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Sample GSM989804 Query DataSets for GSM989804
Status Public on Aug 23, 2012
Title PC 375T
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 375T2
Organism Homo sapiens
Characteristics ethnicity: Caucasian
age: 64
pre-operation treatment: None
individual: PC 648T
disease free survival: 0.03
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/2008-08/81116.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 12428 9777 186 210 12241 9567 14723 11592 233 270 14537 11382 0 0 8568 7036 158 199 100 100 100 94 21808 25919 1.28 .782 .783 .688 .791 1.926 52 380 .79 .98 90 2010 7250 44 53 36 45 0 9071 195 8877 .725 10755 10561 1.379 .726 -.464 -.461
2 8493 7185 219 299 8274 6886 7544 4475 266 375 7325 4175 0 0 7444 6283 165 261 92 86 82 73 15160 11500 1.202 .832 .57 .855 .839 2.266 52 326 .833 .98 90 2160 7260 45 54 51 60 0 6667 277 6389 .772 4152 3874 1.295 .529 -.373 -.919
3 8719 23668 242 355 8476 23312 9514 23747 561 614 9272 23391 0 0 7266 20099 3822 1687 59 69 51 69 31788 32663 .364 2.75 2.523 2.097 2.646 2.52 52 337 2.413 .78 90 2310 7250 44 53 66 75 0 21960 329 21630 2.552 22033 21703 .392 2.341 1.352 1.227
4 9044 7779 203 242 8840 7537 11702 10037 248 360 11498 9794 0 0 5464 4586 175 344 92 92 92 88 16377 21292 1.173 .853 .852 .907 .86 1.426 52 304 .84 .98 90 2470 7250 44 53 82 91 0 7218 225 6993 .791 9313 9087 1.264 .79 -.338 -.339
5 1000 366 192 234 808 132 1033 359 213 258 841 125 0 0 269 102 97 130 96 46 96 9 940 966 6.121 .163 .149 .145 .167 2.432 32 151 .188 .62 60 2610 7260 47 53 98 104 0 340 217 122 .152 333 116 6.597 .138 -2.722 -2.858
6 3387 4536 172 226 3214 4309 683 1155 181 233 510 928 0 0 3931 5078 54 84 99 100 97 99 7523 1438 .746 1.341 1.82 1.612 1.531 1.625 120 573 1.316 .98 130 2770 7260 43 56 110 123 0 4209 210 3998 1.244 1072 861 .804 1.688 .315 .756
7 276 172 170 213 105 -41 302 160 190 240 131 -53 0 0 93 61 88 132 61 0 26 0 64 78 null null null .508 .721 5.043 52 266 1.939 .31 90 2920 7250 44 53 127 136 -50 160 198 -38 null 148 -49 null null null null
8 12579 29129 172 216 12406 28913 15347 35078 259 337 15174 34862 0 0 9176 22663 194 294 88 88 86 82 41319 50036 .429 2.331 2.297 1.943 2.3 2.032 52 291 2.425 .98 90 3070 7240 43 52 142 151 -100 27027 200 26827 2.162 32547 32346 .462 2.132 1.113 1.092
9 208 256 147 154 60 102 172 213 217 264 24 59 0 0 101 142 185 290 9 7 1 0 162 83 .588 1.7 2.458 1.753 1.698 3.796 52 291 1.581 .88 90 3220 7240 43 52 157 166 -50 238 143 95 1.577 198 55 .634 2.281 .657 1.19
10 177 172 132 122 44 50 176 167 140 140 43 45 0 0 57 67 54 82 36 25 5 5 94 88 .88 1.136 1.047 1.074 1.202 2.94 52 309 1.678 .51 90 3370 7240 43 52 172 181 -50 160 113 46 1.054 155 42 .948 .971 .076 -.042
11 360 549 129 144 230 404 388 497 137 156 258 352 0 0 219 396 44 73 63 61 57 57 634 610 .569 1.757 1.364 1.649 1.719 2.039 52 336 1.896 .88 90 3520 7240 43 52 187 196 0 509 134 375 1.63 461 327 .614 1.266 .705 .34
12 442 743 126 141 315 602 464 757 137 150 337 616 0 0 79 149 46 71 100 100 96 100 917 953 .523 1.911 1.828 1.942 1.875 1.468 32 211 2.057 .88 70 3680 7250 45 52 204 211 0 689 131 559 1.773 702 572 .564 1.696 .826 .762
13 312 204 139 157 172 47 317 201 157 169 177 44 0 0 119 71 71 78 76 36 61 5 219 221 3.66 .273 .249 .381 .381 3.275 52 306 .771 .59 90 3830 7250 44 53 218 227 -50 189 146 44 .254 186 41 3.944 .231 -1.98 -2.116
14 303 337 126 158 176 179 310 349 135 158 183 191 0 0 60 43 43 61 100 100 91 91 355 374 .983 1.017 1.044 1.047 1.092 1.904 12 104 1.331 .72 50 3980 7250 46 51 235 240 0 313 147 166 .944 324 177 1.06 .968 -.084 -.046
15 121 67 132 126 -10 -59 120 54 147 137 -11 -72 0 0 35 42 60 67 1 0 1 0 -69 -83 null null null 2.481 2.349 3.738 52 327 2.1 .37 90 4130 7250 44 53 248 257 -50 62 117 -55 null 50 -67 null null null null
16 3813 2299 131 118 3681 2181 3951 2268 147 123 3820 2150 0 0 753 431 70 55 100 100 100 100 5862 5970 1.688 .593 .563 .595 .569 1.259 32 217 .589 .97 70 4280 7250 45 52 264 271 0 2133 109 2024 .55 2104 1995 1.819 .522 -.863 -.937
17 148 232 133 110 14 122 143 226 145 127 9 116 0 0 38 87 66 95 16 66 0 16 136 125 .115 8.714 12.889 2.124 2.036 3.772 12 68 -34.397 -.03 40 4440 7230 45 49 282 286 0 215 102 113 8.085 210 108 .124 11.959 3.015 3.58
18 117 108 129 144 -11 -36 106 86 143 158 -22 -58 0 0 42 70 57 104 3 5 1 0 -47 -80 null null null 2.042 1.921 3.437 52 306 2.776 .62 90 4580 7240 43 52 293 302 -50 100 134 -33 null 80 -54 null null null null
19 331 314 148 167 182 147 361 314 153 176 212 147 0 0 153 140 46 71 73 69 67 50 329 359 1.238 .808 .693 .897 .803 3.044 52 332 .985 .7 90 4730 7240 43 52 308 317 -50 291 155 136 .749 291 136 1.334 .643 -.416 -.636
20 2787 6569 158 164 2628 6405 3160 7200 163 188 3001 7036 0 0 967 1841 52 118 100 100 100 100 9033 10037 .41 2.437 2.345 2.553 2.378 1.428 32 217 2.392 .97 70 4890 7250 45 52 325 332 0 6095 152 5943 2.261 6680 6528 .442 2.175 1.177 1.121

Total number of rows: 44544

Table truncated, full table size 9622 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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