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Sample GSM989754 Query DataSets for GSM989754
Status Public on Aug 23, 2012
Title PC 634N
Sample type RNA
 
Channel 1
Source name Human 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 634N RNA
Organism Homo sapiens
Characteristics individual: PC 634N
disease state: Normal
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/2008-08/80845.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 10204 13193 124 98 10080 13095 5623 6434 138 119 5499 6336 0 0 10364 14134 68 96 80 71 75 63 23175 11835 .77 1.299 1.152 1.029 1.291 7.206 52 378 1.41 .87 90 1760 7030 26 35 31 40 0 10704 80 10625 1.054 5220 5141 .949 .935 .076 -.097
2 9097 13163 137 99 8960 13064 2854 3891 163 131 2717 3792 0 0 10412 15627 267 104 59 67 55 59 22024 6509 .686 1.458 1.396 .952 1.286 5.875 52 325 1.576 .86 90 1910 7030 26 35 46 55 0 10680 80 10600 1.183 3157 3077 .845 1.132 .242 .179
3 6281 10882 135 101 6146 10781 1688 435 163 133 1553 334 0 0 7220 14163 269 105 57 55 55 53 16927 1887 .57 1.754 .215 1.175 1.64 6.065 52 318 2.228 .84 90 2060 7030 26 35 61 70 0 8829 82 8747 1.423 353 271 .703 .174 .509 -2.519
4 12679 17336 138 102 12541 17234 7977 9691 150 129 7839 9589 0 0 12315 17885 69 95 82 69 78 67 29775 17428 .728 1.374 1.223 1.324 1.415 6.457 52 305 1.573 .83 90 2210 7030 26 35 76 85 0 14066 83 13983 1.115 7863 7780 .897 .992 .157 -.011
5 418 218 138 99 280 119 318 174 145 119 180 75 0 0 329 132 64 85 59 46 51 38 399 255 2.353 .425 .417 .422 .427 3.531 52 328 .367 .53 90 2360 7030 26 35 91 100 -50 177 80 97 .345 141 61 2.9 .338 -1.536 -1.565
6 4911 14946 130 108 4781 14838 6188 18347 147 144 6058 18239 0 0 3122 10258 76 175 90 90 90 84 19619 24297 .322 3.104 3.011 1.816 2.903 6.879 52 342 3.717 .84 90 2520 7030 26 35 107 116 0 12127 88 12039 2.518 14886 14798 .397 2.443 1.332 1.289
7 233 186 141 121 92 65 222 163 162 156 81 42 0 0 116 118 85 144 42 23 21 5 157 123 1.415 .707 .519 1.418 1.5 5.51 52 318 2.017 .21 90 2670 7030 26 35 122 131 -50 151 98 53 .573 132 34 1.744 .421 -.803 -1.249
8 9432 19580 137 102 9295 19478 7852 23593 150 136 7715 23491 0 0 7726 16419 74 137 92 80 90 73 28773 31206 .477 2.096 3.045 1.683 2.073 7.069 52 316 2.345 .85 90 2820 7030 26 35 137 146 0 15886 83 15804 1.7 19142 19060 .588 2.47 .766 1.305
9 193 472 146 95 47 377 185 456 148 131 39 361 0 0 93 169 60 113 41 100 25 83 424 400 .125 8.021 9.256 5.88 4.442 2.515 12 104 7.135 .36 50 2970 7030 28 33 154 159 0 383 77 306 6.508 370 293 .154 7.51 2.702 2.909
10 128 210 134 102 -6 108 126 193 150 138 -8 91 0 0 53 120 80 124 3 40 0 13 102 83 null null null 3.084 3.476 5.339 52 294 26.602 .04 90 3120 7030 26 35 167 176 -50 170 83 88 null 157 74 null null null null
11 426 871 140 100 286 771 395 910 156 157 255 810 0 0 274 597 81 166 65 73 55 65 1057 1065 .371 2.696 3.176 2.731 2.737 3.082 52 278 3.047 .69 80 3270 7030 27 35 183 191 0 707 81 626 2.187 738 657 .457 2.577 1.129 1.366
12 397 1051 143 115 254 936 348 1114 161 144 205 999 0 0 148 429 85 125 93 93 68 90 1190 1204 .271 3.685 4.873 3.505 4.406 3.737 32 219 5.227 .56 70 3430 7030 27 34 199 206 0 853 93 759 2.99 904 811 .334 3.954 1.58 1.983
13 305 321 132 82 173 239 297 301 148 122 165 219 0 0 101 122 76 104 83 91 50 66 412 384 .724 1.382 1.327 1.5 1.391 2.728 12 104 1.317 .5 50 3580 7030 28 33 215 220 0 260 67 194 1.121 244 178 .892 1.077 .165 .107
14 205 346 146 99 59 247 196 358 152 136 50 259 0 0 59 102 64 94 41 91 8 66 306 309 .239 4.186 5.18 3.909 4.221 3.297 12 68 4.583 .22 40 3730 7040 30 34 231 235 0 281 80 200 3.397 290 210 .294 4.203 1.764 2.071
15 145 84 128 103 17 -19 134 71 142 129 6 -32 0 0 73 59 75 96 15 3 1 1 -2 -26 null null null .851 1.225 3.022 52 309 9.385 .04 90 3880 7030 26 35 243 252 -50 68 84 -15 null 58 -26 null null null null
16 1273 608 143 107 1130 501 1226 680 154 136 1083 573 0 0 404 295 78 109 100 84 100 78 1631 1656 2.255 .443 .529 .395 .48 2.447 32 209 .422 .62 70 4030 7020 26 33 259 266 0 493 87 406 .36 552 465 2.78 .429 -1.475 -1.22
17 161 154 126 93 35 61 155 111 141 127 29 18 0 0 72 111 66 134 30 23 7 5 96 47 .574 1.743 .621 1.6 1.442 3.515 52 310 -1 -1 90 4170 7020 25 34 272 281 -50 125 75 49 1.414 90 15 .707 .504 .5 -.99
18 122 110 130 106 -8 4 108 78 151 129 -22 -28 0 0 53 101 90 96 7 11 0 9 -4 -50 null null null 1.1 1.414 4.482 52 313 7.919 .08 90 4330 7020 25 34 288 297 -50 89 86 3 null 63 -23 null null null null
19 289 495 127 91 162 404 286 509 146 118 159 418 0 0 99 213 78 102 81 90 50 84 566 577 .401 2.494 2.629 2.627 2.258 2.981 32 227 3.594 .47 70 4480 7020 26 33 304 311 0 402 74 328 2.023 413 339 .494 2.133 1.017 1.093
20 2261 8358 131 113 2130 8245 2705 9276 145 136 2574 9163 0 0 1142 3121 67 104 93 100 87 100 10375 11737 .258 3.871 3.56 5.571 3.997 3.196 32 217 4.051 .85 70 4630 7030 27 34 319 326 0 6781 92 6690 3.141 7526 7435 .318 2.888 1.651 1.53

Total number of rows: 44544

Table truncated, full table size 9490 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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