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Sample GSM989805 Query DataSets for GSM989805
Status Public on Aug 23, 2012
Title PC 411N
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 411N2
Organism Homo sapiens
Characteristics individual: PC 411N
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/2008-08/81202.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) [email protected]
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 36588 14518 48 93 36539 14425 37839 16014 57 122 37791 15921 84 0 3996 4284 32 91 100 100 100 100 50964 53712 2.533 .395 .421 .353 .421 5.207 52 351 .39 .93 90 1800 6710 18 27 11 20 -100 24794 159 24636 .674 27349 27190 1.483 .719 -.569 -.475
2 34937 14499 62 95 34874 14404 37839 16636 81 121 37777 16541 73 0 6867 5798 50 100 100 100 100 100 49278 54318 2.421 .413 .438 .31 .451 7.837 52 252 .406 .92 90 1950 6710 18 27 26 35 -100 24762 162 24600 .705 28412 28249 1.418 .748 -.504 -.419
3 31418 19265 56 96 31361 19168 37839 23307 90 135 37783 23210 75 0 12411 9832 77 114 100 98 100 93 50529 60993 1.636 .611 .614 .452 .647 8.997 80 382 .605 .94 110 2110 6700 16 27 41 52 -100 32901 164 32736 1.044 39805 39639 .958 1.049 .062 .069
4 30614 14776 58 98 30555 14677 37839 18751 92 131 37780 18652 71 0 12931 7824 79 107 100 93 98 88 45232 56432 2.082 .48 .494 .368 .509 7.507 80 376 .485 .95 110 2270 6700 16 27 57 68 -100 25235 167 25066 .82 32024 31855 1.219 .843 -.286 -.246
5 1856 294 61 91 1795 202 2053 280 79 105 1992 188 0 0 614 117 47 64 100 86 100 76 1997 2180 8.886 .113 .094 .104 .101 6.993 80 273 .096 .73 100 2410 6700 17 27 72 82 0 502 155 345 .192 478 321 5.203 .161 -2.379 -2.633
6 15171 7668 68 95 15103 7573 19321 9702 79 105 19253 9606 0 0 7666 4151 35 53 100 98 100 95 22676 28859 1.994 .501 .499 .425 .509 7.778 120 335 .485 .94 120 2560 6710 17 29 86 98 0 13096 162 12933 .856 16569 16405 1.168 .852 -.224 -.231
7 483 219 57 100 425 119 498 228 69 119 440 128 0 0 86 67 35 81 100 70 100 26 544 568 3.571 .28 .291 .25 .293 6.104 80 306 .244 .49 110 2720 6700 16 27 102 113 0 374 171 203 .478 389 219 2.091 .497 -1.064 -1.009
8 31922 17810 55 109 31866 17701 37839 20569 68 138 37784 20460 75 0 11847 7031 34 105 100 98 100 98 49567 58244 1.8 .555 .541 .512 .56 6.973 80 271 .531 .94 100 2870 6700 17 27 118 128 -100 30417 186 30230 .949 35129 34942 1.054 .925 -.076 -.113
9 297 240 58 110 239 129 310 237 65 126 252 126 0 0 82 100 27 76 100 70 97 37 368 378 1.853 .54 .5 .534 .599 7.1 80 382 .546 .64 110 3010 6710 17 28 131 142 0 410 188 220 .922 405 215 1.085 .854 -.117 -.228
10 270 330 57 105 212 225 271 348 62 114 213 242 0 0 35 95 23 53 100 98 100 84 437 455 .942 1.061 1.136 .958 1.114 5.356 52 267 1.035 .74 90 3160 6710 18 27 147 156 0 564 179 384 1.813 594 413 .552 1.94 .858 .956
11 1956 1108 49 96 1907 1011 2144 1181 53 102 2094 1084 0 0 727 445 12 48 100 96 100 95 2918 3178 1.886 .53 .518 .531 .527 6.22 80 313 .501 .91 100 3320 6700 17 27 163 173 0 1892 164 1727 .905 2017 1851 1.104 .884 -.143 -.178
12 808 2109 47 98 761 2010 846 2182 49 105 798 2083 0 0 226 704 11 48 100 100 98 98 2771 2881 .379 2.641 2.61 2.623 2.597 4.505 80 303 2.649 .94 110 3470 6710 17 28 177 188 0 3602 167 3433 4.511 3727 3557 .222 4.458 2.173 2.156
13 882 337 46 102 835 235 961 348 47 110 914 245 0 0 301 136 9 57 100 87 100 78 1070 1159 3.553 .281 .268 .257 .297 6.477 80 285 .26 .78 100 3620 6700 17 27 193 203 0 576 174 401 .481 594 418 2.081 .458 -1.057 -1.127
14 414 374 46 93 367 280 419 374 48 103 372 280 0 0 62 122 8 53 100 97 100 92 647 652 1.311 .763 .753 .715 .777 4.895 80 285 .724 .8 110 3770 6700 16 27 207 218 0 639 159 478 1.303 639 478 .767 1.285 .382 .362
15 64 124 46 88 17 36 64 114 49 98 17 25 0 0 11 57 10 48 68 39 40 12 53 42 .472 2.118 1.471 3.405 3.228 12.202 120 337 10.46 .18 120 3920 6700 16 28 222 234 -50 212 150 61 3.617 195 43 .277 2.512 1.855 1.329
16 5303 2123 45 91 5257 2031 6273 2450 47 98 6227 2358 0 0 2027 891 10 48 100 100 100 100 7288 8585 2.588 .386 .379 .379 .379 5.609 80 212 .37 .93 100 4080 6700 17 27 239 249 0 3626 155 3469 .66 4184 4027 1.516 .647 -.6 -.629
17 117 268 47 93 69 174 122 252 50 103 74 159 0 0 24 100 13 57 100 87 92 72 243 233 .397 2.522 2.149 2.29 2.489 6.067 80 285 3.075 .67 100 4220 6700 17 27 253 263 0 458 159 297 4.307 430 272 .232 3.67 2.107 1.876
18 61 112 59 96 1 15 56 102 62 109 -2 5 0 0 17 60 15 57 25 25 9 9 16 3 .067 15 null 3.309 3.151 8.752 52 219 7.397 .21 80 4370 6730 21 29 269 277 0 191 164 26 25.618 174 9 .039 null 4.679 null
19 1432 524 58 100 1374 424 1456 519 60 110 1397 419 0 0 327 150 15 55 100 100 100 97 1798 1816 3.241 .309 .3 .3 .307 4.782 80 342 .284 .86 110 4520 6700 16 27 282 293 0 895 171 724 .527 886 716 1.897 .512 -.924 -.965
20 8218 6936 57 96 8160 6839 9108 7580 59 110 9050 7483 0 0 2936 2189 18 60 100 100 100 100 14999 16533 1.193 .838 .827 .924 .834 6.566 80 323 .779 .93 100 4680 6700 17 27 299 309 0 11846 164 11680 1.431 12945 12780 .699 1.412 .517 .498

Total number of rows: 44544

Table truncated, full table size 9472 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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