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Sample GSM989718 Query DataSets for GSM989718
Status Public on Aug 23, 2012
Title PC 45N
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 45N2
Organism Homo sapiens
Characteristics individual: PC 45N
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/2008-08/81125.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 13388 17013 111 174 13277 16839 19094 23452 131 213 18983 23277 0 0 9889 11498 78 217 76 82 73 78 30116 42260 .788 1.268 1.226 1.892 1.26 3.053 52 378 1.219 .98 90 2440 6940 37 46 39 48 0 14815 152 14664 1.104 20423 20270 .905 1.068 .143 .095
2 12278 15639 105 169 12173 15470 14698 17649 128 209 14593 17480 0 0 9539 11497 74 214 84 86 75 84 27643 32073 .787 1.271 1.198 2.001 1.295 3.558 52 325 1.244 .97 90 2590 6940 37 46 54 63 0 13619 147 13472 1.107 15369 15222 .904 1.043 .146 .061
3 26182 46410 122 168 26059 46242 39351 66524 157 244 39228 66356 0 30 20109 30388 232 471 80 84 71 80 72301 105584 .564 1.775 1.692 2.617 1.69 2.992 52 325 1.648 .97 90 2740 6940 37 46 69 78 -100 40415 146 40269 1.545 57931 57785 .647 1.473 .628 .559
4 19889 24779 127 164 19762 24614 24473 29006 142 206 24345 28841 0 0 10453 10884 84 147 94 100 88 100 44376 53186 .803 1.246 1.185 2.027 1.186 4.018 52 332 1.177 .98 90 2890 6940 37 46 84 93 -100 21578 143 21435 1.085 25259 25116 .922 1.032 .117 .045
5 713 365 188 220 525 144 732 295 234 254 544 74 0 0 259 198 153 166 90 34 84 15 669 618 3.646 .274 .136 .241 .227 3.943 32 175 .242 .24 60 3050 6940 39 45 102 108 0 318 192 125 .239 257 64 4.187 .118 -2.066 -3.078
6 10944 16817 211 222 10733 16594 11884 17401 284 263 11673 17178 0 0 3388 3779 208 169 100 100 100 100 27327 28851 .647 1.546 1.472 1.679 1.542 1.834 52 303 1.529 .98 90 3200 6940 37 46 115 124 0 14645 193 14450 1.346 15153 14959 .743 1.282 .429 .358
7 289 233 142 180 147 53 303 211 177 214 161 31 0 0 120 133 135 132 55 19 15 7 200 192 2.774 .361 .193 .837 1.042 4.438 52 291 .644 .21 90 3350 6940 37 46 130 139 -50 203 157 46 .314 184 27 3.185 .168 -1.671 -2.576
8 31499 46130 133 185 31365 45944 48692 71977 173 230 48559 71792 0 55 24252 32231 304 254 73 86 71 84 77309 120351 .683 1.465 1.478 2.669 1.433 4.105 52 313 1.401 .98 90 3500 6940 37 46 145 154 -100 40171 161 40009 1.276 62679 62518 .784 1.287 .351 .365
9 206 356 123 194 82 162 183 331 149 236 59 137 0 0 96 213 115 168 33 41 8 33 244 196 .506 1.976 2.322 1.711 1.605 4.41 12 68 5.542 .22 40 3650 6930 39 43 163 167 0 310 169 141 1.72 288 119 .581 2.022 .783 1.016
10 217 459 108 177 109 281 200 434 127 205 91 257 0 0 77 200 64 139 68 71 28 46 390 348 .388 2.578 2.824 2.434 2.593 3.661 32 175 4.34 .42 60 3810 6940 39 45 178 184 0 400 154 245 2.245 378 224 .445 2.459 1.167 1.298
11 631 1199 112 173 518 1025 705 1108 131 214 592 934 0 0 277 439 82 183 87 96 81 96 1543 1526 .505 1.979 1.578 2 1.917 2.536 32 225 1.931 .85 70 3950 6940 38 45 191 198 0 1044 151 893 1.723 965 813 .58 1.374 .785 .458
12 470 1174 120 174 350 999 501 1164 132 243 381 989 0 0 141 280 81 394 96 100 87 78 1349 1370 .35 2.854 2.596 3.074 2.989 2.277 32 224 4.579 .68 70 4100 6940 38 45 206 213 0 1022 152 870 2.486 1014 861 .402 2.26 1.314 1.177
13 407 390 111 166 295 224 374 399 128 199 262 232 0 0 131 150 66 137 96 68 90 37 519 494 1.317 .759 .885 .783 .994 2.381 32 227 .939 .33 70 4250 6940 38 45 221 228 0 340 145 195 .661 347 202 1.512 .771 -.597 -.375
14 313 511 112 175 200 336 315 504 143 244 203 328 0 0 191 311 202 404 50 46 15 7 536 531 .595 1.68 1.616 1.601 1.54 3.303 52 254 2.216 .78 80 4410 6950 39 47 237 245 0 445 152 293 1.463 439 286 .684 1.407 .549 .493
15 94 125 112 159 -18 -34 87 110 134 213 -25 -48 0 0 32 69 109 215 0 0 0 0 -52 -73 null null null 1.601 1.937 4.499 52 291 2.92 .38 90 4560 6940 37 46 251 260 -50 109 138 -30 null 96 -42 null null null null
16 2218 2953 121 173 2097 2779 2474 2895 136 222 2353 2721 0 0 673 780 81 183 98 100 98 100 4876 5074 .755 1.325 1.156 1.356 1.236 1.815 52 253 1.298 .92 80 4710 6940 38 46 267 275 0 2572 151 2420 1.154 2521 2370 .867 1.007 .207 .01
17 147 244 130 200 17 43 153 200 146 238 23 0 0 0 71 129 83 197 15 15 3 1 60 23 .395 2.529 null 2.246 2.389 5.138 52 291 4.625 .3 90 4860 6940 37 46 281 290 -50 212 174 37 2.203 174 0 .454 null 1.139 null
18 113 158 124 196 -10 -38 107 126 152 283 -17 -70 0 0 45 132 223 552 0 0 0 0 -48 -87 null null null 2.254 2.302 5.106 52 301 2.902 .78 90 5010 6940 37 46 296 305 -50 138 171 -33 null 110 -61 null null null null
19 474 494 123 187 350 306 466 467 133 248 342 280 0 0 179 255 70 273 96 50 84 13 656 622 1.144 .874 .819 .913 .875 3.356 52 274 1.934 .36 80 5170 6940 38 46 313 321 0 430 163 266 .761 407 244 1.313 .713 -.393 -.488
20 1870 7268 131 191 1739 7077 2184 8594 142 243 2053 8403 0 0 886 3246 66 283 94 96 92 92 8816 10456 .246 4.07 4.093 3.915 3.879 2.477 52 244 4.106 .95 80 5320 6950 39 47 328 336 0 6329 166 6163 3.544 7484 7318 .282 3.564 1.825 1.834

Total number of rows: 44544

Table truncated, full table size 9837 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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