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Sample GSM989722 Query DataSets for GSM989722
Status Public on Aug 23, 2012
Title PC 184T
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 184T2
Organism Homo sapiens
Characteristics ethnicity: Caucasian
age: 56
pre-operation treatment: None
individual: PC 370T
disease free survival: 15.83
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/2008-08/81107.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 16829 15485 101 61 16727 15423 19081 17904 117 72 18979 17842 0 0 5231 6002 58 42 100 100 100 100 32150 36821 1.085 .922 .94 .861 .948 1.933 32 236 .957 .93 70 1750 7320 40 47 19 26 0 15024 59 14964 .895 17371 17311 1.118 .912 -.161 -.133
2 15002 13551 112 74 14890 13476 16766 18095 121 77 16654 18020 0 0 6076 7909 43 32 100 100 100 96 28366 34674 1.105 .905 1.082 .61 .961 2.944 32 231 .999 .95 70 1910 7320 40 47 35 42 0 13148 72 13075 .878 17556 17484 1.139 1.05 -.188 .07
3 16813 32922 118 76 16694 32846 17313 29416 129 84 17195 29340 0 7 13573 27046 53 43 98 100 98 100 49540 46535 .508 1.968 1.706 1.864 1.938 3.043 52 275 2.04 .95 80 2060 7330 41 49 50 58 0 31942 74 31868 1.909 28540 28467 .524 1.656 .933 .727
4 12875 12596 117 76 12757 12520 16858 15561 140 88 16740 15485 0 0 7088 6957 69 46 100 98 100 96 25277 32225 1.019 .981 .925 .773 .957 2.954 52 273 .978 .95 80 2210 7320 40 48 65 73 0 12221 74 12147 .952 15098 15024 1.05 .897 -.071 -.156
5 1326 338 139 86 1187 252 1434 350 162 97 1294 263 0 0 259 100 73 52 100 96 100 90 1439 1557 4.71 .212 .203 .19 .219 1.835 32 175 .21 .88 60 2360 7320 41 47 81 87 0 328 83 244 .206 340 255 4.855 .197 -2.279 -2.342
6 12255 18748 202 129 12053 18619 14295 21759 211 141 14093 21629 0 0 4388 7476 70 56 100 100 100 100 30672 35722 .647 1.545 1.535 1.393 1.534 2.038 52 292 1.597 .96 80 2510 7320 40 48 95 103 0 18190 125 18065 1.499 21111 20985 .667 1.489 .584 .574
7 408 239 145 102 263 136 413 233 147 109 268 130 0 0 64 36 47 43 100 100 100 91 399 398 1.934 .517 .485 .518 .51 1.589 12 104 .551 .77 50 2660 7330 42 47 111 116 0 232 99 132 .502 226 126 1.993 .471 -.995 -1.087
8 26671 48778 119 86 26552 48692 28549 58635 129 100 28429 58549 0 12 7845 21699 51 58 100 100 100 100 75244 86978 .545 1.834 2.059 1.455 2.014 2.343 32 219 2.059 .95 70 2810 7320 40 47 125 132 -100 47326 83 47242 1.779 56889 56806 .562 1.998 .831 .999
9 146 203 98 66 48 136 141 200 110 78 43 133 0 0 44 41 39 87 50 91 16 8 184 176 .353 2.833 3.093 2.828 2.874 2.637 12 104 4.625 .37 50 2960 7310 40 45 141 146 0 197 64 132 2.749 194 129 .364 3.001 1.459 1.585
10 114 168 92 58 22 110 108 98 95 66 16 40 0 0 31 124 29 35 38 50 9 44 132 56 .2 5 2.5 4.189 3.966 3.993 52 334 4.329 .53 90 3110 7310 38 47 154 163 -50 163 56 107 4.851 95 39 .206 2.426 2.278 1.278
11 796 1100 97 55 699 1044 669 1098 121 67 572 1042 0 0 852 394 148 52 100 100 96 96 1743 1614 .67 1.494 1.822 1.606 1.84 1.98 32 215 .121 .56 70 3270 7320 40 47 171 178 0 1067 53 1013 1.449 1065 1011 .69 1.767 .535 .822
12 318 1044 97 54 221 990 288 1185 129 72 191 1131 0 0 188 438 170 82 53 98 11 98 1211 1322 .223 4.48 5.921 4.917 4.79 2.129 52 298 3.24 .48 90 3410 7320 39 48 184 193 0 1013 52 961 4.346 1150 1097 .23 5.745 2.12 2.522
13 331 281 90 58 240 222 325 286 95 64 235 227 0 0 58 71 32 31 100 100 100 100 462 462 1.081 .925 .966 .895 .908 1.632 32 208 .89 .79 70 3560 7320 40 47 200 207 0 273 56 215 .897 277 220 1.114 .937 -.156 -.094
14 259 266 87 56 171 210 265 275 95 67 177 219 0 0 84 84 34 61 96 90 87 84 381 396 .814 1.228 1.237 1.266 1.253 1.953 32 162 1.184 .84 60 3710 7330 42 48 216 222 0 258 54 204 1.192 267 212 .839 1.2 .253 .264
15 96 45 92 59 3 -14 93 40 97 66 0 -19 0 0 25 22 33 48 11 1 1 0 -11 -19 null null null 1.732 1.678 3.695 52 313 2.666 .38 90 3860 7320 39 48 229 238 -50 44 57 -14 null 39 -18 null null null null
16 2791 2388 94 61 2697 2326 3025 2534 104 71 2931 2472 0 0 807 599 72 45 100 100 100 100 5023 5403 1.16 .862 .843 .873 .852 1.474 32 228 .84 .94 70 4010 7310 39 46 245 252 0 2317 59 2257 .837 2459 2398 1.195 .818 -.257 -.289
17 135 151 93 48 42 102 141 156 99 57 48 108 0 0 26 47 38 30 58 91 0 75 144 156 .412 2.429 2.25 2.933 2.446 3.351 12 104 1.483 .51 50 4170 7310 40 45 262 267 0 147 47 99 2.356 151 105 .424 2.183 1.237 1.126
18 84 48 88 57 -3 -9 81 43 95 67 -6 -14 0 0 24 25 36 40 7 7 1 1 -12 -20 null null null 1.346 1.259 3.613 52 337 .979 .4 90 4320 7310 38 47 275 284 -50 47 55 -9 null 42 -14 null null null null
19 441 444 89 59 351 385 438 461 96 66 348 401 0 0 109 154 35 36 100 100 100 96 736 749 .912 1.097 1.152 1.016 1.037 1.82 52 280 1.155 .86 80 4480 7310 39 47 292 300 0 431 57 374 1.064 447 389 .94 1.118 .09 .161
20 2293 5358 88 53 2205 5304 2804 7036 96 59 2715 6982 0 0 1256 3153 35 31 98 100 96 100 7509 9697 .416 2.405 2.572 2.721 2.524 2.587 52 256 2.524 .95 80 4620 7320 40 48 306 314 0 5198 51 5146 2.334 6827 6774 .428 2.495 1.223 1.319

Total number of rows: 44544

Table truncated, full table size 9366 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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