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Sample GSM989800 Query DataSets for GSM989800
Status Public on Aug 23, 2012
Title PC 473T
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 473T2
Organism Homo sapiens
Characteristics ethnicity: Asian
age: 66
pre-operation treatment: None
individual: PC 473T
disease free survival: 52.83
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/2008-08/81184.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) [email protected]
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 3767 3939 39 171 3728 3767 3953 4035 43 205 3913 3863 0 0 817 870 12 124 100 100 100 100 7495 7776 .99 1.01 .987 1.01 .975 3.018 52 309 .984 .96 80 1690 7340 34 42 45 53 0 2855 124 2730 .732 2924 2799 1.366 .715 -.45 -.483
2 3332 3456 41 176 3290 3280 3760 3909 45 211 3718 3733 0 0 1150 1328 13 137 100 100 100 98 6570 7451 1.003 .997 1.004 .925 .951 3.793 52 264 .98 .94 80 1840 7340 34 42 60 68 0 2505 128 2377 .722 2833 2705 1.384 .728 -.469 -.459
3 3380 5649 41 154 3339 5495 3499 6002 44 183 3457 5848 0 0 675 1338 14 116 100 100 100 100 8834 9305 .608 1.646 1.692 1.629 1.584 3.107 52 263 1.641 .96 80 1990 7340 34 42 75 83 0 4094 112 3982 1.193 4350 4238 .838 1.226 .254 .294
4 3776 4048 41 142 3735 3906 3791 4151 44 173 3750 4008 0 0 621 853 12 118 100 100 100 100 7641 7758 .956 1.046 1.069 1.033 1.026 2.754 52 238 1.036 .96 80 2140 7340 34 42 90 98 0 2934 103 2831 .758 3008 2905 1.319 .775 -.4 -.369
5 178 137 38 128 140 8 185 133 40 148 146 4 0 0 39 60 9 94 98 9 98 1 148 150 17.5 .057 .027 .184 .194 8.209 52 212 -.057 -.03 80 2290 7340 34 42 105 113 0 99 93 6 .041 96 3 24.148 .02 -4.594 -5.654
6 1576 3013 42 146 1533 2867 1540 2987 51 179 1497 2840 0 0 201 456 24 161 100 100 100 100 4400 4337 .535 1.87 1.897 1.862 1.908 2.562 52 240 1.887 .97 90 2440 7340 33 42 119 128 0 2183 106 2078 1.355 2165 2058 .738 1.375 .439 .459
7 79 122 42 158 36 -35 78 105 49 189 35 -53 0 0 28 65 19 127 70 3 45 0 1 -18 null null null 3.308 2.446 11.562 80 281 -1 -1 100 2590 7340 33 43 134 144 -50 88 115 -25 null 76 -38 null null null null
8 3400 5540 39 143 3360 5396 3872 6071 51 219 3832 5928 0 0 1213 1396 79 552 98 100 98 100 8756 9760 .623 1.606 1.547 1.897 1.541 4.423 52 222 1.518 .97 90 2740 7340 33 42 149 158 0 4015 104 3910 1.164 4400 4296 .859 1.121 .219 .165
9 52 133 39 134 13 -1 47 85 47 214 8 -48 0 0 18 207 46 539 6 2 1 1 12 -40 null null null 7.152 10.527 11.179 80 289 18.048 .88 100 2890 7330 32 42 164 174 -50 96 97 -1 null 62 -35 null null null null
10 61 146 37 131 23 14 58 127 42 164 20 -4 0 0 22 65 27 124 35 5 8 0 37 16 1.643 .609 null 3.217 2.767 6.933 80 289 4.865 .55 100 3040 7330 32 42 179 189 -50 106 95 10 .441 92 -3 2.267 null -1.181 null
11 94 185 37 133 56 51 94 183 141 220 56 50 0 0 29 75 1485 879 0 0 0 0 107 106 1.098 .911 .893 1.161 1.158 6.57 52 224 9.286 .2 90 3190 7340 33 42 194 203 0 134 96 37 .66 133 36 1.515 .647 -.6 -.628
12 120 268 39 133 81 134 100 254 110 204 61 121 0 0 152 148 1175 699 1 1 0 0 215 182 .604 1.654 1.984 2.3 2.275 5.874 80 358 .461 .81 110 3340 7320 30 41 208 219 0 194 96 97 1.199 184 88 .834 1.437 .262 .524
13 72 142 37 128 35 13 77 121 39 145 40 -7 0 0 27 84 10 88 77 13 66 3 48 33 2.692 .371 null 3.15 3.954 12.87 80 288 48.478 .05 100 3490 7330 32 42 224 234 -50 103 93 9 .269 88 -5 3.715 null -1.893 null
14 54 130 37 118 17 11 54 127 39 140 16 8 0 0 17 57 10 88 65 10 41 0 28 24 1.545 .647 .5 2.819 3.016 7.4 80 287 26.831 .16 100 3650 7330 32 42 240 250 -50 94 86 8 .469 92 6 2.133 .362 -1.093 -1.465
15 41 102 37 128 4 -26 39 91 41 161 2 -37 0 0 10 66 16 148 6 2 3 1 -22 -35 null null null 9.486 10.747 6.851 80 289 22.233 .42 100 3800 7330 32 42 255 265 -50 74 93 -19 null 66 -27 null null null null
16 252 324 37 142 214 182 259 312 40 168 222 170 0 0 56 106 10 106 100 78 100 34 396 392 1.176 .85 .766 .81 .854 3.547 52 198 .972 .71 80 3960 7330 33 41 272 280 0 235 103 132 .616 226 123 1.623 .555 -.698 -.85
17 48 149 39 154 8 -4 47 122 62 253 8 -31 0 0 14 96 302 857 0 0 0 0 4 -23 null null null 6.789 7.676 8.639 80 277 2.808 .99 100 4100 7320 31 41 285 295 -50 108 112 -3 null 88 -22 null null null null
18 39 116 40 177 -1 -60 37 79 44 213 -3 -97 0 0 9 149 14 152 5 2 1 2 -61 -100 null null null 16.109 15.352 6.069 80 273 29.516 .37 100 4250 7320 31 41 300 310 -50 84 128 -43 null 57 -70 null null null null
19 85 162 39 164 45 -1 91 155 42 199 51 -8 0 0 32 75 14 137 77 3 70 0 44 43 null null null 2.677 1.595 14 80 332 28.836 .1 100 4400 7320 31 41 315 325 -50 117 119 -1 null 112 -6 null null null null
20 465 2076 39 140 426 1935 477 2187 42 162 438 2046 0 0 74 399 14 111 100 100 100 100 2361 2484 .22 4.542 4.671 4.504 4.567 2.697 52 256 4.663 .97 80 4560 7330 33 41 332 340 0 1504 101 1402 3.292 1585 1483 .304 3.385 1.719 1.759

Total number of rows: 44544

Table truncated, full table size 9498 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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