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Sample GSM989735 Query DataSets for GSM989735
Status Public on Aug 23, 2012
Title PC 643T
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 643T2
Organism Homo sapiens
Characteristics ethnicity: Asian
age: 70
pre-operation treatment: None
individual: PC 463T
disease free survival: 52.10
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/2008-08/81094.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 9845 9159 100 107 9744 9051 11903 9629 106 128 11803 9522 0 0 4369 2711 42 82 100 100 100 100 18795 21325 1.077 .929 .807 1.137 .896 2.548 32 208 .859 .93 70 1870 6890 17 24 39 46 0 8137 95 8042 .825 8555 8460 1.212 .717 -.277 -.48
2 7302 8041 123 122 7179 7919 9051 9510 140 149 8927 9387 0 0 5121 4999 63 99 100 100 90 100 15098 18314 .907 1.103 1.052 1.471 1.02 2.7 32 213 1.038 .95 70 2010 6890 17 24 53 60 0 7144 108 7036 .98 8449 8340 1.02 .934 -.029 -.098
3 14512 24029 130 118 14381 23911 14518 27163 140 142 14388 27045 0 0 9272 15587 48 88 100 96 100 93 38292 41433 .601 1.663 1.88 1.264 1.603 2.765 32 234 1.705 .94 70 2170 6880 16 23 69 76 0 21349 105 21244 1.477 24133 24029 .677 1.67 .563 .74
4 15458 12952 117 125 15340 12826 17385 15690 143 158 17268 15564 0 0 5123 5547 136 175 100 96 100 96 28166 32832 1.196 .836 .901 .706 .851 2.259 32 236 .865 .96 70 2320 6880 16 23 84 91 0 11507 111 11396 .743 13940 13828 1.346 .801 -.429 -.32
5 866 274 137 132 729 142 838 254 154 170 701 121 0 0 122 103 59 261 100 16 100 0 871 822 5.134 .195 .173 .148 .157 2.765 12 104 .231 .64 50 2470 6880 17 22 100 105 0 243 117 126 .173 226 108 5.778 .153 -2.531 -2.705
6 6172 5199 194 178 5978 5021 6940 5643 230 203 6746 5464 0 0 2038 1916 158 129 100 100 100 96 10999 12210 1.191 .84 .81 .81 .824 1.787 32 230 .855 .96 70 2610 6880 16 23 113 120 0 4619 158 4461 .746 5014 4855 1.34 .72 -.422 -.475
7 365 189 114 135 251 53 364 194 122 153 249 59 0 0 85 61 39 95 100 33 100 0 304 308 4.736 .211 .237 .285 .298 3.729 12 104 .196 .04 50 2760 6870 16 21 129 134 0 168 120 47 .188 172 52 5.33 .211 -2.414 -2.248
8 20282 34014 139 135 20142 33879 22613 39291 156 181 22474 39155 0 0 7986 16236 89 198 100 100 100 96 54021 61629 .595 1.682 1.742 1.399 1.688 2.016 32 234 1.798 .97 70 2920 6880 16 23 144 151 0 30220 120 30100 1.494 34909 34788 .669 1.548 .58 .63
9 292 258 97 115 195 143 291 221 105 135 194 106 0 0 58 91 37 81 100 58 100 41 338 300 1.364 .733 .546 .616 .484 2.954 12 103 .98 .41 50 3080 6880 17 22 161 166 0 229 102 127 .652 196 94 1.535 .485 -.618 -1.043
10 339 298 91 106 248 191 350 280 100 120 259 174 0 0 94 111 34 68 100 87 96 68 439 433 1.298 .77 .672 .673 .582 2.576 32 158 .814 .59 60 3220 6890 18 24 175 181 0 265 94 170 .684 249 155 1.461 .597 -.547 -.744
11 538 694 101 95 437 598 610 694 110 114 509 598 0 0 218 206 41 73 87 100 84 100 1035 1107 .731 1.368 1.175 1.647 1.222 2.849 32 176 1.289 .83 60 3370 6880 17 23 190 196 0 617 84 531 1.216 617 531 .823 1.044 .282 .062
12 583 1162 105 136 477 1025 596 1166 147 234 490 1030 0 0 138 237 152 340 100 100 87 93 1502 1520 .465 2.149 2.102 2.194 2.153 1.826 32 174 2.357 .85 60 3520 6880 17 23 205 211 0 1032 121 911 1.909 1036 915 .524 1.868 .933 .901
13 545 436 97 105 447 330 529 426 110 128 431 320 0 0 151 139 53 111 100 96 100 75 777 751 1.355 .738 .742 .715 .801 2.168 32 215 .769 .63 70 3670 6880 16 23 219 226 0 387 93 293 .656 378 284 1.525 .66 -.608 -.6
14 329 339 99 99 230 240 352 333 112 122 253 234 0 0 108 162 58 78 90 81 84 75 470 487 .958 1.043 .925 1.037 1.077 2.245 32 169 1.433 .71 60 3810 6880 17 23 234 240 0 301 88 213 .927 296 208 1.079 .822 -.109 -.283
15 136 132 103 115 33 17 124 123 111 143 21 8 0 0 42 66 39 109 42 9 13 1 50 29 1.941 .515 .381 1.106 .723 7.681 52 325 21.673 .1 90 3960 6880 15 24 247 256 -50 117 102 15 .458 109 7 2.185 .338 -1.128 -1.563
16 1775 1714 98 107 1676 1607 1842 1775 106 121 1744 1667 0 0 337 469 34 79 100 100 100 96 3283 3411 1.043 .959 .956 .888 1.045 1.785 32 217 .989 .93 70 4120 6880 16 23 264 271 0 1523 95 1428 .852 1577 1481 1.174 .849 -.231 -.236
17 250 404 104 132 145 272 254 401 129 235 149 269 0 0 52 99 91 368 83 16 16 0 417 418 .533 1.876 1.805 1.818 1.907 2.114 12 104 2.315 .62 50 4270 6880 17 22 280 285 0 359 117 242 1.667 356 239 .6 1.604 .737 .682
18 107 145 101 118 6 26 103 136 111 145 1 18 0 0 29 77 53 128 5 15 0 0 32 19 .231 4.333 18 2.958 2.668 3.603 52 353 5.108 .3 90 4420 6870 14 23 293 302 -50 129 105 23 3.85 121 16 .26 15.992 1.945 3.999
19 523 440 112 134 411 305 549 405 183 331 437 271 0 0 143 192 279 662 84 6 12 0 716 708 1.348 .742 .62 .669 .602 2.545 32 232 .898 .65 70 4580 6870 15 22 310 317 0 391 119 271 .659 360 241 1.517 .551 -.601 -.86
20 3324 8919 117 141 3207 8778 3591 9910 156 236 3474 9769 0 0 1112 3230 222 471 100 100 100 100 11985 13243 .365 2.737 2.812 2.621 2.706 1.674 32 220 2.802 .97 70 4720 6870 15 22 324 331 0 7924 125 7799 2.432 8805 8679 .411 2.498 1.282 1.321

Total number of rows: 44544

Table truncated, full table size 9838 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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