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Sample GSM989771 Query DataSets for GSM989771
Status Public on Aug 23, 2012
Title PC 452T
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 452T2
Organism Homo sapiens
Characteristics ethnicity: Caucasian
age: 67
pre-operation treatment: None
individual: PC 362T
disease free survival: 44.80
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/2008-08/81187.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 GPL9497
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
1 870 1659 47 85 823 1574 1003 1940 54 123 956 1854 0 0 564 1120 29 203 95 82 86 75 2397 2810 .523 1.913 1.939 1.94 1.907 2.708 80 466 2.018 .89 100 1590 6790 22 32 18 28 0 1358 70 1289 1.566 1589 1518 .639 1.588 .647 .667
2 1270 2437 48 81 1222 2355 1492 2679 53 107 1444 2597 0 0 592 959 19 152 92 96 90 96 3577 4041 .519 1.927 1.798 2.345 1.829 2.999 52 240 1.862 .96 80 1730 6810 25 33 33 41 0 1995 66 1928 1.578 2194 2126 .634 1.473 .658 .558
3 9058 11772 49 81 9009 11690 10108 13121 54 125 10059 13039 0 0 3215 5146 27 186 100 96 100 96 20699 23098 .771 1.298 1.296 1.078 1.291 2.702 52 301 1.347 .97 90 1890 6800 23 32 48 57 0 9639 66 9572 1.062 10744 10677 .941 1.061 .087 .086
4 1165 2156 46 78 1119 2078 1031 2377 53 110 984 2298 0 0 627 1090 29 160 100 94 98 94 3197 3282 .538 1.857 2.335 1.849 1.824 2.549 52 273 1.877 .95 90 2040 6800 23 32 63 72 0 1765 64 1702 1.521 1946 1882 .658 1.912 .605 .935
5 283 217 47 75 235 142 289 191 59 107 242 115 0 0 123 137 83 129 86 42 71 9 377 357 1.655 .604 .475 .552 .542 3.589 52 228 .877 .58 90 2190 6810 24 33 78 87 0 178 61 116 .495 156 94 2.021 .389 -1.015 -1.362
6 3688 4996 50 84 3637 4911 3638 5039 67 134 3587 4955 0 0 753 1273 98 247 100 100 100 100 8548 8542 .741 1.35 1.381 1.331 1.292 1.917 52 294 1.362 .95 90 2340 6800 23 32 93 102 0 4091 69 4021 1.106 4126 4057 .904 1.131 .145 .178
7 132 137 51 91 80 45 128 127 70 168 77 36 0 0 31 55 138 433 6 0 0 0 125 113 1.778 .563 .468 .427 .623 5.033 32 222 7.353 .9 70 2500 6790 23 30 110 117 0 112 75 37 .461 104 29 2.171 .383 -1.118 -1.385
8 9830 13162 50 87 9779 13074 10936 14452 64 117 10885 14364 0 0 3747 4402 127 227 100 100 100 100 22853 25249 .748 1.337 1.32 1.389 1.283 2.417 52 260 1.307 .97 80 2640 6800 24 32 124 132 0 10777 71 10705 1.095 11834 11762 .913 1.081 .131 .112
9 142 273 48 81 94 191 143 264 58 117 95 182 0 0 54 105 55 151 73 55 40 17 285 277 .492 2.032 1.916 2.161 1.89 2.813 52 245 7.896 .48 80 2790 6800 24 32 139 147 0 224 66 156 1.664 216 149 .601 1.569 .734 .65
10 157 357 47 84 110 273 154 293 71 168 107 209 0 0 60 253 173 421 17 15 0 5 383 316 .403 2.482 1.953 1.974 1.982 3.31 52 216 3.34 .58 80 2950 6800 24 32 155 163 0 292 69 224 2.032 240 171 .492 1.599 1.023 .678
11 496 875 45 73 450 801 487 866 50 92 442 793 0 0 112 214 16 64 100 100 100 100 1251 1235 .562 1.78 1.794 1.773 1.743 1.922 32 203 1.936 .86 70 3090 6800 24 31 169 176 0 716 60 656 1.457 709 649 .686 1.469 .543 .555
12 450 864 46 77 403 787 486 875 56 121 439 797 0 0 169 256 63 278 90 98 88 80 1190 1236 .512 1.953 1.815 2.306 1.847 3.254 52 254 1.929 .92 80 3250 6800 24 32 185 193 0 707 63 644 1.599 716 653 .625 1.487 .677 .572
13 331 481 45 77 285 404 337 466 54 126 291 389 0 0 99 126 58 279 100 86 90 15 689 680 .705 1.418 1.337 1.454 1.374 2.576 52 253 1.407 .84 80 3400 6800 24 32 200 208 0 394 63 331 1.161 382 319 .862 1.095 .215 .13
14 216 306 44 78 171 228 221 209 50 99 176 131 0 0 98 409 21 77 96 86 92 44 399 307 .75 1.333 .744 1.114 .947 3.541 52 273 3.536 .66 90 3560 6790 22 31 215 224 0 251 64 187 1.092 171 107 .916 .609 .127 -.714
15 63 113 48 101 15 12 58 79 59 148 9 -21 0 0 21 144 55 155 2 3 0 2 27 -12 1.25 .8 null 3.898 3.311 5.234 80 315 5.346 .43 100 3700 6790 22 32 229 239 -50 93 83 10 .655 65 -17 1.527 null -.61 null
16 1540 2496 52 98 1488 2397 1663 2579 59 162 1611 2480 0 0 600 682 44 320 100 100 96 98 3885 4091 .621 1.611 1.539 1.861 1.537 2.703 52 252 1.548 .92 90 3850 6800 23 32 244 253 0 2044 80 1963 1.319 2112 2031 .758 1.261 .399 .334
17 151 269 49 92 102 176 151 256 68 164 102 163 0 0 24 109 109 386 28 3 0 0 278 265 .58 1.725 1.598 1.538 1.54 2.674 32 171 3.573 .92 70 4010 6800 24 31 261 268 0 220 75 144 1.413 210 133 .708 1.309 .499 .388
18 76 115 47 80 29 34 64 84 55 103 17 3 0 0 51 148 49 110 9 5 3 1 63 20 .853 1.172 .176 1.391 2.608 6.035 52 257 6.052 .5 80 4150 6780 22 30 275 283 0 94 66 28 .96 69 2 1.042 .144 -.059 -2.791
19 309 361 44 74 265 286 340 365 51 105 295 291 0 0 171 179 29 139 82 80 78 53 551 586 .927 1.079 .986 1.387 1.008 4.23 80 333 4.045 .41 100 4310 6790 22 32 290 300 0 296 61 234 .884 299 238 1.132 .808 -.178 -.308
20 1727 5340 45 84 1681 5256 1848 5971 52 123 1802 5886 0 0 491 2081 34 166 100 96 100 94 6937 7688 .32 3.127 3.266 2.655 3.117 2.624 52 236 3.317 .97 90 4460 6790 22 31 305 314 0 4372 69 4304 2.56 4889 4820 .391 2.675 1.356 1.419

Total number of rows: 44544

Table truncated, full table size 9520 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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