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Sample GSM989819 Query DataSets for GSM989819
Status Public on Aug 23, 2012
Title PC 564N
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 564N2
Organism Homo sapiens
Characteristics individual: PC 564N
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/2008-08/81201.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 15064 8326 72 125 14991 8201 15459 8637 79 139 15387 8512 0 0 2851 1955 30 72 100 100 100 100 23192 23899 1.828 .547 .553 .535 .549 3.108 52 363 .546 .95 90 1830 7240 31 40 22 31 0 14205 213 13991 .933 14735 14522 1.071 .944 -.1 -.083
2 15823 8926 90 147 15733 8779 16750 8763 97 191 16659 8616 0 0 3350 1065 39 253 100 100 100 100 24512 25275 1.792 .558 .517 .578 .519 3.507 52 251 .521 .96 90 1980 7250 32 41 37 46 0 15228 251 14977 .952 14950 14699 1.05 .882 -.071 -.181
3 16675 9735 75 125 16599 9610 19294 11182 84 158 19218 11057 0 0 6160 3276 37 221 100 100 100 100 26209 30275 1.727 .579 .575 .607 .565 4.06 80 330 .558 .98 100 2140 7230 30 40 53 63 0 16608 213 16395 .988 19077 18864 1.012 .982 -.018 -.027
4 13194 7784 74 112 13119 7671 15180 8596 80 123 15106 8483 0 0 4879 2624 33 61 100 100 100 100 20790 23589 1.71 .585 .562 .613 .562 4.181 80 269 .559 .97 100 2290 7240 31 41 68 78 0 13280 191 13087 .998 14665 14472 1.002 .958 -.004 -.062
5 1309 265 87 110 1221 155 1212 267 114 128 1125 156 0 0 446 106 70 66 100 75 100 53 1376 1281 7.877 .127 .139 .094 .12 6.522 52 220 .336 .38 90 2440 7230 30 39 83 92 0 452 188 264 .217 456 266 4.617 .237 -2.207 -2.08
6 8088 6873 75 106 8012 6767 10362 8377 102 128 10287 8271 0 0 4951 4033 71 93 100 100 100 99 14779 18558 1.184 .845 .804 .852 .807 4.373 120 357 .814 .97 120 2590 7240 30 42 97 109 0 11726 181 11545 1.441 14292 14111 .694 1.372 .527 .456
7 322 243 72 106 250 137 312 227 85 128 240 121 0 0 85 117 53 129 98 43 97 11 387 361 1.825 .548 .504 .444 .514 7.272 80 292 .668 .41 110 2740 7240 30 41 112 123 0 415 181 234 .935 387 206 1.07 .86 -.097 -.217
8 18096 10456 78 121 18017 10334 21801 11744 90 129 21722 11622 0 0 7726 4032 44 61 100 100 100 100 28351 33344 1.743 .574 .535 .625 .559 3.947 80 289 .551 .98 100 2900 7230 30 40 129 139 0 17838 206 17630 .979 20036 19828 1.022 .913 -.031 -.132
9 252 156 75 115 176 41 261 140 83 126 185 25 0 0 59 102 34 61 100 36 95 18 217 210 4.293 .233 .135 .417 .471 8.382 80 248 .087 .07 100 3050 7240 31 41 144 154 0 266 196 70 .397 239 43 2.516 .231 -1.331 -2.117
10 322 327 68 118 253 208 317 322 74 131 249 204 0 0 48 102 26 61 100 96 100 75 461 453 1.216 .822 .819 .755 .854 4.273 52 259 .824 .68 90 3200 7240 31 40 159 168 0 558 201 355 1.403 549 348 .713 1.398 .488 .483
11 815 978 66 115 749 862 829 953 73 126 763 837 0 0 263 353 29 63 100 100 100 100 1611 1600 .869 1.151 1.097 1.142 1.12 4.07 80 351 1.09 .9 100 3350 7230 30 40 174 184 0 1669 196 1471 1.963 1626 1428 .509 1.872 .973 .904
12 622 490 61 123 560 367 636 490 64 132 575 367 0 0 155 155 18 63 100 97 100 95 927 942 1.526 .655 .638 .616 .637 4.509 80 325 .601 .8 110 3500 7230 29 40 188 199 0 836 210 626 1.118 836 626 .894 1.089 .161 .123
13 416 226 63 120 353 106 430 205 67 129 367 85 0 0 111 102 22 61 100 65 97 31 459 452 3.33 .3 .232 .285 .286 7.434 80 297 .221 .39 100 3650 7230 30 40 204 214 0 386 205 181 .512 350 145 1.952 .395 -.965 -1.34
14 318 427 64 121 253 305 325 427 67 137 261 305 0 0 61 125 20 68 100 96 100 92 558 566 .83 1.206 1.169 1.106 1.161 4.321 80 327 1.14 .78 110 3800 7230 29 40 218 229 0 728 206 520 2.057 728 520 .486 1.994 1.04 .995
15 78 159 78 142 0 17 70 102 80 150 -8 -39 0 0 26 145 20 75 28 25 6 12 17 -47 null null null 4.639 4.296 6.291 32 137 8.511 .42 70 3950 7260 34 41 235 242 0 271 242 29 null 174 -67 null null null null
16 1365 1500 66 123 1298 1377 1471 1480 70 132 1404 1356 0 0 441 482 20 61 100 100 98 100 2675 2760 .943 1.061 .966 1.143 1.036 4.241 80 317 1.009 .94 100 4110 7230 30 40 250 260 0 2559 210 2349 1.81 2525 2313 .553 1.648 .856 .72
17 145 180 67 140 78 39 143 155 73 151 75 14 0 0 35 107 24 75 96 31 80 13 117 89 2 .5 .187 1.267 1.299 8.807 80 206 .941 .11 100 4260 7240 31 41 265 275 0 307 239 67 .853 264 24 1.172 .318 -.229 -1.651
18 76 148 68 131 8 17 65 112 72 145 -2 -18 0 0 28 99 22 69 28 25 14 12 25 -20 .471 2.125 null 3.663 4.01 7.491 120 450 4.618 .4 120 4410 7230 29 41 279 291 -50 252 223 29 3.625 191 -31 .276 null 1.858 null
19 519 379 67 128 451 251 540 359 72 139 473 231 0 0 138 125 22 69 100 96 100 81 702 704 1.797 .557 .488 .526 .563 4.702 80 345 .482 .69 110 4560 7230 29 40 294 305 0 647 218 428 .949 612 394 1.053 .833 -.075 -.263
20 3904 8849 66 128 3838 8721 4162 9629 70 142 4095 9501 0 0 1145 2733 21 72 100 100 100 100 12559 13596 .44 2.272 2.32 2.258 2.245 3.404 80 273 2.275 .97 100 4710 7220 29 39 310 320 0 15097 218 14878 3.877 16427 16209 .258 3.958 1.955 1.985

Total number of rows: 44544

Table truncated, full table size 9686 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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