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Sample GSM989697 Query DataSets for GSM989697
Status Public on Aug 23, 2012
Title PC 584N
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 584N2
Organism Homo sapiens
Characteristics individual: PC 584N
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/2008-08/81200.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 5901 5375 60 134 5840 5241 6994 5984 69 175 6934 5850 0 0 4457 4422 47 329 91 77 80 75 11081 12784 1.114 .897 .844 1.009 .816 10.242 120 593 .809 .77 120 2060 6820 28 40 40 52 0 5505 137 5368 .919 6129 5992 1.088 .864 -.122 -.211
2 7268 5270 74 158 7193 5111 7738 5437 78 167 7663 5278 0 0 1854 1421 25 72 100 100 100 100 12304 12941 1.407 .711 .689 .708 .703 5.306 52 239 .609 .84 90 2220 6800 27 36 57 66 0 5398 162 5235 .728 5569 5406 1.374 .705 -.458 -.503
3 4835 4792 72 162 4763 4630 5539 5614 74 168 5467 5452 0 0 2099 2089 22 72 98 100 98 98 9393 10919 1.029 .972 .997 1.092 .974 8.288 80 318 .899 .89 100 2380 6800 27 37 73 83 0 4908 166 4742 .996 5750 5584 1.004 1.021 -.006 .031
4 6191 4697 65 139 6125 4558 6840 5090 68 152 6774 4951 0 0 2337 1700 21 67 100 98 100 97 10683 11725 1.344 .744 .731 .743 .738 7.106 80 308 .678 .9 110 2530 6800 26 37 87 98 0 4811 142 4669 .762 5214 5071 1.312 .749 -.392 -.418
5 326 194 61 132 264 62 339 180 67 145 277 47 0 0 103 94 25 65 97 43 95 20 326 324 4.258 .235 .17 .346 .316 8.78 80 226 .075 .11 100 2680 6800 27 37 103 113 0 199 135 64 .241 184 48 4.157 .174 -2.056 -2.525
6 2559 2261 62 132 2496 2129 2632 2373 70 152 2569 2240 0 0 520 730 28 98 100 100 100 100 4625 4809 1.172 .853 .872 .791 .88 3.974 80 257 .844 .88 110 2830 6790 25 36 117 128 0 2316 135 2181 .874 2431 2294 1.145 .893 -.195 -.163
7 136 199 61 139 75 60 130 171 67 157 69 32 0 0 43 111 23 96 91 32 71 10 135 101 1.25 .8 .464 1.096 1.353 8.934 120 305 1.106 .25 120 2980 6800 26 38 132 144 -100 204 142 61 .819 175 33 1.22 .475 -.287 -1.074
8 3602 4130 72 137 3530 3993 4273 4653 76 153 4201 4515 0 0 1688 1703 28 70 98 98 96 97 7523 8716 .884 1.131 1.075 1.284 1.089 9.953 80 186 .929 .83 100 3130 6810 28 38 148 158 0 4230 140 4090 1.159 4766 4625 .863 1.101 .212 .139
9 105 168 61 142 43 26 103 165 70 153 42 22 0 0 28 72 32 76 65 20 20 6 69 64 1.654 .605 .524 1.171 1.38 9.875 120 355 1.03 .05 120 3280 6790 25 37 162 174 -100 172 145 27 .619 169 23 1.615 .537 -.691 -.898
10 119 209 62 144 56 65 117 201 69 153 55 57 0 0 31 90 28 78 83 43 48 16 121 112 .862 1.161 1.036 1.472 1.509 10.143 120 405 1.096 .16 120 3430 6790 25 37 177 189 -100 214 147 67 1.189 206 58 .841 1.062 .25 .086
11 251 434 68 157 183 276 253 434 76 171 185 276 0 0 74 131 32 83 98 92 92 78 459 461 .663 1.508 1.492 1.432 1.448 6.707 80 304 1.236 .6 100 3590 6800 27 37 194 204 0 445 161 283 1.545 445 283 .647 1.528 .627 .612
12 216 946 63 152 152 794 213 869 66 163 149 717 0 0 51 327 17 75 100 100 98 100 946 866 .191 5.224 4.812 5.097 4.975 4.415 80 268 6.426 .76 110 3740 6800 26 37 208 219 0 969 156 813 5.35 890 734 .187 4.929 2.42 2.301
13 213 211 61 147 152 63 212 222 62 150 150 75 0 0 50 103 15 63 100 52 100 26 215 225 2.413 .414 .5 .669 .732 5.987 80 263 .302 .2 110 3890 6790 25 36 223 234 0 216 151 65 .425 227 77 2.356 .512 -1.236 -.965
14 136 245 57 132 79 113 134 235 59 147 76 103 0 0 31 96 15 101 95 50 92 18 192 179 .699 1.43 1.355 1.316 1.48 9.363 120 340 1.492 .33 120 4040 6800 26 38 238 250 0 251 135 116 1.465 241 105 .683 1.388 .551 .473
15 72 144 57 139 14 4 67 135 60 149 9 -3 0 0 20 83 16 99 34 10 20 3 18 6 3.5 .286 null 3.936 3.468 10.455 120 374 23.014 .19 120 4190 6800 26 38 253 265 -50 147 142 4 .293 138 -3 3.417 null -1.773 null
16 681 910 57 160 623 750 760 976 60 175 703 815 0 0 233 335 15 76 100 98 100 93 1373 1518 .831 1.204 1.159 1.191 1.197 5.075 80 217 1.111 .85 100 4350 6800 27 37 270 280 0 932 164 768 1.233 1000 835 .811 1.187 .302 .248
17 87 208 62 150 25 57 86 189 65 167 24 39 0 0 20 113 20 81 63 36 25 23 82 63 .439 2.28 1.625 3.697 4.141 13.878 52 238 18.312 .15 90 4480 6770 24 33 283 292 -100 213 154 58 2.335 194 40 .428 1.664 1.224 .735
18 67 165 58 144 9 21 65 145 61 155 7 1 0 0 17 124 18 68 25 27 6 16 30 8 .429 2.333 .143 5.492 6.073 11.547 120 389 16.77 .24 120 4640 6780 24 36 298 310 -50 169 147 22 2.39 149 1 .418 .146 1.257 -2.773
19 246 379 58 165 187 214 243 373 59 165 184 208 0 0 60 122 14 65 100 88 100 73 401 392 .874 1.144 1.13 1.01 1.176 6.627 80 238 1.024 .61 110 4800 6800 26 37 314 325 0 388 169 219 1.172 382 213 .853 1.158 .229 .211
20 1158 4656 57 150 1100 4505 1453 5940 59 158 1396 5789 0 0 721 2898 15 68 98 93 93 90 5605 7185 .244 4.095 4.147 3.875 4.036 10.292 120 331 4.288 .89 120 4950 6800 26 38 329 341 0 4769 154 4614 4.195 6084 5930 .238 4.247 2.069 2.087

Total number of rows: 44544

Table truncated, full table size 9795 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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