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Sample GSM989698 Query DataSets for GSM989698
Status Public on Aug 23, 2012
Title PC 393T
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 393T2
Organism Homo sapiens
Characteristics ethnicity: Caucasian
age: 48
pre-operation treatment: None
individual: PC 229T
disease free survival: 54.67
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/2008-08/81197.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 GPL15971
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 2606 1785 95 184 2510 1601 2771 1827 98 187 2676 1642 0 0 555 474 25 67 100 100 100 100 4111 4318 1.568 .638 .614 .626 .619 4.173 52 230 .621 .92 90 1770 6810 28 37 0 9 0 1725 178 1548 .617 1766 1587 1.622 .593 -.698 -.754
2 2642 1994 100 170 2542 1823 2723 2039 104 180 2623 1868 0 0 534 340 31 66 100 100 100 100 4365 4491 1.394 .717 .712 .724 .71 3.776 52 267 .684 .95 90 1930 6820 29 38 16 25 0 1927 164 1762 .693 1971 1806 1.443 .688 -.529 -.539
3 5158 5766 105 187 5052 5578 5426 5959 128 224 5320 5771 0 0 1035 1216 174 232 100 100 100 100 10630 11091 .906 1.104 1.085 1.111 1.118 3.804 52 285 1.069 .97 90 2080 6800 27 36 31 40 0 5574 181 5392 1.067 5760 5578 .937 1.049 .094 .068
4 3227 2213 106 192 3121 2020 3279 2204 139 231 3172 2011 0 0 335 448 203 236 100 100 100 100 5141 5183 1.545 .647 .634 .633 .661 3.786 52 308 .626 .95 90 2230 6800 27 36 46 55 0 2139 186 1953 .626 2130 1944 1.598 .613 -.677 -.706
5 288 260 102 175 185 85 293 262 115 189 190 86 0 0 77 71 105 90 85 43 41 12 270 276 2.176 .459 .453 .487 .522 9.864 80 404 .382 .54 110 2390 6800 26 37 61 72 0 251 169 82 .444 253 83 2.252 .438 -1.171 -1.193
6 4323 3723 105 180 4218 3543 4314 3654 108 189 4209 3473 0 0 885 771 27 67 100 100 100 100 7761 7682 1.191 .84 .825 .849 .838 3.719 80 336 .819 .97 110 2530 6810 27 38 75 86 0 3599 174 3425 .812 3532 3357 1.232 .798 -.301 -.326
7 194 274 111 194 83 79 195 274 121 199 83 79 0 0 46 78 65 73 63 51 15 19 162 162 1.051 .952 .952 1.175 1.238 8.265 52 264 .651 .32 90 2680 6820 29 38 91 100 0 265 188 76 .92 265 76 1.087 .92 -.12 -.12
8 5840 6293 104 191 5735 6102 5815 6284 123 212 5711 6093 0 0 522 549 118 144 100 100 100 100 11837 11804 .94 1.064 1.067 1.064 1.034 3.465 52 214 1.022 .97 80 2840 6800 28 36 108 116 0 6083 185 5898 1.028 6074 5890 .972 1.031 .041 .044
9 142 227 94 166 47 60 139 219 101 182 44 52 0 0 33 79 76 111 23 25 0 3 107 96 .783 1.277 1.182 1.677 1.575 9.97 120 388 1.089 .69 120 2980 6800 26 38 120 132 -50 219 160 58 1.234 212 50 .81 1.142 .303 .192
10 180 255 102 186 78 69 175 250 106 205 73 64 0 0 41 74 26 126 94 25 76 0 147 137 1.13 .885 .877 .957 1.11 11.085 52 215 .773 .31 80 3130 6800 28 36 137 145 0 246 180 67 .855 242 62 1.169 .847 -.226 -.239
11 313 412 98 172 214 239 319 408 101 182 220 236 0 0 72 92 24 62 98 96 95 87 453 456 .895 1.117 1.073 1.134 1.196 5.093 80 365 1.004 .79 100 3290 6800 27 37 152 162 0 398 166 231 1.08 394 228 .926 1.037 .11 .052
12 257 391 96 170 161 220 253 377 100 182 157 206 0 0 53 109 28 73 98 92 96 75 381 363 .732 1.366 1.312 1.303 1.427 5.281 80 374 1.388 .72 110 3450 6790 25 36 167 178 0 378 164 213 1.321 364 199 .757 1.268 .401 .343
13 238 309 95 165 142 144 225 278 100 175 129 113 0 0 75 140 29 69 100 75 93 40 286 242 .986 1.014 .876 .785 1.019 7.807 80 256 1.175 .71 100 3590 6790 26 36 182 192 0 299 159 139 .98 269 109 1.02 .847 -.029 -.24
14 174 363 97 184 77 179 176 361 101 196 78 177 0 0 37 106 25 74 91 83 76 64 256 255 .43 2.325 2.269 2.236 2.468 7.152 120 381 2.368 .58 120 3750 6790 25 37 197 209 0 351 178 173 2.247 349 171 .445 2.194 1.168 1.133
15 131 307 113 250 17 57 128 293 116 257 14 43 0 0 37 123 29 88 32 30 17 13 74 57 .298 3.353 3.071 3.143 2.825 7.805 52 131 3.245 .35 80 3900 6840 32 40 214 222 0 297 242 55 3.241 283 42 .309 2.969 1.696 1.57
16 521 752 114 234 407 518 545 771 116 241 431 537 0 0 124 175 24 79 98 98 98 96 925 968 .786 1.273 1.246 1.297 1.257 5.107 80 250 1.201 .87 100 4050 6800 27 37 228 238 0 727 226 501 1.23 745 519 .813 1.204 .299 .268
17 165 380 111 234 54 146 166 373 113 238 55 139 0 0 31 104 24 74 79 74 56 45 200 194 .37 2.704 2.527 2.72 3.048 10.01 120 349 2.801 .41 130 4190 6800 25 38 240 253 0 367 226 141 2.613 361 134 .383 2.443 1.386 1.289
18 134 295 113 238 20 57 129 297 116 241 16 59 0 0 38 93 25 69 38 43 23 21 77 75 .351 2.85 3.688 2.767 2.998 10.237 120 296 1.65 .31 120 4340 6810 27 39 256 268 0 285 230 55 2.755 287 57 .363 3.564 1.462 1.834
19 368 549 113 234 255 314 376 521 115 241 263 286 0 0 78 152 26 71 100 98 98 87 569 549 .812 1.231 1.087 1.161 1.185 5.288 80 324 1.231 .78 110 4510 6800 26 37 273 284 0 531 226 304 1.19 504 276 .84 1.051 .251 .072
20 788 3035 112 234 675 2800 796 3023 117 248 683 2788 0 0 85 379 35 113 100 100 100 100 3475 3471 .241 4.148 4.082 4.143 4.177 3.689 52 234 4.109 .94 90 4650 6790 26 35 288 297 0 2934 226 2707 4.01 2922 2695 .249 3.946 2.004 1.98

Total number of rows: 44544

Table truncated, full table size 9468 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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