100 98 3673 3654 .678 1.475 1.575 1.403 1.506 2.106 80 269 1.532 .94 110 4090 6780 16 27 251 262 0 2111 71 2039 1.374 2154 2082 .728 1.467 .459 .553
17 148 183 52 79 95 104 144 166 55 87 92 87 0 0 67 122 14 58 83 60 76 37 199 179 .913 1.095 .946 1.197 1.176 3.73 120 322 1.802 .63 120 4240 6770 15 27 266 278 -100 170 74 97 1.02 155 81 .981 .881 .028 -.183
18 73 94 53 72 19 21 68 70 54 86 14 -2 0 0 24 71 13 56 50 25 27 8 40 12 .905 1.105 null 2.552 2.415 4.055 120 298 11.745 .21 120 4390 6770 15 27 281 293 -100 88 67 20 1.03 65 -2 .971 null .042 null
19 525 617 50 75 475 542 521 607 52 90 471 531 0 0 255 313 13 64 93 92 92 90 1017 1002 .876 1.141 1.127 1.208 1.072 3.323 120 292 1.138 .87 120 4540 6780 16 28 296 308 0 575 70 505 1.063 565 495 .941 1.05 .088 .071
20 2368 6456 47 68 2321 6387 2528 6965 49 84 2481 6896 0 0 1181 3058 13 60 98 99 98 97 8708 9377 .363 2.752 2.78 3.059 2.773 2.681 120 312 2.756 .97 120 4690 6780 16 28 311 323 0 6014 63 5950 2.563 6488 6424 .39 2.589 1.358 1.373

Total number of rows: 44544

Table truncated, full table size 9571 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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