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Sample GSM989725 Query DataSets for GSM989725
Status Public on Aug 23, 2012
Title PC 574T
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 574T2
Organism Homo sapiens
Characteristics individual: PC 574T
disease state: Tumor
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/2008-08/81144.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) [email protected]
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 33604 21252 119 204 33485 21048 36654 23282 127 229 36535 23078 0 0 8969 6603 51 112 100 100 100 100 54533 59613 1.591 .629 .632 .588 .634 1.973 52 367 .637 .99 90 2100 6750 26 35 41 50 0 18737 180 18557 .554 20526 20347 1.804 .557 -.852 -.844
2 34216 22909 145 220 34071 22689 37135 23671 163 256 36990 23450 0 0 7516 4102 97 182 100 100 100 100 56760 60440 1.502 .666 .634 .678 .654 1.801 52 311 .646 .98 90 2260 6730 24 33 57 66 0 20198 194 20004 .587 20869 20675 1.703 .559 -.768 -.839
3 49687 72437 164 250 49523 72187 54931 78185 178 272 54766 77935 80 82 13016 15026 96 127 100 100 100 100 121710 132701 .686 1.458 1.423 1.525 1.423 1.942 52 289 1.463 .98 90 2410 6730 24 33 72 81 -100 63864 220 63643 1.285 68932 68711 .778 1.255 .362 .327
4 36394 23816 150 237 36243 23579 38468 24429 161 251 38317 24192 0 0 8810 4269 62 102 100 100 100 100 59822 62509 1.537 .651 .631 .682 .628 1.884 52 246 .628 .98 80 2550 6740 26 34 87 95 0 20997 209 20788 .574 21538 21329 1.743 .557 -.802 -.845
5 1706 521 134 230 1571 291 1818 526 156 262 1683 295 0 0 440 158 85 156 100 76 98 48 1862 1978 5.399 .185 .175 .166 .188 2.667 52 270 .168 .64 90 2710 6730 24 33 102 111 0 459 203 257 .163 464 260 6.123 .155 -2.614 -2.694
6 24482 27126 308 377 24173 26749 28015 29404 651 498 27707 29027 0 0 9738 9791 798 440 100 100 94 100 50922 56734 .904 1.107 1.048 1.129 1.061 1.952 52 267 1.082 .98 90 2850 6730 24 33 116 125 0 23916 332 23583 .976 25924 25592 1.025 .924 -.036 -.115
7 625 387 247 326 378 60 573 369 523 443 326 42 0 0 150 152 764 427 3 1 0 0 438 368 6.3 .159 .129 .273 .357 3.957 52 277 .362 .54 90 3010 6730 24 33 132 141 -50 341 287 53 .14 325 37 7.146 .114 -2.837 -3.138
8 50352 74912 143 252 50208 74659 54931 78185 181 275 54787 77932 73 88 10309 10392 109 141 100 100 100 100 124867 132719 .672 1.487 1.422 1.516 1.422 1.759 52 265 1.46 .98 90 3160 6740 25 34 147 156 -100 66046 222 65823 1.311 68932 68708 .763 1.254 .391 .327
9 429 351 129 250 299 101 429 350 140 270 299 100 0 0 83 103 71 136 98 38 98 3 400 399 2.96 .338 .334 .338 .488 4.451 52 213 .509 .32 80 3310 6740 26 34 163 171 0 309 220 89 .298 309 88 3.358 .295 -1.748 -1.762
10 486 428 116 224 370 204 496 415 121 261 379 190 0 0 82 125 34 152 100 61 100 21 574 569 1.814 .551 .501 .45 .594 4.028 52 292 .92 .42 90 3460 6720 23 32 177 186 0 377 197 180 .486 366 168 2.057 .442 -1.041 -1.178
11 2056 3727 114 225 1941 3501 2194 3752 120 254 2079 3526 0 0 599 1028 36 162 100 100 100 100 5442 5605 .554 1.804 1.696 1.812 1.768 1.848 52 257 1.785 .97 80 3610 6730 25 33 193 201 0 3286 198 3087 1.59 3308 3109 .629 1.495 .669 .58
12 1676 3438 115 223 1560 3215 1634 3409 121 257 1518 3186 0 0 286 614 35 157 100 100 100 100 4775 4704 .485 2.061 2.099 2.053 2.062 1.786 52 286 2.119 .96 90 3770 6730 24 33 208 217 0 3031 197 2834 1.817 3006 2809 .55 1.85 .862 .888
13 1180 653 113 237 1067 416 1234 650 119 267 1121 412 0 0 235 143 33 144 100 98 100 78 1483 1533 2.565 .39 .368 .361 .383 2.697 52 253 .372 .72 80 3920 6720 24 32 224 232 0 576 209 367 .344 573 363 2.909 .324 -1.541 -1.626
14 448 428 108 214 339 213 461 423 113 246 352 208 0 0 106 125 35 139 98 69 98 28 552 560 1.592 .628 .591 .603 .631 2.277 52 242 .809 .63 80 4070 6730 25 33 239 247 0 377 189 188 .554 373 183 1.805 .521 -.852 -.941
15 67 94 105 213 -37 -119 64 85 113 250 -41 -127 0 0 19 66 36 146 1 1 0 0 -156 -168 null null null 3.167 3.167 2.438 52 281 4.93 .63 90 4220 6730 24 33 253 262 -50 83 188 -105 null 75 -112 null null null null
16 5786 6441 108 217 5677 6224 5861 6710 112 245 5752 6493 0 0 1377 1282 25 127 100 100 100 100 11901 12245 .912 1.096 1.129 1.112 1.081 1.704 52 239 1.076 .97 80 4370 6740 26 34 269 277 0 5679 191 5487 .967 5916 5725 1.035 .995 -.049 -.007
17 227 388 124 236 102 152 218 366 137 267 93 130 0 0 31 119 46 151 100 41 50 8 254 223 .671 1.49 1.398 1.431 1.401 2.623 12 102 2.566 .42 50 4510 6740 27 32 284 289 0 342 208 134 1.314 323 115 .761 1.232 .394 .301
18 66 90 108 212 -42 -121 59 79 113 236 -49 -132 0 0 24 63 33 113 1 3 0 0 -163 -181 null null null 3.026 2.93 2.54 52 330 5.664 .58 90 4660 6730 24 33 297 306 -50 79 187 -107 null 70 -116 null null null null
19 1750 1746 118 212 1631 1534 1774 1723 123 240 1656 1511 0 0 414 402 31 133 100 100 100 100 3165 3167 1.063 .941 .912 .94 .893 1.981 52 314 .914 .94 90 4820 6720 23 32 313 322 0 1539 187 1352 .829 1519 1332 1.206 .804 -.27 -.314
20 6770 19271 125 227 6645 19043 7509 20573 129 258 7383 20346 0 0 2252 5701 35 136 100 100 100 100 25688 27729 .349 2.866 2.756 3.03 2.806 2.152 52 258 2.866 .98 90 4960 6730 24 33 327 336 0 16990 200 16789 2.527 18138 17938 .396 2.43 1.337 1.281

Total number of rows: 44544

Table truncated, full table size 9859 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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