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Sample GSM989706 Query DataSets for GSM989706
Status Public on Aug 23, 2012
Title PC 648T
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 648T2
Organism Homo sapiens
Characteristics ethnicity: Asian
age: 59
pre-operation treatment: None
individual: PC 544T
disease free survival: 0.03
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/2008-08/81143.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 46747 29155 207 251 46540 28904 57545 33819 216 260 57337 33568 21 0 20005 11920 61 82 100 100 100 100 75444 90905 1.61 .621 .585 .702 .613 2.117 52 293 .6 .95 80 2080 7210 29 37 40 48 -100 28764 248 28516 .613 33365 33118 1.632 .578 -.707 -.792
2 59478 37451 279 327 59198 37124 62088 37845 326 377 61808 37518 62 0 5644 5208 200 199 100 100 100 100 96322 99326 1.595 .627 .607 .624 .617 1.234 32 210 .597 .96 70 2230 7190 27 34 55 62 -100 36949 323 36626 .619 37337 37015 1.616 .599 -.693 -.74
3 50121 59313 375 529 49746 58783 62088 69173 414 590 61713 68643 73 78 22104 21314 200 270 100 100 98 100 108529 130356 .846 1.182 1.112 1.461 1.112 2.223 52 268 1.146 .95 80 2380 7200 28 36 70 78 -100 58517 522 57994 1.166 68245 67722 .858 1.097 .221 .134
4 54953 33744 335 400 54617 33344 59971 35901 355 478 59636 35501 42 0 13077 9982 131 244 100 100 100 100 87961 95137 1.638 .611 .595 .597 .61 1.341 52 271 .615 .97 90 2540 7220 29 38 85 94 -100 33291 395 32897 .602 35419 35025 1.66 .587 -.731 -.768
5 4502 917 306 366 4196 550 4804 844 381 486 4498 478 0 0 1350 338 260 410 98 57 98 15 4746 4976 7.629 .131 .106 .117 .116 2.218 52 232 .102 .39 80 2700 7190 27 35 102 110 0 905 361 543 .129 833 472 7.733 .105 -2.951 -3.254
6 27642 31054 403 492 27238 30561 36990 37297 533 649 36586 36804 0 0 21059 23125 348 459 100 100 98 99 57799 73390 .891 1.122 1.006 1.212 1.124 1.9 120 461 1.108 .96 120 2840 7190 25 37 114 126 0 30637 485 30151 1.107 36797 36310 .903 .992 .147 -.011
7 1030 714 329 468 701 245 1027 662 459 593 698 194 0 0 352 303 320 376 76 23 59 7 946 892 2.861 .35 .278 .322 .359 4.5 52 287 .762 .57 90 2990 7190 26 35 130 139 0 704 462 242 .345 653 191 2.9 .274 -1.536 -1.867
8 35862 43547 307 446 35554 43100 54683 68066 352 562 54375 67620 47 50 28319 30512 325 662 91 93 81 87 78654 121995 .825 1.212 1.244 1.558 1.112 2.509 80 368 1.153 .95 100 3150 7200 27 37 146 156 -100 42963 440 42522 1.196 67153 66713 .836 1.227 .258 .295
9 680 1549 219 292 460 1257 560 1260 246 371 341 967 0 0 331 1208 120 312 90 63 68 56 1717 1308 .366 2.733 2.836 1.798 2.197 2.798 80 414 3.53 .86 110 3310 7190 25 36 161 172 0 1528 288 1240 2.696 1243 954 .371 2.798 1.431 1.484
10 388 770 199 277 188 492 370 738 210 289 170 461 0 0 85 129 60 98 96 100 81 100 680 631 .382 2.617 2.712 2.884 2.45 1.975 32 193 2.606 .7 70 3440 7200 28 35 176 183 0 760 273 485 2.582 728 455 .387 2.675 1.368 1.42
11 2163 2637 198 261 1965 2375 2111 2575 199 268 1913 2313 0 0 603 850 55 83 100 100 100 100 4340 4226 .827 1.209 1.209 1.18 1.276 1.473 52 245 1.247 .95 80 3600 7210 29 37 192 200 0 2602 257 2343 1.192 2540 2282 .839 1.193 .254 .254
12 1804 4416 177 224 1627 4191 1840 4260 192 239 1663 4035 0 0 558 1075 146 137 100 100 98 100 5818 5698 .388 2.576 2.426 2.715 2.517 1.639 52 276 2.471 .93 80 3750 7200 28 36 207 215 0 4357 221 4135 2.541 4203 3981 .393 2.394 1.346 1.259
13 1115 1020 163 206 951 813 1074 992 171 211 910 785 0 0 232 202 47 62 100 100 100 100 1764 1695 1.17 .855 .863 .854 .834 1.467 32 232 .831 .9 70 3900 7180 26 33 222 229 0 1006 203 802 .843 979 774 1.186 .851 -.246 -.233
14 958 980 169 198 789 782 913 998 174 204 743 800 0 0 195 175 57 63 100 100 100 100 1571 1543 1.009 .991 1.077 .995 .959 1.402 32 231 .894 .91 70 4050 7180 26 33 237 244 0 967 195 772 .978 985 789 1.023 1.062 -.032 .087
15 232 254 167 201 64 52 218 251 173 207 51 49 0 0 61 67 52 69 48 38 25 11 116 100 1.231 .813 .961 1.078 .853 2.549 52 332 2.23 .17 90 4200 7190 26 35 251 260 -50 251 198 51 .802 248 48 1.248 .948 -.319 -.077
16 13153 9998 171 207 12982 9790 13232 9972 183 214 13060 9764 0 0 3385 2609 57 64 100 100 100 100 22772 22824 1.326 .754 .748 .753 .752 1.652 52 252 .743 .95 80 4360 7200 28 36 268 276 0 9864 204 9659 .744 9838 9633 1.344 .738 -.427 -.439
17 302 337 199 216 102 121 302 338 206 225 102 122 0 0 74 84 63 73 67 71 34 34 223 224 .843 1.186 1.196 1.25 1.257 3.337 52 298 1.522 .32 90 4500 7190 26 35 281 290 -50 332 213 119 1.17 333 120 .854 1.18 .227 .239
18 214 144 185 206 28 -62 210 144 197 214 24 -62 0 0 54 44 71 64 28 1 0 0 -34 -38 null null null 1.755 1.56 5.841 52 331 3.074 .12 90 4650 7190 26 35 296 305 -50 142 203 -61 null 142 -61 null null null null
19 2065 1986 188 223 1876 1762 2020 1900 194 231 1832 1677 0 0 708 531 53 67 98 100 98 100 3638 3509 1.065 .939 .915 .968 .935 1.594 52 351 .891 .95 90 4810 7180 25 34 312 321 0 1959 220 1738 .927 1875 1655 1.079 .903 -.11 -.147
20 9860 30621 196 229 9664 30392 10605 31178 201 239 10409 30949 0 0 3944 7730 55 74 100 100 100 100 40056 41358 .318 3.145 2.973 3.691 2.962 1.975 52 274 2.948 .94 80 4960 7180 26 34 328 336 0 30210 226 29984 3.103 30760 30534 .322 2.933 1.634 1.553

Total number of rows: 44544

Table truncated, full table size 9968 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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