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Sample GSM989690 Query DataSets for GSM989690
Status Public on Aug 23, 2012
Title PC 229T
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 PT 229
Organism Homo sapiens
Characteristics ethnicity: Caucasian
age: 59
pre-operation treatment: None
individual: PC 636T
disease free survival: 4.63
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/2008-11/81779.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 GPL15972
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 7501 5601 60 140 7441 5461 7615 5541 62 148 7555 5400 0 0 1917 1312 15 47 100 100 100 100 12902 12955 1.363 .734 .715 .74 .746 1.549 52 363 .716 .97 90 1670 8020 29 38 30 39 0 4959 124 4835 .65 4906 4781 1.539 .633 -.622 -.66
2 9041 6348 60 136 8980 6212 9754 6799 62 142 9693 6663 0 0 3341 2455 14 47 100 100 100 100 15192 16356 1.446 .692 .687 .668 .695 1.598 52 319 .69 .99 90 1820 8020 29 38 45 54 0 5620 120 5500 .612 6020 5899 1.633 .609 -.707 -.716
3 10237 22710 60 133 10176 22576 10585 24132 63 140 10524 23998 0 0 2391 6904 15 52 100 100 100 100 32752 34522 .451 2.219 2.28 2.132 2.292 1.593 52 312 2.297 .98 90 1980 8020 29 38 61 70 0 20107 118 19988 1.964 21366 21247 .509 2.019 .974 1.014
4 11644 8434 65 137 11579 8297 13771 9725 68 145 13706 9588 0 0 5517 4111 22 54 100 100 100 100 19876 23294 1.396 .717 .7 .728 .732 2.052 52 310 .715 .98 90 2130 8020 29 38 76 85 0 7467 121 7346 .634 8610 8489 1.576 .619 -.656 -.691
5 514 236 66 136 447 100 568 231 71 139 501 94 0 0 238 82 21 54 100 67 96 46 547 595 4.47 .224 .188 .211 .25 2.676 52 238 .253 .65 80 2280 8020 30 38 92 100 0 209 120 89 .198 205 83 5.049 .166 -2.336 -2.59
6 7265 10032 96 185 7168 9847 7050 9810 112 194 6953 9625 0 0 2072 2838 65 97 100 100 100 100 17015 16578 .728 1.374 1.384 1.361 1.383 1.607 52 294 1.353 .97 90 2420 8010 28 37 105 114 0 8882 164 8718 1.216 8685 8522 .822 1.226 .282 .294
7 284 301 78 172 206 128 277 292 97 186 198 119 0 0 63 89 60 82 98 65 92 32 334 317 1.609 .621 .601 .603 .642 2.556 52 237 .759 .61 80 2580 8030 31 39 122 130 0 266 152 113 .55 259 105 1.818 .532 -.862 -.91
8 18261 40615 69 166 18191 40448 20056 44473 73 174 19986 44307 0 0 5589 14221 19 61 100 100 100 100 58639 64293 .45 2.224 2.217 2.154 2.275 1.574 52 257 2.28 .99 90 2730 8020 29 38 136 145 0 35959 147 35812 1.969 39375 39228 .508 1.963 .977 .973
9 134 181 61 143 72 37 141 170 63 154 79 26 0 0 50 77 12 59 86 33 73 16 109 105 1.946 .514 .329 1.196 1.313 5.388 80 302 10.46 .05 100 2870 8010 28 38 150 160 0 160 127 33 .455 151 23 2.198 .291 -1.136 -1.779
10 190 242 57 127 133 114 200 239 60 135 143 112 0 0 60 70 29 64 92 75 84 40 247 255 1.167 .857 .783 .849 .834 2.578 52 244 1.102 .62 80 3030 8010 29 37 167 175 0 214 112 101 .759 212 99 1.318 .693 -.398 -.528
11 337 559 56 122 281 436 353 565 57 127 296 443 0 0 100 162 12 45 100 98 98 98 717 739 .644 1.552 1.497 1.563 1.606 1.715 52 306 1.648 .93 90 3190 8010 28 37 182 191 0 495 108 386 1.374 500 392 .728 1.325 .458 .406
12 370 760 57 133 313 626 378 745 59 136 320 611 0 0 115 262 12 43 100 100 100 98 939 931 .5 2 1.909 1.963 1.919 1.678 52 208 2.107 .94 80 3330 8020 30 38 197 205 0 673 118 554 1.771 660 541 .565 1.691 .824 .757
13 248 250 59 137 189 112 240 238 60 146 180 101 0 0 65 72 11 54 100 78 100 42 301 281 1.688 .593 .561 .488 .559 3.235 52 233 .64 .57 80 3480 8010 29 37 212 220 0 221 121 99 .525 211 89 1.906 .497 -.931 -1.009
14 225 360 59 138 166 222 222 358 60 143 163 219 0 0 48 80 12 53 100 96 100 92 388 382 .748 1.337 1.344 1.279 1.308 1.809 52 261 1.587 .8 90 3630 8010 28 37 226 235 0 319 122 197 1.184 317 194 .845 1.19 .244 .25
15 73 133 56 133 17 0 72 122 57 136 16 -11 0 0 14 70 12 43 56 31 26 10 17 5 null null null 4.148 3.664 4.948 80 305 24.436 .13 100 3780 8010 28 38 241 251 -50 118 118 0 null 108 -10 null null null null
16 1246 2529 56 136 1189 2392 1281 2657 59 145 1224 2521 0 0 348 729 13 51 100 100 100 100 3581 3745 .497 2.012 2.06 1.961 2.015 1.764 52 241 2.051 .97 80 3930 8010 29 37 257 265 0 2239 120 2118 1.781 2352 2232 .561 1.824 .833 .867
17 97 193 58 139 39 53 98 181 63 156 40 42 0 0 27 68 29 88 59 28 21 3 92 82 .736 1.359 1.05 1.595 1.401 3.613 32 216 5.994 .39 70 4090 7980 26 33 273 280 0 171 123 47 1.203 160 37 .831 .93 .267 -.105
18 67 122 60 136 7 -13 65 102 75 159 5 -33 0 0 15 66 148 117 0 3 0 0 -6 -28 null null null 4.386 5.294 6.709 80 410 .515 .67 100 4230 7990 26 36 286 296 -50 108 120 -12 null 90 -29 null null null null
19 310 372 60 140 249 232 297 354 77 154 237 214 0 0 80 101 166 100 88 94 11 53 481 451 1.073 .932 .903 .883 .888 1.811 52 324 .609 .78 90 4380 8000 27 36 301 310 0 329 124 205 .825 313 189 1.212 .799 -.278 -.323
20 1593 7952 59 137 1534 7814 1661 7913 66 151 1601 7775 0 0 483 2505 56 101 100 100 100 100 9348 9376 .196 5.094 4.856 5.148 5.361 1.744 52 292 5.309 .95 90 4530 8000 27 36 316 325 0 7040 121 6918 4.51 7006 6884 .222 4.3 2.173 2.104

Total number of rows: 44544

Table truncated, full table size 9473 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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