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Sample GSM989693 Query DataSets for GSM989693
Status Public on Aug 23, 2012
Title PC 361T
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 361T2.0
Organism Homo sapiens
Characteristics ethnicity: Hispanic
age: 73
pre-operation treatment: None
individual: PC 99T
disease free survival: 83.60
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/2008-08/81242.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 GPL15971
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 35447 20848 57 104 35390 20744 37591 21276 66 142 37533 21171 13 0 10423 7627 33 258 100 98 100 98 56134 58704 1.706 .586 .564 .53 .545 3.481 80 413 .587 .96 100 1770 6630 22 32 32 42 0 20697 103 20594 .582 21122 21018 1.718 .56 -.781 -.837
2 25824 16728 61 110 25763 16617 32586 19596 71 152 32525 19485 1 0 14089 8683 34 143 100 98 100 97 42380 52010 1.55 .645 .599 .703 .639 4.183 80 334 .621 .97 100 1900 6630 22 32 45 55 0 16607 109 16497 .64 19454 19344 1.562 .595 -.643 -.75
3 22984 28728 78 130 22906 28598 25571 30259 93 169 25493 30129 0 0 9022 9590 73 213 100 98 100 98 51504 55622 .801 1.248 1.182 1.275 1.167 4.793 80 316 1.191 .95 100 2080 6660 25 35 63 73 0 28520 129 28391 1.239 30040 29911 .807 1.173 .31 .231
4 31336 16600 77 127 31259 16472 33579 17686 93 169 33501 17558 1 0 11060 6008 73 248 100 100 100 100 47731 51059 1.898 .527 .524 .545 .526 3.624 80 313 .533 .97 100 2230 6650 24 34 78 88 0 16480 126 16353 .523 17558 17431 1.912 .52 -.935 -.943
5 1658 424 66 120 1592 304 1728 426 72 140 1662 305 0 0 593 208 32 94 98 82 97 70 1896 1967 5.237 .191 .184 .173 .181 4.728 80 371 .183 .75 100 2370 6620 21 31 92 102 0 421 119 302 .19 423 303 5.275 .182 -2.399 -2.457
6 9358 8435 75 132 9282 8303 9791 8795 108 344 9715 8663 0 0 4928 4199 188 2733 100 86 98 75 17585 18378 1.118 .895 .892 .917 .872 3.723 120 420 .863 .96 120 2520 6650 23 35 106 118 0 8374 131 8243 .888 8731 8600 1.126 .885 -.171 -.176
7 452 265 69 123 382 142 468 253 107 169 398 130 0 0 122 133 112 238 95 23 91 1 524 528 2.69 .372 .327 .304 .362 5.674 80 368 .876 .53 110 2670 6620 20 31 121 132 0 263 122 141 .369 251 129 2.71 .324 -1.438 -1.625
8 27432 30514 73 162 27358 30352 26475 29830 303 451 26401 29668 0 0 3517 4310 2159 2439 100 100 100 100 57710 56069 .901 1.109 1.124 1.108 1.11 2.217 52 317 1.13 .98 90 2820 6620 21 30 137 146 0 30293 161 30132 1.101 29614 29453 .908 1.116 .139 .158
9 298 285 64 142 234 143 324 258 252 374 260 116 0 0 99 176 1983 2235 0 0 0 0 377 376 1.636 .611 .446 .714 .834 5.072 80 376 1.03 .96 110 2980 6650 23 34 152 163 0 283 141 142 .607 256 115 1.648 .443 -.721 -1.175
10 320 378 57 126 263 252 324 375 62 143 267 249 0 0 97 143 24 97 96 83 96 60 515 516 1.044 .958 .933 .863 .939 4.563 80 320 .959 .64 110 3120 6640 22 33 166 177 0 375 125 250 .951 372 247 1.051 .926 -.072 -.111
11 1053 1611 55 110 998 1500 1122 1625 58 127 1067 1515 0 0 464 717 21 91 96 97 95 93 2498 2582 .665 1.503 1.42 1.734 1.553 4.149 80 263 1.486 .94 100 3280 6640 23 33 183 193 0 1599 109 1489 1.492 1613 1504 .67 1.41 .577 .495
12 846 1021 56 123 790 898 804 997 61 198 748 873 0 0 195 364 37 695 100 68 100 11 1688 1621 .88 1.137 1.167 1.076 1.088 3.174 80 304 2.44 .52 110 3430 6650 23 34 197 208 0 1014 122 892 1.128 990 867 .886 1.159 .174 .212
13 663 380 59 123 603 256 692 341 66 186 632 218 0 0 186 193 39 611 97 3 97 0 859 850 2.355 .425 .345 .349 .384 4.567 80 400 4.208 .23 110 3580 6630 21 32 212 223 0 377 122 254 .421 339 216 2.373 .342 -1.246 -1.546
14 252 440 59 123 193 317 255 436 65 150 195 312 0 0 52 167 25 134 100 88 100 63 510 507 .609 1.642 1.6 1.552 1.578 4.024 80 373 2.068 .65 110 3720 6640 22 33 226 237 0 437 122 315 1.631 433 310 .613 1.588 .705 .668
15 62 114 57 134 4 -20 61 103 65 195 3 -31 0 0 16 70 94 532 0 0 0 0 -16 -28 null null null 4.341 5.427 7.435 120 423 55.906 .18 120 3880 6630 21 33 242 254 -50 113 133 -20 null 102 -31 null null null null
16 1239 1256 59 144 1180 1111 1259 1264 64 179 1200 1119 0 0 459 540 25 167 100 93 98 90 2291 2319 1.062 .942 .933 .939 .895 3.267 80 252 .949 .92 100 4040 6630 22 32 259 269 0 1247 143 1103 .935 1255 1111 1.07 .926 -.097 -.111
17 135 304 59 149 75 154 137 282 70 289 77 133 0 0 50 156 90 1047 37 0 1 0 229 210 .487 2.053 1.727 2.037 2.327 5.93 120 273 12.768 .81 120 4180 6650 23 35 272 284 0 302 148 153 2.038 280 132 .491 1.715 1.027 .778
18 69 219 66 149 2 70 57 84 81 282 -9 -64 0 0 87 922 85 946 1 1 1 1 72 -73 .029 35 null 5.484 5.137 6.394 120 365 8.696 .6 120 4330 6640 22 34 287 299 -50 217 148 69 34.747 83 -64 .029 null 5.119 null
19 842 835 72 157 770 677 787 836 87 241 715 678 0 0 308 299 50 598 100 61 100 3 1447 1393 1.137 .879 .948 .834 .945 3.724 80 332 .844 .83 110 4480 6640 22 33 302 313 0 829 156 672 .873 830 673 1.146 .941 -.196 -.087
20 4673 16072 62 143 4610 15928 4588 16551 71 179 4525 16408 0 0 1492 5513 34 210 100 98 100 98 20538 20933 .289 3.455 3.626 3.448 3.451 3.032 80 347 3.547 .98 110 4640 6630 21 32 318 329 0 15956 142 15813 3.43 16431 16289 .292 3.6 1.778 1.848

Total number of rows: 44544

Table truncated, full table size 9797 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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