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Sample GSM989746 Query DataSets for GSM989746
Status Public on Aug 23, 2012
Title PC 163T
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 163T2
Organism Homo sapiens
Characteristics ethnicity: Caucasian
age: 61
pre-operation treatment: None
individual: PC 103T
disease free survival: 5.90
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/2008-09/81278.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 2477 1962 60 76 2417 1886 2868 2101 63 86 2808 2025 0 0 985 940 21 49 100 97 98 93 4303 4833 1.282 .78 .721 .715 .779 5.214 80 447 .768 .93 100 1780 7210 32 42 25 35 0 1824 71 1753 .725 1953 1883 1.378 .67 -.463 -.577
2 3633 2673 65 82 3568 2591 3777 2817 68 95 3711 2734 0 0 575 807 23 54 100 100 100 100 6159 6445 1.377 .726 .737 .677 .74 3.292 52 275 .725 .94 90 1930 7210 32 41 40 49 0 2485 76 2409 .675 2619 2542 1.481 .685 -.567 -.546
3 13247 15131 72 101 13174 15030 15045 17470 75 115 14973 17369 0 0 4389 5672 27 68 100 100 100 100 28204 32342 .877 1.141 1.16 1.056 1.167 4.021 80 324 1.144 .97 100 2090 7210 32 42 56 66 0 14068 94 13974 1.061 16243 16149 .943 1.079 .085 .109
4 3836 2946 69 95 3766 2850 3913 3029 72 109 3843 2934 0 0 493 748 25 65 100 100 100 100 6616 6777 1.321 .757 .763 .714 .767 3.255 80 335 .767 .95 110 2240 7210 31 42 70 81 0 2739 88 2650 .704 2816 2728 1.421 .71 -.507 -.494
5 785 360 67 92 717 268 809 331 75 112 741 238 0 0 219 143 36 74 100 93 100 77 985 979 2.675 .374 .321 .337 .338 4.81 80 270 .319 .72 100 2380 7210 32 42 85 95 0 335 86 249 .348 308 221 2.878 .299 -1.525 -1.744
6 9377 9820 92 133 9285 9686 9442 9677 112 158 9349 9544 0 0 1183 1087 65 104 100 100 100 100 18971 18893 .959 1.043 1.021 1.046 1.041 2.389 80 336 1.011 .98 110 2530 7210 31 42 99 110 0 9130 124 9005 .97 8997 8873 1.031 .949 -.044 -.075
7 245 172 94 142 151 30 245 155 109 161 151 13 0 0 62 79 59 99 92 17 71 5 181 164 5.033 .199 .086 .319 .381 8.675 52 216 .458 .3 90 2690 7220 33 42 116 125 0 160 132 28 .185 144 12 5.414 .08 -2.437 -3.643
8 12311 14187 78 106 12232 14080 15027 17333 85 123 14948 17226 0 0 5579 6605 34 71 100 100 100 100 26312 32174 .869 1.151 1.152 1.125 1.164 3.683 120 390 1.138 .97 120 2840 7210 31 43 130 142 0 13190 99 13091 1.07 16115 16016 .934 1.071 .098 .1
9 310 255 78 115 231 139 315 238 83 127 236 123 0 0 70 99 33 70 100 77 98 40 370 359 1.662 .602 .521 .5 .577 4.76 80 289 .576 .59 100 2990 7210 32 42 146 156 0 237 107 129 .559 221 114 1.787 .485 -.838 -1.045
10 287 291 66 89 221 202 278 252 70 101 212 162 0 0 148 209 26 55 100 91 96 72 423 374 1.094 .914 .764 .785 .845 5.591 80 286 .77 .52 100 3140 7210 32 42 161 171 0 271 83 188 .85 234 151 1.177 .71 -.235 -.493
11 908 1462 61 76 847 1386 1019 1610 64 86 957 1534 0 0 433 716 23 51 96 94 95 93 2233 2491 .611 1.636 1.603 1.554 1.684 4.699 120 329 1.598 .93 120 3290 7210 31 43 175 187 0 1359 71 1289 1.521 1497 1426 .657 1.49 .605 .576
12 764 1280 62 74 702 1206 854 1395 66 87 791 1320 0 0 339 542 22 54 95 97 92 94 1908 2111 .582 1.718 1.669 1.885 1.733 3.895 120 344 1.652 .94 120 3430 7210 31 43 189 201 0 1190 69 1121 1.597 1297 1227 .626 1.552 .676 .634
13 560 482 63 82 497 400 547 482 67 93 484 400 0 0 142 167 23 60 100 98 100 96 897 884 1.243 .805 .826 .746 .784 3.549 80 352 .745 .86 110 3590 7200 30 41 205 216 0 448 76 372 .748 448 372 1.336 .768 -.418 -.38
14 317 345 60 82 256 263 307 322 64 90 246 240 0 0 81 128 22 54 100 100 100 96 519 486 .973 1.027 .976 .975 .998 3.981 80 301 .95 .73 110 3740 7200 30 41 220 231 0 321 76 245 .955 299 223 1.047 .907 -.066 -.141
15 184 168 60 77 124 90 180 146 64 87 120 68 0 0 70 104 22 46 91 61 85 40 214 188 1.378 .726 .567 .697 .724 5.709 120 356 .673 .48 120 3890 7200 30 42 235 247 0 156 72 84 .675 136 63 1.482 .527 -.567 -.925
16 1937 2431 68 85 1868 2346 1972 2431 74 95 1903 2346 0 0 392 552 25 52 100 100 100 100 4214 4249 .796 1.256 1.233 1.253 1.234 2.759 80 301 1.228 .95 110 4040 7200 30 41 250 261 0 2260 79 2181 1.168 2260 2181 .856 1.146 .224 .197
17 341 430 72 79 269 351 326 392 75 89 254 313 0 0 91 181 25 51 100 100 100 97 620 567 .766 1.305 1.232 1.22 1.226 3.47 80 324 1.266 .81 110 4190 7200 30 41 265 276 0 400 73 326 1.213 364 291 .824 1.146 .279 .196
18 133 136 66 79 67 57 130 117 68 89 64 38 0 0 55 79 22 49 75 44 64 23 124 102 1.175 .851 .594 .85 .964 8.185 120 376 .662 .33 120 4340 7200 30 42 280 292 -100 126 73 53 .791 109 35 1.264 .552 -.338 -.857
19 816 924 66 77 749 847 819 895 70 89 753 817 0 0 168 288 24 49 100 100 100 100 1596 1570 .884 1.131 1.085 1.093 1.106 3.105 80 290 1.021 .87 110 4490 7200 30 41 295 306 0 859 72 787 1.051 832 760 .951 1.009 .072 .013
20 3294 7683 68 83 3225 7599 3379 7669 72 93 3311 7586 0 0 562 926 25 52 100 100 100 100 10824 10897 .424 2.356 2.291 2.388 2.321 2.629 80 320 2.309 .96 110 4640 7200 30 41 310 321 0 7143 77 7065 2.191 7130 7053 .456 2.13 1.131 1.091

Total number of rows: 44544

Table truncated, full table size 9646 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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