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Sample GSM989811 Query DataSets for GSM989811
Status Public on Aug 23, 2012
Title PC 527T
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 527T
Organism Homo sapiens
Characteristics individual: PC 527T
disease state: Tumor
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/2007-12/77939.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 1198 528 45 66 1153 462 1331 541 46 86 1286 475 0 0 777 350 8 66 96 78 96 73 1615 1761 2.496 .401 .369 .393 .394 3.253 80 436 .371 .84 100 1790 6770 20 30 34 44 0 951 119 832 .722 975 856 1.385 .666 -.47 -.587
2 3119 1342 48 67 3071 1275 2941 1206 50 86 2893 1139 0 0 994 574 11 66 100 100 100 100 4346 4032 2.409 .415 .394 .397 .413 1.322 52 233 .42 .95 90 1940 6780 21 30 49 58 0 2418 121 2297 .748 2173 2052 1.337 .709 -.419 -.495
3 7729 4690 52 93 7677 4597 7472 4340 158 163 7420 4247 0 0 2078 1508 1075 561 100 100 100 100 12274 11667 1.67 .599 .572 .587 .612 1.198 52 339 .583 .96 90 2080 6740 17 26 63 72 0 8451 168 8283 1.079 7820 7653 .927 1.031 .11 .045
4 7199 3617 55 118 7144 3499 7424 3472 167 183 7369 3354 0 0 2478 1254 1101 573 93 96 92 95 10643 10723 2.042 .49 .455 .525 .479 2.013 80 323 .491 .95 100 2240 6770 20 30 79 89 0 6517 213 6305 .883 6256 6044 1.133 .82 -.18 -.286
5 564 158 60 119 504 39 546 151 71 133 486 32 0 0 121 93 32 83 100 30 100 9 543 518 12.923 .077 .066 .171 .183 2.157 52 234 .069 .18 90 2390 6770 20 29 94 103 0 285 214 70 .139 272 58 7.172 .119 -2.842 -3.075
6 5864 2678 82 118 5782 2560 5373 2467 91 135 5291 2349 0 0 1679 932 39 93 100 100 100 100 8342 7640 2.259 .443 .444 .431 .439 1.233 80 310 .472 .94 110 2540 6770 19 30 108 119 0 4825 213 4613 .798 4445 4233 1.253 .8 -.326 -.322
7 163 137 63 123 100 14 181 128 78 144 118 5 0 0 81 89 44 97 65 15 58 4 114 123 7.143 .14 .042 .877 .67 6.5 120 420 5.903 .07 120 2690 6770 19 31 123 135 -50 247 222 25 .252 231 9 3.964 .076 -1.987 -3.711
8 14750 9148 56 106 14694 9042 15842 9594 67 130 15786 9488 0 0 5375 3091 35 94 100 100 100 100 23736 25274 1.625 .615 .601 .661 .607 1.829 80 398 .61 .96 110 2840 6770 19 30 138 149 0 16484 191 16293 1.109 17287 17096 .902 1.083 .149 .115
9 167 102 80 98 87 4 167 102 93 115 87 4 0 0 28 58 45 81 91 8 50 0 91 91 21.75 .046 .046 .479 .696 1.996 12 89 -2.105 -.27 50 3000 6800 25 30 157 162 0 184 177 7 .083 184 7 12.071 .083 -3.593 -3.593
10 195 103 55 106 140 -3 194 78 70 119 139 -28 0 0 44 79 41 81 100 12 90 3 137 111 null null null .473 .414 2.229 32 130 -2.904 -.18 60 3160 6780 23 29 173 179 0 186 191 -5 null 141 -50 null null null null
11 540 453 50 108 490 345 507 431 52 128 457 323 0 0 246 246 11 85 97 85 96 72 835 780 1.42 .704 .707 .658 .684 3.113 80 277 .742 .81 100 3300 6770 20 30 185 195 0 816 195 622 1.269 777 582 .788 1.274 .343 .349
12 389 367 50 102 339 265 363 369 51 117 313 267 0 0 109 177 10 77 100 87 100 71 604 580 1.279 .782 .853 .676 .766 2.09 80 287 .998 .7 110 3440 6770 19 30 198 209 0 661 184 477 1.409 665 481 .71 1.537 .494 .62
13 323 126 50 128 273 -2 315 117 52 156 265 -11 0 0 71 74 11 109 100 2 100 1 271 254 null null null .161 .185 2.76 80 224 -.042 -.04 100 3590 6770 20 30 214 224 0 227 231 -4 null 211 -20 null null null null
14 205 225 49 113 156 112 209 199 51 137 160 86 0 0 42 112 9 91 100 47 100 26 268 246 1.393 .718 .538 .586 .661 2.818 80 236 2.111 .37 110 3730 6770 19 30 227 238 0 405 204 202 1.294 359 155 .773 .969 .371 -.046
15 61 71 51 113 10 -42 60 46 58 133 9 -67 0 0 13 59 35 97 3 2 0 0 -32 -58 null null null 5.704 8.125 3.843 120 420 -32.42 -.09 120 3880 6760 18 30 242 254 -100 128 204 -76 null 83 -121 null null null null
16 1063 1041 51 107 1012 934 1074 978 58 128 1023 871 0 0 395 382 34 102 98 98 98 96 1946 1894 1.084 .923 .851 .969 .932 1.681 80 314 .922 .92 110 4040 6760 18 29 258 269 0 1876 193 1683 1.663 1762 1569 .601 1.534 .734 .617
17 110 92 50 107 60 -15 110 66 51 124 60 -41 0 0 37 80 10 81 88 12 80 5 45 19 null null null 1.36 1.632 5.063 120 314 -9.982 -.2 120 4190 6760 18 30 273 285 -50 166 193 -27 null 119 -74 null null null null
18 56 83 53 110 3 -27 55 64 59 130 2 -46 0 0 10 67 27 88 0 7 0 0 -24 -44 null null null 9.574 10.857 2.639 120 400 -1 -1 120 4340 6760 18 30 288 300 -100 150 198 -49 null 115 -83 null null null null
19 451 258 57 122 394 136 433 232 90 149 376 110 0 0 155 144 170 150 97 41 61 13 530 486 2.897 .345 .293 .302 .408 2.465 80 355 .427 .51 100 4500 6770 20 30 305 315 0 465 220 245 .622 418 198 1.608 .527 -.685 -.924
20 1913 4477 54 122 1859 4355 1801 4234 81 147 1747 4112 0 0 482 1118 169 150 100 100 100 100 6214 5859 .427 2.343 2.354 2.355 2.317 1.216 80 358 2.433 .95 110 4640 6760 18 29 318 329 0 8067 220 7847 4.221 7629 7409 .237 4.241 2.078 2.084

Total number of rows: 44544

Table truncated, full table size 9539 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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