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Sample GSM989816 Query DataSets for GSM989816
Status Public on Aug 23, 2012
Title PC 343T
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 343T2
Organism Homo sapiens
Characteristics ethnicity: Caucasian
age: 64
pre-operation treatment: None
individual: PC 83T
disease free survival: 31.23
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/2008-08/81114.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 6476 6009 74 119 6402 5889 6378 7088 85 195 6303 6968 0 0 4899 4570 49 571 90 76 86 71 12291 13271 1.087 .92 1.106 1.029 .923 5.266 52 314 .905 .93 80 2040 7040 28 36 52 60 0 4920 97 4822 .753 5803 5705 1.328 .905 -.409 -.144
2 7808 6713 89 151 7719 6562 9411 8153 100 240 9322 8002 0 0 3522 3714 54 656 100 81 100 81 14281 17324 1.176 .85 .858 .542 .898 6.323 32 231 .869 .95 70 2190 7030 27 34 67 74 0 5496 124 5373 .696 6675 6552 1.437 .703 -.523 -.509
3 12388 35880 99 176 12288 35703 15820 40300 108 192 15720 40123 0 0 6293 14197 41 98 100 100 100 100 47991 55843 .344 2.906 2.552 3.524 2.743 3.57 32 232 2.844 .95 70 2340 7040 28 35 82 89 0 29376 144 29232 2.379 32995 32850 .42 2.09 1.25 1.063
4 10451 8299 104 169 10347 8130 10888 9155 113 194 10784 8985 0 0 1716 2220 41 135 100 100 100 100 18477 19769 1.273 .786 .833 .749 .806 2.16 32 174 .781 .95 60 2490 7040 29 35 98 104 0 6795 138 6656 .643 7496 7356 1.554 .682 -.636 -.552
5 642 209 86 167 555 42 667 195 95 191 581 28 0 0 205 115 37 130 100 9 100 3 597 609 13.214 .076 .048 .096 .099 4.418 32 169 .076 .15 60 2640 7040 29 35 113 119 0 171 137 34 .062 160 23 16.14 .039 -4.013 -4.664
6 6595 9989 95 143 6499 9845 8528 12684 104 167 8432 12540 0 0 3649 5765 44 101 100 100 98 96 16344 20972 .66 1.515 1.487 1.573 1.528 4.254 52 263 1.541 .93 80 2790 7040 28 36 127 135 0 8178 117 8061 1.24 10385 10267 .806 1.218 .311 .284
7 181 124 86 143 95 -19 181 113 93 183 95 -30 0 0 85 57 38 141 67 1 53 0 76 65 null null null .859 .418 15.712 52 319 3.059 .37 90 2940 7030 26 35 141 150 -50 102 117 -16 null 93 -25 null null null null
8 10613 25839 86 157 10527 25681 9954 27748 92 186 9868 27591 0 0 8189 20331 33 115 100 92 98 88 36208 37459 .41 2.44 2.796 1.718 2.412 4.832 52 301 2.508 .96 90 3090 7030 26 35 156 165 0 21155 129 21026 1.997 22718 22590 .501 2.289 .998 1.195
9 104 150 81 133 22 17 100 140 87 163 19 7 0 0 34 56 33 112 28 3 11 0 39 26 1.294 .773 .368 1.319 1.572 7.3 52 291 28.574 .18 90 3240 7030 26 35 171 180 -50 123 109 14 .633 115 6 1.581 .302 -.66 -1.729
10 104 147 70 130 33 17 105 151 77 153 35 20 0 0 29 64 30 103 53 11 17 0 50 55 1.941 .515 .571 1.74 1.372 5.201 52 333 9.053 .26 90 3390 7030 26 35 186 195 -50 120 106 14 .422 124 16 2.371 .468 -1.245 -1.096
11 445 715 68 125 377 589 441 749 73 162 373 623 0 0 87 266 23 125 100 93 100 84 966 996 .64 1.562 1.67 1.316 1.558 3.24 32 236 1.859 .79 70 3550 7030 27 34 203 210 0 585 102 482 1.279 613 510 .782 1.367 .355 .452
12 332 577 71 117 261 460 354 591 77 147 282 474 0 0 91 124 26 112 100 100 90 96 721 756 .567 1.762 1.681 1.913 1.758 2.586 32 223 1.728 .79 70 3700 7040 28 35 218 225 0 472 96 377 1.443 484 388 .693 1.376 .529 .461
13 280 203 71 130 208 73 277 197 77 169 205 67 0 0 61 80 34 174 100 9 100 0 281 272 2.849 .351 .327 .41 .376 3.485 32 175 .321 .1 60 3850 7030 28 34 234 240 0 166 106 60 .287 161 55 3.48 .268 -1.799 -1.902
14 175 225 71 137 104 87 186 213 95 186 115 75 0 0 72 133 176 222 21 5 0 1 191 190 1.195 .837 .652 .934 .806 4.662 52 303 .542 .45 90 4000 7030 26 35 247 256 -50 184 112 71 .685 174 61 1.46 .534 -.546 -.905
15 68 86 74 141 -5 -54 67 67 84 194 -7 -74 0 0 18 59 57 241 1 0 0 0 -59 -81 null null null 4.952 4.493 4.877 52 319 112.403 .03 90 4150 7030 26 35 262 271 -50 70 115 -44 null 55 -61 null null null null
16 1844 1009 76 143 1768 865 2015 1203 90 202 1939 1059 0 0 1181 557 95 190 90 76 84 71 2633 2998 2.044 .489 .546 .482 .466 3.639 52 257 .441 .89 80 4310 7030 27 35 279 287 0 826 117 708 .401 985 867 2.496 .447 -1.32 -1.161
17 83 146 76 162 7 -15 81 139 85 213 4 -23 0 0 26 69 44 211 5 1 0 0 -8 -19 null null null 2.315 2.185 5.047 52 279 18.075 .21 90 4450 7030 26 35 292 301 -50 120 133 -12 null 114 -19 null null null null
18 88 169 78 142 9 26 75 91 85 196 -3 -51 0 0 71 291 35 201 11 7 5 3 35 -54 .346 2.889 null 6.627 4.93 6.321 52 311 5.763 .61 90 4600 7030 26 35 307 316 -50 138 116 21 2.365 75 -42 .423 null 1.242 null
19 426 336 75 137 351 198 421 351 84 185 345 213 0 0 78 69 37 187 100 62 100 0 549 558 1.773 .564 .617 .54 .576 2.38 32 233 .578 .55 70 4760 7030 27 34 324 331 0 275 112 162 .462 287 174 2.165 .505 -1.114 -.984
20 2590 6091 72 131 2518 5959 2839 7046 84 185 2767 6914 0 0 731 2519 57 212 100 96 100 93 8477 9681 .423 2.367 2.499 1.972 2.43 3.497 32 227 2.601 .9 70 4910 7030 27 34 339 346 0 4987 107 4879 1.938 5769 5661 .516 2.046 .954 1.033

Total number of rows: 44544

Table truncated, full table size 9637 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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