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Sample GSM989810 Query DataSets for GSM989810
Status Public on Aug 23, 2012
Title PC 474T
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 474T2
Organism Homo sapiens
Characteristics ethnicity: Caucasian
age: 68
pre-operation treatment: None
individual: PC 474T
disease free survival: 43.30
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/2008-08/81182.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 GPL9497
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 11957 15512 51 61 11905 15450 12037 15508 56 72 11985 15447 0 0 2372 3195 17 46 100 100 100 100 27355 27432 .771 1.298 1.289 1.297 1.275 1.575 52 376 1.297 .98 90 1670 7620 21 30 34 43 0 13199 52 13146 1.104 13196 13144 .906 1.097 .143 .133
2 11267 14710 56 78 11210 14631 12130 15497 60 86 12073 15418 0 0 3297 4024 19 44 100 100 100 100 25841 27491 .766 1.305 1.277 1.346 1.246 1.805 52 292 1.294 .98 90 1820 7620 21 30 49 58 0 12517 66 12450 1.111 13186 13119 .9 1.087 .151 .12
3 8926 12627 55 74 8871 12553 9832 13942 61 85 9777 13868 0 0 3025 3896 22 47 100 100 100 100 21424 23645 .707 1.415 1.418 1.508 1.386 1.981 52 287 1.388 .98 90 1970 7620 21 30 64 73 0 10744 63 10681 1.204 11863 11800 .831 1.207 .268 .271
4 13235 16933 56 71 13178 16861 13882 17716 61 82 13825 17645 0 0 3527 4111 22 51 100 100 100 100 30039 31470 .782 1.279 1.276 1.314 1.256 1.746 52 285 1.264 .99 90 2120 7620 21 30 79 88 0 14408 60 14347 1.089 15075 15014 .919 1.086 .123 .119
5 502 236 57 82 444 153 521 232 63 88 463 150 0 0 111 76 21 43 100 94 100 78 597 613 2.902 .345 .324 .286 .33 3.299 52 210 .344 .8 80 2280 7620 22 30 96 104 0 201 70 130 .293 197 128 3.41 .276 -1.77 -1.859
6 3125 3870 80 95 3044 3774 3536 4397 112 116 3456 4301 0 0 1460 1907 78 75 100 98 100 97 6818 7757 .807 1.24 1.245 1.166 1.218 2.135 80 305 1.264 .98 100 2430 7620 21 31 110 120 0 3293 81 3211 1.055 3741 3660 .948 1.059 .077 .083
7 192 144 60 67 131 77 198 138 69 77 137 70 0 0 45 65 27 45 100 65 98 36 208 207 1.701 .588 .511 .573 .613 3.244 52 226 .609 .52 80 2580 7620 22 30 126 134 0 123 57 66 .5 117 60 1.999 .435 -1 -1.202
8 10020 13276 56 68 9964 13208 11089 14558 60 83 11033 14490 0 0 2783 3653 23 47 100 100 100 100 23172 25523 .754 1.326 1.313 1.34 1.321 1.65 52 291 1.294 .97 90 2730 7610 20 29 140 149 0 11297 58 11239 1.128 12387 12330 .887 1.118 .174 .16
9 104 112 55 63 49 49 107 91 59 74 52 27 0 0 35 96 19 44 73 36 62 22 98 79 1 1 .519 .902 1.041 3.459 80 398 3.085 .46 110 2890 7610 19 30 155 166 0 95 54 42 .851 77 23 1.175 .442 -.233 -1.178
10 113 140 54 66 58 74 115 130 56 77 61 63 0 0 21 45 13 38 100 84 93 37 132 124 .784 1.276 1.033 1.101 1.456 3.65 32 182 1.639 .49 70 3040 7610 21 28 172 179 0 119 56 63 1.086 111 54 .921 .879 .119 -.186
11 291 674 55 74 235 599 291 674 57 82 236 599 0 0 66 181 14 41 100 100 100 100 834 835 .392 2.549 2.538 2.538 2.449 1.773 52 284 2.63 .92 90 3180 7610 20 29 185 194 0 574 63 510 2.169 574 510 .461 2.16 1.117 1.111
12 252 745 56 68 196 677 250 737 60 80 194 669 0 0 66 168 20 55 100 100 98 100 873 863 .29 3.454 3.448 3.596 3.646 1.927 52 284 3.541 .91 80 3330 7610 21 29 201 209 0 634 58 576 2.939 627 569 .34 2.934 1.555 1.553
13 201 217 54 78 147 139 191 197 58 90 136 118 0 0 59 100 17 55 100 84 98 55 286 254 1.058 .946 .868 .8 .95 2.921 52 231 1.218 .66 80 3490 7610 21 29 217 225 0 185 66 118 .805 168 100 1.243 .738 -.314 -.438
14 137 199 63 88 74 110 106 136 71 106 43 47 0 0 188 236 35 101 58 25 30 8 184 90 .673 1.486 1.093 1.2 1.397 3.955 80 316 1.629 .67 100 3630 7600 19 29 230 240 -50 169 75 94 1.265 116 40 .791 .93 .339 -.105
15 339 466 62 78 277 387 82 139 70 85 20 60 0 0 615 1091 27 46 25 50 25 33 664 80 .716 1.397 3 3.637 3.668 4.175 12 68 1.824 .84 40 3770 7590 21 25 247 251 0 397 66 329 1.189 118 51 .841 2.553 .25 1.352
16 558 740 64 99 494 641 568 743 75 124 504 644 0 0 103 187 49 111 100 100 100 98 1135 1148 .771 1.298 1.278 1.269 1.234 1.794 52 326 1.335 .92 90 3940 7610 20 29 261 270 0 630 84 545 1.104 632 548 .906 1.087 .143 .121
17 85 133 61 90 23 43 77 123 70 110 15 33 0 0 36 66 33 101 27 21 8 2 66 48 .535 1.87 2.2 2.443 2.285 4.443 80 367 2.791 .48 100 4080 7600 19 29 275 285 -50 113 77 37 1.591 105 28 .629 1.872 .67 .905
18 315 322 58 78 256 244 226 254 64 91 167 175 0 0 294 247 26 52 83 75 75 58 500 342 1.049 .953 1.048 1.095 .923 2.947 12 104 .911 .8 50 4230 7600 21 26 292 297 0 274 66 208 .811 216 149 1.233 .892 -.302 -.165
19 220 279 56 87 163 191 215 270 67 101 158 182 0 0 54 101 35 55 98 92 96 71 354 340 .853 1.172 1.152 1.05 1.146 2.386 52 316 1.313 .78 90 4400 7600 19 28 307 316 0 237 74 163 .997 230 155 1.003 .98 -.004 -.029
20 1109 5664 56 74 1052 5590 1158 5977 66 95 1101 5903 0 0 279 1589 35 92 100 100 100 100 6642 7004 .188 5.314 5.361 5.266 5.334 1.756 52 275 5.423 .98 90 4540 7610 20 29 321 330 0 4819 63 4757 4.521 5086 5023 .221 4.562 2.177 2.19

Total number of rows: 44544

Table truncated, full table size 9362 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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