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Sample GSM989700 Query DataSets for GSM989700
Status Public on Aug 23, 2012
Title PC 47N
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 47N2
Organism Homo sapiens
Characteristics individual: PC 47N
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/2008-08/81089.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 9870 11017 101 153 9768 10863 8132 9110 111 216 8031 8956 0 0 9357 10524 64 273 76 71 71 61 20631 16987 .899 1.112 1.115 1.113 1.148 5.085 52 348 1.098 .93 90 1850 7250 28 37 36 45 0 9157 127 9029 .924 7572 7444 1.082 .927 -.113 -.109
2 8114 9635 106 159 8007 9475 4172 1332 117 221 4066 1172 0 0 8876 11091 61 231 73 61 65 57 17482 5238 .845 1.183 .288 1.118 1.235 4.249 52 332 1.223 .94 90 2000 7250 28 37 51 60 0 8008 132 7875 .984 1107 974 1.017 .24 -.024 -2.061
3 15863 20928 99 153 15764 20774 20948 25931 110 206 20849 25777 0 0 8745 10420 60 212 100 100 96 100 36538 46626 .759 1.318 1.236 1.834 1.311 3.896 32 232 1.279 .95 70 2160 7260 30 37 68 75 0 17395 127 17267 1.095 21553 21425 .913 1.028 .131 .039
4 15297 17242 105 170 15191 17072 17260 20555 117 207 17154 20384 0 0 4204 6810 49 150 100 100 100 100 32263 37538 .89 1.124 1.188 .986 1.182 2.777 32 227 1.164 .94 70 2320 7250 29 36 84 91 0 14331 141 14190 .934 17085 16943 1.071 .988 -.098 -.018
5 1128 324 103 145 1025 179 1054 275 115 195 951 129 0 0 189 152 54 181 100 25 100 16 1204 1080 5.726 .175 .136 .131 .129 3.329 12 104 .093 .25 50 2460 7250 30 35 99 104 0 269 121 149 .145 229 107 6.889 .113 -2.784 -3.149
6 6940 12357 138 170 6801 12186 6992 13151 149 219 6853 12980 0 0 878 3148 74 207 100 100 100 100 18987 19833 .558 1.792 1.894 1.709 1.875 2.035 32 230 1.926 .95 70 2610 7250 29 36 113 120 0 10271 141 10129 1.489 10931 10789 .671 1.574 .575 .655
7 237 275 119 187 118 87 204 230 136 235 85 43 0 0 129 157 74 198 50 17 40 1 205 128 1.356 .737 .506 .957 1.405 6.652 52 342 5.807 .25 90 2760 7250 28 37 127 136 -50 229 155 72 .613 191 36 1.632 .42 -.706 -1.25
8 13246 19338 119 167 13126 19171 14981 21506 132 224 14861 21339 0 0 6199 6778 61 230 100 100 100 100 32297 36200 .685 1.461 1.436 1.818 1.431 2.926 32 201 1.365 .95 70 2910 7250 29 36 143 150 0 16073 139 15935 1.214 17875 17737 .824 1.193 .28 .255
9 143 187 109 171 34 15 136 162 218 397 27 -9 0 0 48 110 1006 1897 0 0 0 0 49 18 2.267 .441 null 1.811 1.13 5.145 52 295 8.95 .3 90 3050 7240 27 36 156 165 -50 155 142 12 .367 135 -7 2.727 null -1.447 null
10 133 270 109 198 24 72 126 228 119 284 16 30 0 0 46 177 54 306 23 13 7 0 96 46 .333 3 1.875 3.366 3.203 6.942 52 304 29.36 .19 90 3200 7240 27 36 171 180 -50 224 165 60 2.494 190 25 .401 1.558 1.318 .64
11 693 1313 107 174 585 1139 685 1273 114 241 578 1099 0 0 183 414 46 299 100 96 100 84 1724 1677 .514 1.947 1.901 1.828 2.142 2.525 32 174 2.139 .84 60 3350 7250 30 36 188 194 0 1091 145 947 1.618 1058 913 .618 1.58 .694 .66
12 377 4797 102 186 275 4611 369 4835 113 231 267 4648 0 0 99 807 43 182 100 100 100 100 4886 4915 .06 16.767 17.408 17.703 18.023 2.243 32 176 18.187 .83 60 3510 7250 30 36 204 210 0 3987 155 3833 13.937 4019 3863 .072 14.469 3.801 3.855
13 309 377 104 185 204 192 313 343 115 234 208 158 0 0 114 182 52 200 86 40 78 17 396 366 1.063 .941 .76 .852 .862 3.787 52 269 3.699 .34 80 3660 7250 29 37 218 226 0 313 154 160 .782 285 131 1.278 .631 -.354 -.663
14 208 330 109 181 99 148 194 240 122 243 84 58 0 0 101 465 64 319 63 13 25 3 247 142 .669 1.495 .69 1.362 1.767 4.824 52 291 6.454 .54 90 3810 7240 27 36 232 241 -50 274 150 123 1.243 199 48 .805 .574 .313 -.801
15 129 151 105 168 24 -16 127 145 114 231 21 -22 0 0 36 75 49 227 23 1 1 0 8 -1 null null null 1.481 1.186 8.055 52 335 12.68 .29 90 3960 7240 27 36 247 256 -50 126 140 -13 null 121 -18 null null null null
16 1751 742 108 153 1643 588 1790 773 116 221 1682 620 0 0 377 228 47 236 100 87 100 75 2231 2302 2.794 .358 .369 .332 .354 2.203 32 218 .347 .78 70 4110 7240 28 35 263 270 0 617 127 489 .297 643 515 3.362 .306 -1.749 -1.707
17 143 255 109 197 34 58 131 237 119 261 22 40 0 0 63 121 54 248 32 11 11 0 92 62 .586 1.706 1.818 1.639 1.393 7.46 52 303 6.337 .51 90 4260 7240 27 36 277 286 -50 212 164 48 1.418 197 33 .705 1.511 .504 .596
18 161 266 104 197 56 69 113 171 111 257 8 -25 0 0 256 287 47 221 19 13 5 5 125 -17 .812 1.232 null 4.349 2.496 10.416 52 304 2.714 .18 90 4410 7240 27 36 292 301 -50 221 164 57 1.024 142 -21 .976 null .034 null
19 462 502 105 209 357 293 456 480 117 271 351 271 0 0 141 212 59 302 96 43 96 9 650 622 1.218 .821 .772 .734 .754 3.265 32 218 1.196 .61 70 4560 7250 29 36 308 315 0 417 174 244 .682 399 225 1.466 .642 -.552 -.64
20 2970 6719 111 229 2858 6489 3238 7227 122 285 3126 6998 0 0 972 2418 48 317 100 100 100 96 9347 10124 .44 2.27 2.239 2.254 2.272 2.976 32 170 2.474 .91 60 4720 7240 29 35 325 331 0 5585 190 5394 1.887 6007 5817 .53 1.861 .916 .896

Total number of rows: 44544

Table truncated, full table size 9699 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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