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Sample GSM989711 Query DataSets for GSM989711
Status Public on Aug 23, 2012
Title PC 599T
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 599T2
Organism Homo sapiens
Characteristics ethnicity: Caucasian
age: 70
pre-operation treatment: None
individual: PC 634T
disease free survival: 11.70
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/2008-08/81156.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 7568 8808 66 70 7501 8738 8348 9825 69 76 8282 9754 0 0 3179 3747 18 41 100 100 100 100 16239 18036 .858 1.165 1.178 1.277 1.208 2.314 52 280 1.17 .95 80 1760 6960 20 28 12 20 0 8159 65 8094 1.079 9101 9036 .927 1.091 .11 .126
2 7452 7615 77 85 7375 7529 8924 8857 80 105 8847 8772 0 0 3424 4099 24 71 100 100 100 98 14904 17619 .98 1.021 .992 .99 1.055 2.589 52 248 1.058 .94 80 1910 6950 19 27 27 35 0 7054 79 6975 .946 8205 8126 1.057 .918 -.081 -.123
3 10521 23907 85 118 10435 23788 12071 28480 97 148 11985 28361 0 0 4708 11683 57 131 100 100 100 98 34223 40346 .439 2.28 2.366 2.129 2.328 3.246 52 250 2.441 .93 80 2050 6950 19 27 41 49 0 22146 109 22036 2.112 26383 26272 .474 2.192 1.078 1.132
4 6344 7006 91 115 6252 6890 9397 9425 202 289 9306 9310 0 0 5118 6136 715 986 67 63 63 59 13142 18616 .907 1.102 1 1.063 1.17 3.272 52 338 1.141 .95 90 2200 6940 17 26 55 64 0 6490 107 6383 1.021 8731 8624 .98 .927 .03 -.11
5 724 352 98 114 625 237 744 374 107 132 645 259 0 0 129 97 48 90 100 93 100 68 862 904 2.637 .379 .402 .338 .386 2.1 32 213 .366 .78 70 2360 6940 18 25 72 79 0 326 106 220 .351 346 240 2.847 .372 -1.509 -1.427
6 4397 4009 108 133 4289 3875 3676 1271 118 152 3568 1137 0 0 4176 4121 49 115 97 89 95 67 8164 4705 1.107 .903 .319 .792 .95 2.842 120 492 .946 .95 120 2510 6940 16 28 85 97 0 3714 123 3590 .837 1177 1053 1.195 .295 -.257 -1.76
7 180 129 94 127 86 2 193 124 103 148 98 -3 0 0 59 54 38 89 75 5 61 1 88 95 43 .023 null .292 .321 5.699 52 292 4.834 .12 90 2660 6940 17 26 101 110 -50 119 118 2 .022 115 -3 46.419 null -5.537 null
8 13272 23021 91 119 13181 22901 15562 27490 99 146 15471 27370 0 0 5285 10790 45 97 100 98 100 98 36082 42841 .576 1.737 1.769 1.578 1.833 3.167 52 256 1.845 .94 80 2810 6950 19 27 117 125 0 21326 110 21214 1.609 25465 25354 .621 1.639 .687 .713
9 133 167 89 120 43 46 133 162 97 153 43 42 0 0 38 54 42 120 50 11 11 0 89 85 .935 1.07 .977 .996 1.005 2.844 52 309 3.714 .5 90 2960 6940 17 26 131 140 -50 155 111 43 .991 150 39 1.009 .905 -.013 -.144
10 122 201 85 117 37 84 117 197 97 151 32 79 0 0 34 85 60 136 25 19 1 1 121 111 .44 2.27 2.469 1.941 2.273 4.293 52 310 2.342 .59 90 3110 6940 17 26 146 155 -50 186 108 78 2.103 182 73 .475 2.287 1.072 1.193
11 590 864 82 104 507 760 607 948 93 126 524 844 0 0 217 381 38 78 96 94 94 88 1267 1368 .667 1.499 1.611 1.394 1.583 2.258 52 260 1.646 .89 80 3270 6950 19 27 163 171 0 800 96 704 1.389 878 782 .72 1.492 .474 .577
12 359 1419 78 104 280 1315 368 1491 88 124 289 1386 0 0 82 420 35 77 100 100 100 100 1595 1675 .213 4.696 4.796 4.628 4.374 1.471 52 255 5.123 .89 80 3420 6950 19 27 178 186 0 1314 96 1218 4.351 1381 1284 .23 4.443 2.121 2.151
13 287 259 81 124 205 135 289 251 89 140 207 127 0 0 58 73 30 80 100 68 100 31 340 334 1.519 .659 .614 .596 .602 2.119 32 185 .866 .65 70 3570 6960 20 27 193 200 0 240 115 125 .61 233 118 1.639 .568 -.713 -.815
14 157 126 83 108 74 17 160 118 90 125 77 10 0 0 48 56 30 76 80 13 63 1 91 87 4.353 .23 .13 .573 .771 5.524 52 296 4.49 .21 90 3710 6940 17 26 206 215 -50 117 100 16 .213 109 9 4.699 .12 -2.232 -3.055
15 85 69 83 104 1 -34 85 56 89 124 1 -47 0 0 16 50 30 78 3 3 0 1 -33 -46 null null null 4.354 3.707 3.14 52 300 5.257 .52 90 3860 6940 17 26 221 230 -50 64 96 -31 null 52 -44 null null null null
16 2287 1342 81 104 2205 1238 2570 1471 87 123 2488 1366 0 0 907 452 30 76 98 98 98 98 3443 3854 1.781 .561 .549 .629 .578 1.809 52 282 .524 .95 90 4010 6950 18 27 236 245 0 1243 96 1147 .52 1363 1265 1.923 .509 -.943 -.975
17 116 118 81 104 34 14 116 114 93 131 35 10 0 0 36 57 47 124 34 3 3 1 48 45 2.429 .412 .286 1.609 1.203 5.33 52 301 4.531 .48 90 4160 6940 17 26 251 260 -50 109 96 13 .381 106 9 2.622 .265 -1.39 -1.918
18 84 67 81 109 2 -42 80 56 91 134 0 -52 0 0 19 42 38 98 3 1 0 0 -40 -52 null null null 5.104 4.553 3.765 52 329 4.509 .47 90 4320 6930 16 25 267 276 -50 62 101 -39 null 52 -48 null null null null
19 479 358 81 108 397 250 484 354 88 133 402 246 0 0 104 100 33 87 100 98 100 76 647 648 1.588 .63 .612 .601 .614 1.759 52 290 .618 .72 90 4480 6940 17 26 283 292 0 332 100 232 .583 328 228 1.714 .567 -.778 -.819
20 2168 5534 80 105 2087 5428 2414 6485 89 129 2333 6380 0 0 695 2276 35 93 100 92 100 90 7515 8713 .384 2.601 2.735 2.024 2.676 3.258 52 248 2.757 .97 80 4620 6940 18 26 298 306 0 5126 97 5028 2.409 6007 5910 .415 2.533 1.269 1.341

Total number of rows: 44544

Table truncated, full table size 9349 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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