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Sample GSM989758 Query DataSets for GSM989758
Status Public on Aug 23, 2012
Title PC 551T
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 551T2
Organism Homo sapiens
Characteristics ethnicity: Caucasian
age: 49
pre-operation treatment: None
individual: PC 599T
disease free survival: 24.50
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/2008-08/81122.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 33737 31317 160 265 33577 31051 38991 33425 193 329 38831 33159 0 0 14181 10305 126 338 98 100 96 100 64628 71990 1.081 .925 .854 1.196 .904 3.784 52 290 .879 .98 80 2480 6270 31 39 36 44 0 28469 241 28227 .841 30385 30144 1.19 .776 -.25 -.365
2 39768 36967 219 291 39549 36675 40923 37093 238 325 40704 36801 0 0 9395 6267 120 171 100 100 100 100 76224 77505 1.078 .927 .904 .949 .888 1.815 32 176 .881 .99 60 2630 6270 32 38 52 58 0 33605 265 33340 .843 33720 33454 1.186 .822 -.246 -.283
3 44203 78929 306 397 43897 78532 50877 81076 348 658 50571 80679 43 84 12731 7281 201 2268 100 100 100 100 122429 131250 .559 1.789 1.595 1.925 1.595 2.273 32 225 1.705 .92 70 2780 6270 31 38 66 73 -100 71751 361 71390 1.626 73703 73342 .615 1.45 .702 .536
4 32387 29437 270 348 32116 29089 33742 31072 320 608 33471 30723 0 0 9534 9976 202 2198 100 100 100 100 61205 64194 1.104 .906 .918 .891 .91 1.814 52 241 .919 .98 80 2940 6270 31 39 82 90 0 26760 316 26444 .823 28246 27929 1.215 .834 -.28 -.261
5 1761 1567 188 343 1572 1223 1634 1624 237 400 1446 1280 0 0 558 431 174 320 100 100 100 87 2795 2726 1.285 .778 .885 .767 .724 2.494 32 183 .686 .81 70 3080 6270 31 38 96 103 0 1424 312 1112 .707 1476 1164 1.414 .805 -.5 -.313
6 15009 21260 306 429 14703 20831 19056 27094 387 502 18750 26665 0 0 10145 13932 286 356 100 98 100 93 35534 45415 .706 1.417 1.422 1.277 1.386 3.271 80 378 1.414 .98 110 3240 6270 29 40 110 121 0 19327 390 18937 1.288 24630 24240 .776 1.293 .365 .371
7 660 858 245 390 414 467 590 784 324 431 345 393 0 0 259 337 267 246 63 73 30 38 881 738 .887 1.128 1.139 1.032 1.228 3.488 52 244 .879 .48 90 3380 6270 30 39 125 134 -50 780 355 425 1.025 713 357 .975 1.036 .036 .05
8 50547 80112 193 361 50353 79751 52972 81076 615 747 52778 80715 84 93 7535 4312 3293 3560 100 100 100 100 130104 133493 .631 1.584 1.529 1.612 1.529 1.825 32 215 1.558 .97 70 3530 6270 31 38 141 148 -100 72827 328 72498 1.44 73703 73375 .695 1.39 .526 .475
9 434 1277 123 314 310 963 375 1238 145 356 252 924 0 0 220 498 84 218 96 100 78 81 1273 1176 .322 3.106 3.667 3.36 3.584 3.212 32 223 3.603 .59 70 3690 6260 30 37 157 164 0 1161 285 875 2.824 1125 840 .354 3.333 1.498 1.737
10 425 1605 134 310 290 1295 401 1540 157 369 266 1229 0 0 167 559 107 247 87 100 68 90 1585 1495 .224 4.466 4.62 4.832 4.537 3.245 32 224 4.259 .75 70 3840 6260 30 37 172 179 0 1459 282 1177 4.059 1400 1117 .246 4.2 2.021 2.07
11 2040 5374 123 305 1916 5068 2025 5438 153 371 1901 5132 0 0 451 1266 97 261 100 100 100 100 6984 7033 .378 2.645 2.7 2.638 2.51 2.029 32 226 2.725 .94 70 3990 6260 30 37 187 194 0 4885 277 4607 2.405 4943 4665 .416 2.454 1.266 1.295
12 1474 5228 134 324 1340 4904 1477 5266 183 475 1343 4942 0 0 333 1198 243 585 100 100 100 100 6244 6285 .273 3.66 3.68 3.676 3.575 2.085 32 197 3.927 .91 70 4140 6260 30 37 202 209 0 4753 295 4458 3.327 4787 4493 .301 3.345 1.734 1.742
13 988 1688 143 352 845 1336 927 1487 193 476 784 1134 0 0 349 686 210 520 96 92 90 59 2181 1918 .632 1.581 1.446 1.548 1.518 2.903 52 236 1.928 .8 80 4290 6270 31 39 217 225 0 1534 320 1215 1.437 1352 1031 .696 1.315 .523 .395
14 813 1923 122 357 691 1566 850 1696 177 503 728 1338 0 0 243 710 166 463 93 100 90 71 2257 2066 .441 2.266 1.838 2.338 2.091 3.02 32 196 2.763 .81 70 4440 6260 30 37 232 239 0 1748 325 1424 2.06 1542 1216 .485 1.671 1.043 .741
15 198 1040 131 364 66 675 156 838 189 482 25 473 0 0 146 838 175 395 18 59 3 25 741 498 .098 10.227 18.92 8.106 6.825 4.138 32 145 8.96 .37 60 4590 6270 32 38 248 254 0 945 331 614 9.297 762 430 .108 17.199 3.217 4.104
16 6681 7161 131 320 6549 6841 6709 7330 174 415 6578 7009 0 0 1275 1307 166 357 100 100 100 100 13390 13587 .957 1.045 1.066 1.047 1.023 1.908 52 247 1 .95 80 4740 6260 30 38 262 270 0 6510 291 6219 .95 6663 6372 1.053 .969 -.075 -.046
17 345 2344 120 290 224 2053 345 2440 148 355 224 2150 0 0 132 716 123 300 78 100 37 100 2277 2374 .109 9.165 9.598 10.256 8.67 3.465 32 210 10.178 .74 70 4900 6250 29 36 278 285 0 2131 264 1866 8.332 2218 1954 .12 8.725 3.059 3.125
18 173 946 126 289 47 656 151 955 151 346 25 665 0 0 88 513 94 231 25 81 9 71 703 690 .072 13.957 26.6 7.368 6.052 4.702 32 219 17.269 .3 70 5040 6240 28 35 292 299 0 860 263 596 12.688 868 605 .079 24.181 3.665 4.596
19 1203 2162 124 304 1079 1858 1157 2089 163 373 1033 1785 0 0 618 841 149 322 90 94 86 88 2937 2818 .581 1.722 1.728 1.874 1.696 3.392 52 288 1.685 .84 90 5190 6260 29 38 306 315 0 1965 276 1689 1.565 1899 1623 .639 1.571 .647 .652
20 7350 19731 130 314 7220 19417 7171 19383 165 356 7041 19069 0 0 1003 2550 130 227 100 100 100 100 26637 26110 .372 2.689 2.708 2.693 2.819 1.794 32 225 2.722 .98 70 5350 6250 29 36 323 330 0 17937 285 17651 2.445 17620 17335 .409 2.462 1.29 1.3

Total number of rows: 44544

Table truncated, full table size 9997 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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