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Sample GSM989824 Query DataSets for GSM989824
Status Public on Aug 23, 2012
Title PC 188T
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 188T2
Organism Homo sapiens
Characteristics ethnicity: Caucasian
age: 64
pre-operation treatment: None
individual: PC 405T
disease free survival: 2.50
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/2008-08/81106.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 18431 23108 60 150 18371 22957 20197 26695 63 172 20137 26545 0 0 4716 8176 19 93 100 100 100 100 41328 46682 .8 1.25 1.318 1.168 1.294 3.177 32 230 1.284 .98 70 1840 7240 32 39 28 35 0 19391 126 19264 1.049 22401 22275 .954 1.106 .068 .146
2 9896 10941 68 168 9827 10772 8626 7761 70 195 8557 7592 0 0 8723 9846 22 161 100 90 100 90 20599 16149 .912 1.096 .887 1.024 1.112 4.183 52 301 1.099 .98 80 1990 7240 32 40 43 51 0 9181 141 9039 .92 6513 6371 1.087 .745 -.121 -.426
3 13638 35012 75 185 13563 34826 15850 41636 84 221 15774 41451 0 0 4948 14478 41 149 100 100 100 100 48389 57225 .389 2.568 2.628 2.453 2.558 3.58 32 226 2.62 .98 70 2140 7230 31 38 58 65 0 29380 155 29224 2.155 34938 34783 .464 2.205 1.107 1.141
4 12965 14913 74 196 12890 14716 16530 19007 86 238 16455 18811 0 0 6491 8511 41 156 100 96 98 94 27606 35266 .876 1.142 1.143 .974 1.16 4.094 52 308 1.167 .98 90 2290 7240 31 40 72 81 0 12514 164 12349 .958 15949 15785 1.044 .959 -.062 -.06
5 934 444 70 179 863 264 986 394 79 218 916 215 0 0 247 181 35 135 100 68 100 43 1127 1131 3.269 .306 .235 .255 .281 4.727 32 210 .299 .67 70 2440 7230 31 38 88 95 0 373 150 222 .257 331 180 3.896 .197 -1.962 -2.344
6 4344 5003 89 182 4255 4821 5246 5246 101 222 5157 5063 0 0 2938 3486 50 150 100 95 97 87 9076 10220 .883 1.133 .982 1.069 1.123 3.864 80 359 1.135 .98 100 2590 7240 31 41 102 112 0 4198 153 4045 .951 4402 4249 1.052 .824 -.073 -.28
7 201 324 70 198 131 125 216 313 85 245 145 115 0 0 87 170 44 204 78 26 63 7 256 260 1.048 .954 .793 1.518 1.167 8.188 52 307 5.325 .25 90 2740 7230 30 39 117 126 -50 272 166 105 .801 263 97 1.249 .666 -.321 -.587
8 7032 20261 68 207 6963 20054 8043 22767 78 242 7974 22559 0 0 4735 14515 37 172 98 100 96 94 27017 30533 .347 2.88 2.829 2.862 2.864 3.798 52 274 2.958 .99 80 2890 7230 31 39 133 141 0 17002 174 16828 2.417 19105 18930 .414 2.374 1.273 1.247
9 158 354 57 201 100 153 149 314 67 238 91 113 0 0 74 172 32 168 82 36 65 11 253 204 .654 1.53 1.242 1.522 1.804 6.503 52 305 4.476 .49 90 3040 7230 30 39 147 156 -50 297 169 128 1.284 263 95 .779 1.042 .361 .059
10 154 354 52 178 102 176 146 310 56 215 93 132 0 0 64 182 21 198 88 36 82 9 278 225 .58 1.725 1.419 1.99 1.885 7.113 52 254 3.24 .4 80 3190 7240 32 40 163 171 0 297 149 148 1.448 260 111 .691 1.191 .534 .252
11 407 951 54 173 353 777 392 871 71 215 338 697 0 0 129 364 98 179 96 93 90 90 1130 1035 .454 2.201 2.062 2.108 2.167 3.717 32 176 2.42 .82 60 3350 7230 32 38 180 186 0 798 145 652 1.847 731 585 .541 1.73 .885 .791
12 536 1364 52 179 484 1184 536 1351 55 213 484 1172 0 0 78 457 20 168 100 100 100 100 1668 1656 .409 2.446 2.421 2.291 2.569 3.568 32 231 2.679 .86 70 3500 7220 30 37 194 201 0 1145 150 994 2.053 1134 983 .487 2.032 1.038 1.023
13 321 314 51 179 270 135 339 293 54 201 288 113 0 0 121 145 16 125 100 48 96 21 405 401 2 .5 .392 .495 .454 5.857 52 279 .497 .43 80 3650 7230 31 39 209 217 0 263 150 113 .42 246 95 2.383 .329 -1.253 -1.603
14 221 440 51 156 169 284 217 437 56 193 165 281 0 0 57 164 21 162 100 71 96 40 453 446 .595 1.68 1.703 1.4 1.637 4.984 32 158 2.32 .68 60 3800 7240 33 39 225 231 0 369 131 238 1.41 367 236 .709 1.429 .496 .515
15 76 221 52 184 24 36 68 133 57 228 16 -50 0 0 36 356 20 192 40 13 21 3 60 -34 .667 1.5 null 6.043 6.563 11.188 52 325 12.4 .58 90 3950 7230 30 39 238 247 -50 185 154 30 1.259 112 -42 .794 null .332 null
16 1008 1619 53 168 954 1450 1033 1574 56 196 980 1405 0 0 166 327 16 129 100 100 100 100 2404 2385 .658 1.52 1.434 1.516 1.464 2.97 32 205 1.497 .93 70 4100 7230 31 38 254 261 0 1359 141 1217 1.275 1321 1179 .784 1.203 .351 .267
17 120 331 52 152 68 179 115 296 54 181 63 144 0 0 61 185 17 165 67 48 61 25 247 207 .38 2.632 2.286 2.608 2.626 9.134 52 295 4.866 .52 90 4240 7220 29 38 267 276 -50 278 128 150 2.209 248 121 .453 1.918 1.143 .94
18 60 164 52 170 7 -6 56 130 55 201 3 -39 0 0 22 130 16 141 25 9 7 5 1 -36 null null null 6.739 6.407 8.209 52 319 43.137 .15 90 4390 7220 29 38 282 291 -50 138 143 -5 null 109 -33 null null null null
19 457 702 54 165 403 536 440 617 57 205 386 451 0 0 106 233 18 156 100 100 100 90 939 837 .752 1.33 1.168 1.258 1.163 3.95 32 235 1.398 .69 70 4560 7220 30 37 300 307 0 589 138 450 1.116 518 378 .896 .98 .158 -.028
20 2722 16253 55 187 2666 16065 2790 17194 59 207 2734 17007 0 0 554 4244 19 135 100 100 100 100 18731 19741 .166 6.026 6.221 5.895 6.19 2.892 32 217 6.216 .96 70 4710 7230 31 38 315 322 0 13638 157 13481 5.057 14428 14271 .198 5.22 2.338 2.384

Total number of rows: 44544

Table truncated, full table size 9675 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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