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Sample GSM989806 Query DataSets for GSM989806
Status Public on Aug 23, 2012
Title PC 477T
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 477T2
Organism Homo sapiens
Characteristics ethnicity: Caucasian
age: 58
pre-operation treatment: None
individual: PC 477T
disease free survival: 11.90
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/2008-08/81174.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 8958 11185 36 92 8922 11092 11390 14045 37 99 11354 13953 0 0 4050 4856 7 37 100 100 100 100 20014 25307 .804 1.243 1.229 1.257 1.249 3.404 52 309 1.221 .98 80 2070 7230 19 27 51 59 0 9860 81 9778 1.096 12381 12300 .912 1.083 .132 .115
2 9730 12182 37 92 9693 12090 12530 15281 38 99 12492 15189 0 0 4897 6023 7 36 100 100 100 100 21783 27681 .802 1.247 1.216 1.251 1.252 3.281 52 266 1.234 .98 80 2220 7230 19 27 66 74 0 10739 81 10658 1.1 13471 13390 .909 1.072 .137 .1
3 12296 17430 38 96 12258 17334 15586 21621 40 99 15548 21524 0 0 5618 7690 7 34 100 100 100 100 29592 37072 .707 1.414 1.384 1.473 1.413 3.034 52 307 1.394 .99 90 2370 7230 18 27 80 89 0 15365 85 15281 1.247 19060 18974 .802 1.22 .318 .287
4 11830 13894 40 95 11790 13799 14685 16856 42 102 14645 16761 0 0 4973 5918 11 47 100 100 100 100 25589 31406 .854 1.17 1.144 1.16 1.181 2.938 52 251 1.163 .98 80 2520 7230 19 27 96 104 0 12248 84 12164 1.032 14859 14776 .969 1.009 .045 .013
5 620 257 40 93 580 163 722 248 42 99 682 155 0 0 206 82 9 33 100 90 100 86 743 837 3.558 .281 .227 .265 .278 3.35 52 208 .259 .84 80 2670 7230 19 27 111 119 0 227 82 144 .248 219 137 4.036 .2 -2.013 -2.319
6 4039 4117 43 96 3995 4021 1354 1335 46 102 1310 1239 0 0 4101 4140 12 37 100 97 100 90 8016 2549 .994 1.007 .946 .975 1.017 3.283 120 453 .999 .99 120 2830 7230 17 29 125 137 0 3629 85 3545 .887 1177 1092 1.127 .834 -.173 -.262
7 227 187 43 96 183 90 231 185 46 100 187 89 0 0 25 50 10 34 100 84 100 62 273 276 2.033 .492 .476 .39 .489 4.574 32 198 .552 .69 70 2970 7220 18 25 141 148 0 165 85 79 .434 163 78 2.307 .42 -1.206 -1.253
8 13850 20039 40 114 13809 19924 16739 23506 43 124 16698 23391 0 0 5579 7500 19 55 100 100 100 100 33733 40089 .693 1.443 1.401 1.543 1.436 2.819 52 326 1.42 .98 90 3120 7230 18 27 155 164 0 17665 100 17564 1.272 20722 20620 .786 1.235 .347 .304
9 202 335 44 127 158 208 200 333 47 139 156 206 0 0 30 79 24 104 100 93 100 50 366 362 .76 1.316 1.321 1.264 1.307 3.038 32 204 1.532 .79 70 3270 7230 19 26 171 178 0 295 112 183 1.161 294 182 .862 1.164 .215 .219
10 169 347 40 115 128 231 172 366 42 120 131 250 0 0 24 74 8 39 100 96 100 96 359 381 .554 1.805 1.908 1.794 1.881 2.573 32 214 1.952 .9 70 3420 7220 18 25 186 193 0 306 101 204 1.591 323 220 .629 1.682 .67 .75
11 557 1240 40 118 516 1122 634 1386 42 125 594 1267 0 0 200 435 8 47 98 98 98 94 1638 1861 .46 2.174 2.133 2.033 2.183 3.342 52 323 2.192 .97 90 3580 7220 17 26 201 210 0 1093 104 989 1.917 1222 1117 .522 1.88 .939 .911
12 527 1958 39 108 488 1849 562 2012 40 113 523 1903 0 0 110 317 7 41 100 100 100 100 2337 2426 .264 3.789 3.639 3.865 3.737 2.252 32 212 3.805 .98 70 3720 7220 18 25 216 223 0 1726 95 1630 3.34 1774 1678 .299 3.208 1.74 1.682
13 302 294 39 111 263 183 360 301 40 117 321 190 0 0 115 97 7 41 100 88 100 86 446 511 1.437 .696 .592 .681 .688 3.346 52 257 .694 .82 80 3870 7220 18 26 231 239 0 259 98 161 .613 265 167 1.63 .522 -.705 -.938
14 126 264 42 122 84 141 126 252 42 128 84 129 0 0 15 60 8 40 100 96 100 84 225 213 .596 1.679 1.536 1.527 1.563 3.301 32 196 2.079 .77 70 4020 7220 18 25 246 253 0 233 108 124 1.48 222 114 .676 1.354 .565 .437
15 43 86 42 113 1 -26 43 83 44 118 1 -29 0 0 7 40 12 43 6 3 0 2 -25 -28 null null null 6.406 8.367 6.773 80 346 11.851 .27 100 4170 7220 17 27 260 270 -50 76 100 -23 null 73 -26 null null null null
16 797 855 40 122 757 732 991 1007 42 129 951 884 0 0 346 308 10 57 100 100 98 100 1489 1835 1.034 .967 .93 1.049 .998 3.138 52 250 .933 .96 80 4320 7220 18 26 276 284 0 754 108 645 .852 888 779 1.173 .819 -.23 -.287
17 77 181 42 117 35 64 78 167 43 124 36 50 0 0 19 62 8 47 84 53 84 25 99 86 .547 1.829 1.389 2.05 2.206 5.866 32 156 3.336 .5 60 4480 7210 18 24 293 299 0 160 103 56 1.612 147 44 .62 1.224 .689 .292
18 42 99 41 121 0 -22 40 88 43 131 0 -33 0 0 9 60 13 69 6 7 1 3 -22 -33 null null null 8.515 7.607 5.593 80 358 6.823 .67 100 4620 7210 16 26 305 315 -50 87 107 -19 null 78 -29 null null null null
19 443 468 42 132 400 335 453 461 46 150 410 328 0 0 90 118 20 102 100 100 100 90 735 738 1.194 .838 .8 .813 .761 2.702 32 224 .82 .91 70 4770 7210 17 24 321 328 0 413 116 295 .738 406 289 1.354 .705 -.438 -.504
20 2242 11410 43 129 2198 11280 2642 13531 52 160 2598 13401 0 0 840 4476 41 164 100 100 100 100 13478 15999 .195 5.132 5.158 5.105 5.223 3.057 52 250 5.254 .98 80 4930 7220 18 26 337 345 0 10058 114 9944 4.524 11928 11814 .221 4.547 2.178 2.185

Total number of rows: 44544

Table truncated, full table size 9337 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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