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Sample GSM989822 Query DataSets for GSM989822
Status Public on Aug 23, 2012
Title PC 537N
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 537N2
Organism Homo sapiens
Characteristics individual: PC 537N
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/2008-08/81132.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 13353 25326 169 74 13184 25252 14199 28610 185 87 14030 28535 0 0 4476 10536 117 78 100 100 100 98 38436 42565 .522 1.915 2.034 1.55 1.977 1.78 52 303 2.069 .95 80 1780 7020 18 26 26 34 0 26143 76 26067 1.977 29533 29456 .506 2.099 .983 1.07
2 9797 18394 163 76 9633 18317 12304 24170 182 100 12141 24093 0 0 5203 10271 125 100 98 100 98 100 27950 36234 .526 1.901 1.984 1.77 2.013 1.43 52 255 1.977 .96 80 1930 7020 18 26 41 49 0 18987 78 18908 1.963 24950 24870 .509 2.048 .973 1.035
3 12733 15594 158 83 12574 15511 16500 21173 172 96 16341 21089 0 0 7198 10144 70 58 96 94 92 90 28085 37430 .811 1.234 1.291 .907 1.243 1.486 52 274 1.338 .97 90 2080 7030 18 27 55 64 0 16097 86 16011 1.273 21856 21769 .785 1.332 .349 .414
4 10706 19937 154 82 10552 19855 11058 21225 165 92 10904 21143 0 0 2619 6110 64 47 100 100 100 100 30407 32047 .531 1.882 1.939 1.808 1.971 1.151 52 324 1.983 .96 90 2240 7010 16 25 71 80 0 20580 85 20496 1.942 21910 21825 .515 2.002 .958 1.001
5 834 236 168 80 666 155 825 234 185 93 657 153 0 0 112 68 83 50 100 90 100 78 821 810 4.297 .233 .233 .21 .226 1.349 32 214 .236 .76 70 2390 7010 17 24 87 94 0 244 83 160 .24 242 158 4.162 .24 -2.057 -2.057
6 12220 13756 213 103 12006 13652 11950 13124 228 107 11736 13021 0 0 2006 2225 76 46 100 100 100 100 25658 24757 .879 1.137 1.109 1.14 1.134 .881 52 255 1.142 .97 80 2540 7020 18 26 102 110 0 14200 106 14092 1.174 13547 13441 .852 1.145 .231 .196
7 482 156 145 69 337 87 485 147 160 79 340 78 0 0 110 47 68 44 100 84 100 43 424 418 3.874 .258 .229 .264 .252 1.215 32 173 .233 .6 60 2690 7010 18 24 118 124 0 161 71 90 .266 152 81 3.753 .237 -1.908 -2.078
8 26032 23375 129 62 25902 23313 26345 24871 139 72 26216 24809 0 0 3250 5021 57 45 100 100 100 100 49215 51025 1.111 .9 .946 .88 .938 .928 32 235 .948 .97 70 2840 7010 17 24 132 139 0 24129 64 24065 .929 25673 25609 1.076 .977 -.106 -.034
9 158 210 118 55 40 155 153 208 131 65 34 153 0 0 42 56 53 49 31 96 6 81 195 187 .258 3.875 4.5 4.106 3.09 2.004 32 174 4.522 .36 60 2990 7010 18 24 148 154 0 217 57 160 4 215 158 .25 4.645 2 2.216
10 174 222 121 53 53 168 164 223 131 66 43 169 0 0 50 59 46 41 44 100 19 94 221 212 .315 3.17 3.93 3.425 3.187 1.886 52 256 3.302 .38 80 3140 7010 17 25 162 170 0 229 55 173 3.272 230 174 .306 4.057 1.71 2.02
11 526 677 125 56 401 620 523 679 146 71 397 622 0 0 128 134 98 95 100 100 93 100 1021 1019 .647 1.546 1.567 1.61 1.562 1.098 32 210 1.472 .91 70 3290 7010 17 24 177 184 0 699 58 640 1.596 701 642 .627 1.617 .674 .694
12 378 2548 124 56 253 2491 395 2645 132 67 270 2588 0 0 138 981 46 38 88 100 82 98 2744 2858 .102 9.846 9.585 9.627 9.94 1.365 52 259 10.246 .86 80 3440 7010 17 25 192 200 0 2630 58 2571 10.163 2730 2671 .098 9.894 3.345 3.307
13 329 228 124 58 204 169 325 220 129 63 201 161 0 0 66 63 38 31 100 98 100 96 373 362 1.207 .828 .801 .801 .795 1.231 52 262 .862 .83 80 3600 7000 16 24 208 216 0 235 60 174 .855 227 166 1.169 .827 -.226 -.274
14 286 310 126 55 160 254 299 335 147 83 172 279 0 0 106 147 99 198 69 65 32 15 414 451 .63 1.588 1.622 1.727 1.509 1.927 52 236 3.093 .72 80 3750 7010 17 25 223 231 0 320 57 262 1.639 346 288 .61 1.674 .713 .744
15 112 56 134 57 -22 0 105 49 144 72 -29 -7 0 0 27 37 57 61 1 3 0 1 -22 -36 null null null .506 .541 2.362 52 291 1.659 .55 90 3900 7000 15 24 237 246 -50 58 59 0 null 51 -7 null null null null
16 3495 1350 130 55 3364 1295 3557 1349 142 68 3427 1294 0 0 589 265 58 60 100 100 100 100 4659 4721 2.598 .385 .378 .385 .38 1.005 52 264 .375 .95 80 4050 7000 16 24 253 261 0 1394 57 1337 .397 1393 1336 2.517 .39 -1.331 -1.359
17 161 174 133 60 27 113 154 166 149 69 20 105 0 0 35 55 68 41 12 96 0 65 140 125 .239 4.185 5.25 4.159 4.253 2.838 32 172 4.078 .2 60 4200 7010 18 24 269 275 0 180 62 117 4.32 171 108 .231 5.419 2.111 2.438
18 113 49 125 58 -12 -8 115 48 139 69 -10 -10 0 0 28 19 58 41 1 1 0 0 -20 -20 null null null .803 .737 2.73 52 334 .51 .33 90 4350 7000 15 24 282 291 -50 51 60 -8 null 50 -10 null null null null
19 472 244 128 54 344 190 478 237 142 66 350 182 0 0 105 75 66 44 100 100 96 90 534 532 1.811 .552 .52 .537 .558 1.217 52 330 .55 .8 90 4510 7000 15 24 298 307 0 252 56 196 .57 245 188 1.754 .537 -.811 -.898
20 2780 4140 126 58 2653 4081 3103 4793 142 71 2976 4734 0 0 1116 1611 69 63 98 100 96 100 6734 7710 .65 1.538 1.591 1.744 1.573 1.648 52 249 1.566 .96 80 4660 7000 16 24 314 322 0 4274 60 4213 1.588 4948 4887 .63 1.642 .667 .715

Total number of rows: 44544

Table truncated, full table size 9452 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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