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Sample GSM989815 Query DataSets for GSM989815
Status Public on Aug 23, 2012
Title PC 97N
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 97N2
Organism Homo sapiens
Characteristics individual: PC 97N
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/2008-08/81120.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 20419 31181 84 135 20335 31045 22574 31808 93 165 22490 31673 0 0 6167 2988 34 153 100 100 100 100 51380 54163 .655 1.527 1.408 1.736 1.373 2.724 52 354 1.483 .89 90 1780 6970 28 37 21 30 0 26023 113 25909 1.274 26546 26433 .785 1.175 .35 .233
2 20114 31436 102 127 20011 31309 25579 36927 109 145 25477 36799 0 0 9162 11506 35 83 100 100 100 100 51320 62276 .639 1.565 1.444 1.768 1.435 3.106 52 282 1.538 .91 90 1930 6970 28 37 36 45 0 26236 106 26130 1.306 30818 30711 .766 1.205 .385 .27
3 18267 24580 100 127 18166 24452 25040 31810 109 153 24939 31682 0 0 12601 14132 40 98 98 98 96 98 42618 56621 .743 1.346 1.27 1.896 1.249 5.377 80 290 1.257 .9 100 2090 6980 29 39 52 62 0 20514 106 20407 1.123 26548 26441 .89 1.06 .168 .084
4 20877 32369 99 151 20778 32218 26797 37515 107 184 26698 37363 0 0 10160 11639 42 209 100 100 100 98 52996 64061 .645 1.551 1.399 1.998 1.437 4.536 80 346 1.481 .93 110 2240 6970 27 38 66 77 0 27014 126 26888 1.294 31309 31182 .773 1.168 .372 .224
5 986 331 106 151 880 179 981 324 116 196 875 172 0 0 114 115 52 265 100 21 100 0 1059 1047 4.916 .203 .197 .154 .187 3.116 32 196 .198 .62 70 2380 6960 28 35 82 89 0 276 126 149 .17 270 144 5.891 .164 -2.558 -2.608
6 12364 25296 139 168 12225 25128 14069 26576 176 187 13929 26407 0 0 4729 5690 101 111 100 100 100 100 37353 40336 .487 2.055 1.896 2.482 1.882 3.433 80 390 2.014 .92 110 2540 6970 27 38 96 107 0 21111 140 20971 1.715 22180 22038 .583 1.582 .779 .662
7 300 267 104 163 196 103 313 237 110 194 208 73 0 0 74 169 42 145 94 25 90 3 299 281 1.903 .526 .351 .51 .453 3.782 52 203 1.133 .39 80 2690 6960 28 36 113 121 0 223 136 86 .439 198 61 2.28 .293 -1.189 -1.772
8 28728 45900 100 166 28627 45734 36373 49300 112 195 36272 49134 0 0 14170 11339 53 143 100 100 100 100 74361 85406 .626 1.598 1.355 2.503 1.386 5.645 52 278 1.465 .9 90 2840 6970 28 37 127 136 0 38307 139 38168 1.333 41144 41006 .75 1.131 .415 .177
9 209 250 87 132 122 118 191 248 93 159 104 116 0 0 56 84 30 90 100 62 90 25 240 220 1.034 .967 1.115 .949 1.193 2.733 32 160 2.143 .36 60 2980 6950 28 34 143 149 0 209 110 98 .807 207 97 1.239 .931 -.309 -.103
10 186 289 81 141 105 148 200 287 84 166 119 145 0 0 76 103 24 97 75 76 69 26 253 264 .709 1.41 1.218 1.656 1.356 3.741 52 276 2.312 .57 90 3120 6950 26 35 155 164 -50 241 118 124 1.176 240 121 .85 1.017 .234 .024
11 562 1555 80 139 482 1416 667 1616 87 161 587 1477 0 0 337 541 30 94 80 98 76 94 1898 2064 .34 2.938 2.516 3.716 2.634 4.195 52 247 2.753 .84 80 3270 6960 28 36 171 179 0 1298 116 1182 2.452 1349 1233 .408 2.1 1.294 1.07
12 512 3101 81 148 430 2953 623 3082 87 183 542 2934 0 0 237 583 30 191 86 100 84 100 3383 3476 .146 6.867 5.413 8.484 5.407 3.9 52 278 6.885 .83 90 3430 6960 27 36 186 195 0 2588 124 2464 5.731 2572 2449 .174 4.518 2.519 2.176
13 371 382 83 141 288 240 422 375 87 163 339 233 0 0 134 188 25 100 96 80 96 57 528 572 1.2 .833 .687 .758 .724 2.815 52 286 1.187 .54 90 3590 6950 26 35 202 211 0 319 118 200 .695 313 194 1.438 .574 -.524 -.802
14 303 462 83 162 220 299 300 457 90 189 217 295 0 0 51 126 25 136 100 93 100 59 519 512 .736 1.359 1.359 1.241 1.302 2.332 32 196 2.434 .55 70 3730 6950 27 34 217 224 0 386 135 250 1.134 381 246 .882 1.135 .182 .182
15 65 88 80 148 -15 -59 62 87 89 183 -17 -61 0 0 14 42 30 167 0 0 0 0 -74 -78 null null null 4.154 2.928 3.627 52 271 34.268 .15 90 3880 6950 26 35 231 240 -50 73 124 -49 null 73 -51 null null null null
16 1506 1783 86 148 1419 1635 1820 1909 93 213 1733 1761 0 0 757 555 48 382 92 93 86 90 3054 3494 .868 1.152 1.016 1.429 1.003 3.8 80 295 1.01 .86 100 4040 6960 27 37 247 257 0 1488 124 1365 .962 1593 1470 1.04 .848 -.056 -.238
17 136 301 81 137 54 163 122 266 88 195 41 128 0 0 72 189 37 202 53 23 17 7 217 169 .331 3.019 3.122 3.175 2.5 3.642 52 228 9.897 .38 80 4200 6940 26 34 264 272 0 251 114 136 2.519 222 107 .397 2.605 1.333 1.382
18 74 99 76 137 -2 -38 70 92 84 183 -6 -45 0 0 21 64 34 153 3 1 1 0 -40 -51 null null null 4.816 4.004 4.232 52 249 6.172 .58 90 4340 6940 25 34 277 286 -50 83 114 -32 null 77 -38 null null null null
19 416 588 76 137 339 451 474 594 82 168 397 456 0 0 195 175 24 114 88 96 83 93 790 853 .752 1.33 1.149 1.466 1.221 3.36 80 293 1.336 .62 100 4490 6950 26 36 292 302 0 491 114 376 1.11 496 381 .901 .959 .151 -.061
20 1424 6699 84 146 1339 6552 1674 8213 100 192 1589 8066 0 0 1049 3264 120 171 73 96 68 93 7891 9655 .204 4.893 5.076 8.52 4.293 5.098 80 293 4.678 .86 100 4650 6950 26 36 308 318 0 5591 122 5468 4.084 6854 6732 .245 4.236 2.03 2.083

Total number of rows: 44544

Table truncated, full table size 9647 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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