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Sample GSM989760 Query DataSets for GSM989760
Status Public on Aug 23, 2012
Title PC 610T
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 610T2
Organism Homo sapiens
Characteristics ethnicity: Caucasian
age: 53
pre-operation treatment: None
individual: PC 22T
disease free survival: 85.33
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/2008-09/81299.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
1 267 481 57 139 209 341 171 336 63 146 114 196 0 0 254 422 23 99 96 65 87 50 550 310 .613 1.632 1.719 1.568 1.69 4.948 32 235 1.712 .79 70 1830 7080 36 43 19 26 0 381 110 270 1.294 266 155 .773 1.363 .372 .447
2 1660 2206 60 156 1600 2050 2005 2625 63 170 1945 2469 0 0 977 1477 23 115 98 80 96 78 3650 4414 .78 1.281 1.269 1.246 1.228 3.732 52 236 1.334 .91 80 1990 7110 39 47 35 43 0 1749 124 1626 1.016 2082 1958 .984 1.007 .023 .01
3 1406 2038 63 161 1342 1877 1481 2002 66 182 1417 1840 0 0 483 818 24 137 96 98 95 96 3219 3257 .715 1.399 1.299 1.494 1.337 4.056 80 287 1.429 .91 100 2140 7100 37 47 49 59 0 1616 128 1488 1.109 1588 1459 .902 1.03 .149 .042
4 2721 3445 66 177 2654 3268 2727 3483 71 195 2660 3306 0 0 442 786 30 136 100 100 100 100 5922 5966 .812 1.231 1.243 1.21 1.22 2.555 80 317 1.235 .93 110 2280 7100 36 47 62 73 0 2732 140 2592 .976 2762 2622 1.024 .986 -.034 -.021
5 216 219 72 164 144 54 210 189 78 196 137 25 0 0 57 123 34 139 98 23 92 5 198 162 2.667 .375 .182 .567 .997 7.818 52 211 .126 .03 90 2450 7100 37 46 80 89 0 174 130 43 .297 150 20 3.363 .145 -1.75 -2.789
6 1344 1588 68 164 1275 1423 1346 1577 76 195 1277 1412 0 0 291 474 37 137 100 100 100 100 2698 2689 .896 1.116 1.106 1.083 1.134 2.785 80 360 1.095 .9 110 2580 7100 36 47 92 103 0 1259 130 1128 .885 1251 1120 1.13 .877 -.176 -.19
7 122 180 61 150 60 29 116 140 66 180 54 -9 0 0 48 128 26 139 67 23 50 5 89 45 2.069 .483 null 2.957 3.215 9.322 52 247 -37.983 -.06 80 2740 7080 36 44 110 118 0 143 119 23 .383 111 -7 2.609 null -1.383 null
8 1741 2449 67 178 1673 2270 1774 2428 79 218 1707 2249 0 0 392 713 41 153 100 100 100 100 3943 3956 .737 1.357 1.318 1.344 1.32 2.815 80 436 1.332 .93 110 2880 7100 36 47 122 133 0 1942 141 1800 1.076 1925 1783 .929 1.045 .106 .063
9 132 323 82 166 50 157 137 384 95 209 55 218 0 0 31 230 50 246 58 50 8 8 207 273 .318 3.14 3.964 2.426 4.643 14.764 12 104 -45.544 -.05 50 3020 7070 36 41 139 144 0 256 132 125 2.49 305 173 .402 3.143 1.316 1.652
10 104 232 69 220 34 11 101 216 78 251 31 -4 0 0 44 129 41 181 41 10 12 1 45 27 3.091 .324 null 2.367 2.457 11.169 120 540 22.9 .09 120 3180 7070 33 45 152 164 -50 184 174 9 .257 171 -3 3.898 null -1.963 null
11 200 424 73 199 127 225 190 393 85 236 117 194 0 0 83 301 49 146 78 53 56 34 352 311 .564 1.772 1.658 2.268 2.157 4.456 32 213 3.284 .49 70 3340 7070 35 42 170 177 0 336 158 178 1.405 312 154 .712 1.315 .491 .395
12 202 344 72 223 130 121 198 323 81 240 126 99 0 0 95 189 37 157 82 36 65 13 251 225 1.074 .931 .786 1.353 1.399 9.933 52 370 2.231 .44 90 3490 7070 34 43 184 193 0 273 177 96 .738 256 79 1.355 .623 -.438 -.682
13 270 408 73 202 196 205 248 327 80 220 174 125 0 0 115 249 34 149 98 48 94 32 401 299 .956 1.046 .718 .87 1.121 7.511 52 260 1.605 .41 80 3650 7090 37 45 201 209 0 324 160 163 .829 259 99 1.206 .57 -.27 -.812
14 135 285 71 247 63 37 100 264 78 271 28 16 0 0 90 208 42 174 46 25 28 6 100 44 1.703 .587 .571 2.706 3.434 8.154 32 158 5.618 .34 60 3790 7080 37 43 216 222 0 226 196 29 .466 209 13 2.147 .453 -1.102 -1.142
15 115 151 67 212 47 -60 110 132 78 244 42 -80 0 0 39 104 41 164 50 5 14 0 -13 -38 null null null 1.36 1.048 11.552 120 501 -24.967 -.09 120 3940 7090 35 47 228 240 -100 120 168 -48 null 105 -63 null null null null
16 216 350 63 180 152 170 213 337 73 218 149 157 0 0 65 194 39 156 97 50 83 18 322 306 .894 1.118 1.054 1.199 1.342 5.406 80 286 3.149 .27 100 4100 7100 37 47 245 255 0 278 143 135 .887 267 125 1.127 .836 -.173 -.259
17 115 233 63 199 51 33 116 208 69 225 52 8 0 0 43 216 28 160 68 12 44 5 84 60 1.545 .647 .154 2.04 1.665 10.058 120 440 -1 -1 120 4240 7080 34 46 258 270 -100 185 158 26 .513 165 6 1.949 .122 -.963 -3.035
18 90 175 68 192 22 -16 87 143 76 213 19 -49 0 0 38 122 37 151 31 11 6 0 6 -30 null null null 3.069 3.201 8.818 120 466 -32.048 -.08 120 4390 7080 34 46 273 285 -100 139 152 -13 null 113 -39 null null null null
19 142 275 74 174 68 101 135 249 92 194 60 74 0 0 53 156 50 123 59 40 25 18 169 134 .673 1.485 1.233 2.485 1.896 10.647 32 144 4.84 .29 60 4520 7070 36 42 289 295 0 218 138 80 1.178 197 59 .849 .978 .236 -.032
20 287 1508 73 189 213 1318 282 1473 89 213 208 1283 0 0 88 588 56 143 97 98 88 97 1531 1491 .162 6.188 6.168 6.146 6.709 3.477 80 463 7.181 .81 110 4690 7100 36 47 303 314 0 1196 150 1045 4.907 1168 1017 .204 4.892 2.295 2.29

Total number of rows: 44544

Table truncated, full table size 9746 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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