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Sample GSM989721 Query DataSets for GSM989721
Status Public on Aug 23, 2012
Title PC 453T
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 453T2
Organism Homo sapiens
Characteristics ethnicity: Caucasian
age: 61
pre-operation treatment: None
individual: PC 375T
disease free survival: 16.53
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/2008-08/81188.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 GPL9497
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 17927 13869 82 127 17845 13741 19999 15505 93 149 19917 15378 0 0 5957 4933 42 91 100 100 100 100 31586 35295 1.299 .77 .772 .754 .771 1.93 52 299 .766 .97 80 1650 6730 25 33 37 45 0 10842 99 10742 .602 12121 12022 1.661 .604 -.732 -.728
2 13780 11158 91 151 13688 11006 14698 11939 119 191 14607 11788 0 0 4958 4320 274 186 100 100 98 100 24694 26395 1.244 .804 .807 .804 .817 2.323 52 253 .796 .96 80 1800 6730 25 33 52 60 0 8723 118 8604 .629 9333 9215 1.591 .631 -.67 -.665
3 18447 19015 85 158 18362 18857 21100 22380 115 194 21015 22222 0 0 6617 7426 273 187 100 100 100 100 37219 43237 .974 1.027 1.057 1.022 1.029 2.001 52 257 1.033 .97 80 1950 6730 25 33 67 75 0 14865 124 14742 .803 17496 17372 1.246 .827 -.317 -.275
4 15818 12313 82 145 15736 12168 17734 13598 89 161 17652 13452 0 0 5512 4902 40 96 100 100 100 100 27904 31104 1.293 .773 .762 .716 .782 1.972 52 231 .779 .98 80 2100 6730 25 33 82 90 0 9626 113 9512 .604 10630 10516 1.654 .596 -.726 -.747
5 963 263 86 151 876 112 1012 264 117 181 925 113 0 0 251 100 181 119 100 42 90 7 988 1038 7.821 .128 .122 .099 .13 4.284 52 208 .169 .57 80 2250 6730 25 33 97 105 0 206 118 88 .1 206 88 10.005 .096 -3.323 -3.388
6 6692 6065 111 154 6580 5910 8208 7091 138 186 8097 6936 0 0 4073 3565 157 143 100 100 93 97 12490 15033 1.113 .898 .857 .948 .886 2.2 80 317 .882 .98 100 2400 6730 24 34 111 121 0 4741 120 4620 .702 5543 5422 1.424 .67 -.51 -.578
7 334 198 87 128 246 69 340 192 97 158 253 64 0 0 114 73 72 137 90 15 86 3 315 317 3.565 .28 .253 .281 .308 3.791 52 256 .871 .56 90 2550 6730 24 33 126 135 0 155 100 54 .219 150 50 4.561 .198 -2.189 -2.338
8 21927 23446 81 134 21846 23312 25183 25803 95 160 25102 25669 0 0 8846 7505 50 104 100 100 100 100 45158 50771 .937 1.067 1.023 1.226 1.033 2.237 52 223 1.012 .98 80 2700 6730 25 33 142 150 0 18329 105 18224 .834 20172 20067 1.199 .799 -.262 -.323
9 142 143 77 119 64 24 131 124 88 145 54 5 0 0 69 97 47 98 55 11 28 6 88 59 2.667 .375 .093 .944 .852 6.319 80 343 3.043 .37 100 2850 6730 24 34 156 166 -50 112 93 19 .293 97 4 3.411 .072 -1.77 -3.788
10 228 200 76 114 151 85 229 176 80 128 152 61 0 0 49 87 25 68 100 46 100 21 236 213 1.776 .563 .401 .5 .657 3.829 32 187 .954 .45 70 3010 6730 25 32 173 180 0 156 89 66 .44 138 48 2.272 .314 -1.184 -1.672
11 437 559 75 107 362 451 430 543 79 136 355 435 0 0 107 169 30 116 100 96 100 90 813 790 .803 1.246 1.225 1.19 1.234 2.104 52 240 1.403 .82 80 3160 6730 25 33 188 196 0 437 84 353 .974 424 340 1.027 .958 -.038 -.062
12 399 704 74 108 325 596 427 745 83 132 353 636 0 0 126 244 36 80 96 96 94 92 921 989 .545 1.834 1.802 1.872 1.705 2.934 52 243 1.917 .9 80 3310 6730 25 33 203 211 0 550 84 466 1.434 582 497 .698 1.408 .52 .494
13 338 298 75 121 262 176 340 280 84 145 264 159 0 0 99 118 34 93 96 76 96 40 438 423 1.489 .672 .602 .589 .612 2.347 52 252 .955 .53 80 3460 6720 24 32 218 226 0 233 95 138 .525 219 124 1.904 .471 -.929 -1.087
14 246 206 72 120 174 85 257 223 168 162 184 103 0 0 76 83 905 194 0 9 0 0 259 287 2.047 .489 .56 .552 .588 4.769 52 260 .134 .6 90 3610 6720 23 32 232 241 0 161 94 66 .382 174 81 2.619 .438 -1.389 -1.192
15 98 88 71 113 27 -25 99 69 144 146 27 -43 0 0 29 66 775 173 0 2 0 0 2 -16 null null null 2.333 2.412 6.102 80 355 .137 .62 100 3760 6720 23 33 247 257 -50 69 88 -20 null 54 -34 null null null null
16 1780 1424 77 120 1703 1304 1950 1545 85 152 1873 1424 0 0 484 483 41 149 100 98 100 94 3007 3297 1.306 .766 .76 .732 .739 1.652 52 238 .789 .96 80 3920 6720 24 32 264 272 0 1113 94 1019 .599 1208 1113 1.671 .594 -.74 -.751
17 198 236 75 122 123 113 196 210 83 149 121 88 0 0 65 152 35 135 94 25 75 11 236 209 1.088 .919 .727 .926 .919 3.906 52 233 2.724 .55 90 4070 6720 23 32 278 287 0 184 95 88 .718 164 69 1.392 .569 -.478 -.815
18 88 90 71 118 17 -27 85 69 82 154 13 -48 0 0 42 59 38 138 13 3 2 0 -10 -35 null null null 2.512 2.585 4.011 80 265 1.841 .94 100 4220 6720 23 33 293 303 -50 70 92 -21 null 54 -38 null null null null
19 310 237 71 115 239 121 330 229 80 136 259 113 0 0 155 123 34 89 86 57 78 28 360 372 1.975 .506 .436 .506 .453 4.807 80 299 .681 .47 100 4370 6720 23 33 308 318 0 185 90 95 .396 179 88 2.527 .341 -1.337 -1.552
20 1574 2568 75 110 1498 2458 1697 2695 82 144 1621 2585 0 0 421 738 34 130 100 100 100 98 3956 4206 .609 1.641 1.595 1.604 1.625 1.81 52 223 1.66 .96 80 4520 6720 24 32 324 332 0 2008 86 1922 1.283 2107 2021 .78 1.247 .359 .318

Total number of rows: 44544

Table truncated, full table size 9534 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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