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Sample GSM989765 Query DataSets for GSM989765
Status Public on Aug 23, 2012
Title PC 646T
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 646T2
Organism Homo sapiens
Characteristics ethnicity: Caucasian
age: 66
pre-operation treatment: None
individual: PC 488T
disease free survival: 28.87
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/2008-08/81136.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
1 105 429 69 162 35 267 90 151 76 227 20 -10 0 0 85 753 32 206 31 28 18 15 302 10 .131 7.629 null 3.509 3.809 6.439 32 236 12.883 .59 70 1940 6770 21 28 42 49 0 307 116 191 5.462 108 -7 .183 null 2.449 null
2 4678 4325 71 182 4606 4142 5264 4896 79 231 5192 4714 0 0 1908 2224 34 235 100 90 100 88 8748 9906 1.112 .899 .908 .789 .93 6.867 52 290 .883 .89 80 2120 6770 21 29 60 68 0 3097 130 2966 .644 3506 3375 1.553 .65 -.635 -.621
3 4420 3970 80 196 4339 3773 5209 4715 82 243 5129 4519 0 0 2002 2157 29 211 98 90 98 84 8112 9648 1.15 .87 .881 .824 .956 6.299 52 273 .853 .91 80 2270 6770 21 29 75 83 0 2842 140 2701 .623 3376 3236 1.606 .631 -.684 -.665
4 6059 10032 78 186 5980 9845 6975 11561 84 227 6896 11375 0 0 2385 4782 34 217 100 98 100 98 15825 18271 .607 1.646 1.65 1.464 1.765 4.834 52 258 1.684 .93 80 2420 6770 21 29 90 98 0 7183 133 7049 1.179 8278 8144 .848 1.181 .237 .24
5 3837 2510 76 191 3761 2319 5069 3203 96 253 4993 3012 0 0 2414 1818 105 344 80 69 78 63 6080 8005 1.622 .617 .603 .574 .696 4.899 52 289 .68 .93 90 2570 6770 20 29 104 113 0 1797 137 1660 .441 2293 2157 2.265 .432 -1.18 -1.211
6 319 208 75 188 244 20 307 209 86 227 232 21 0 0 76 108 66 175 100 9 96 0 264 253 12.2 .082 .091 .29 .317 5.344 32 202 46.742 .12 70 2720 6770 21 28 120 127 0 149 135 14 .059 150 15 17.039 .065 -4.091 -3.948
7 2800 5956 92 198 2707 5757 2727 6254 107 259 2635 6055 0 0 463 2095 60 316 100 98 100 92 8464 8690 .47 2.127 2.298 1.92 2.259 4.087 52 291 2.324 .92 90 2870 6770 20 29 134 143 0 4264 142 4122 1.523 4478 4335 .657 1.645 .607 .718
8 141 180 78 186 63 -5 127 147 88 206 49 -39 0 0 49 212 42 146 53 13 30 1 58 10 null null null 1.886 2.316 15.516 52 284 42.795 .06 90 3020 6770 20 29 149 158 -50 129 133 -4 null 105 -28 null null null null
9 5864 8754 77 193 5786 8560 6597 10282 81 222 6520 10088 0 0 2115 4317 30 146 100 94 100 88 14346 16608 .676 1.479 1.547 1.149 1.537 5.152 52 234 1.55 .94 80 3180 6770 21 29 166 174 0 6268 138 6129 1.059 7362 7223 .944 1.108 .083 .148
10 110 186 76 175 33 11 96 147 84 211 20 -27 0 0 52 147 38 193 40 11 19 3 44 -7 3 .333 null 3.112 4.083 9.008 52 281 -1 -1 90 3320 6760 19 28 179 188 -50 133 125 8 .239 105 -19 4.19 null -2.067 null
11 107 175 71 185 36 -10 98 141 80 221 27 -43 0 0 37 117 33 209 46 5 21 0 26 -16 null null null 7.049 7.063 17.219 52 313 31.395 .22 90 3470 6760 19 28 194 203 -50 125 132 -7 null 101 -31 null null null null
12 271 455 74 192 196 263 268 460 83 244 194 267 0 0 49 179 35 257 100 50 100 9 459 461 .745 1.342 1.376 1.163 1.359 4.781 32 202 4.691 .34 70 3630 6770 21 28 211 218 0 326 137 188 .961 329 191 1.041 .985 -.058 -.021
13 158 392 69 182 89 209 152 350 80 228 82 167 0 0 77 227 46 238 65 42 44 13 298 249 .426 2.348 2.037 2.478 3.236 5.806 52 296 15.695 .24 90 3770 6760 19 28 224 233 -50 281 130 150 1.681 251 120 .595 1.458 .75 .544
14 132 235 71 183 61 52 134 193 78 234 63 10 0 0 48 175 40 328 63 7 34 1 113 73 1.173 .852 .159 1.306 .884 16.085 52 292 18.983 .08 90 3920 6760 19 28 239 248 -50 168 131 37 .61 138 7 1.638 .114 -.712 -3.137
15 107 169 75 185 31 -15 102 151 83 243 27 -33 0 0 33 112 42 328 36 1 5 0 16 -6 null null null 3.744 2.838 10.802 52 292 15.133 .29 90 4070 6760 19 28 254 263 -50 121 132 -11 null 108 -24 null null null null
16 99 159 76 175 22 -15 87 138 90 230 11 -36 0 0 40 94 100 277 3 0 0 0 7 -25 null null null 3.577 2.945 9.168 52 292 -1 -1 90 4220 6760 19 28 269 278 -50 114 125 -11 null 99 -26 null null null null
17 507 353 76 170 431 182 583 316 82 205 507 146 0 0 303 211 35 144 82 50 78 28 613 653 2.368 .422 .288 .589 .501 6.199 52 292 .373 .41 90 4370 6760 19 28 284 293 0 253 122 130 .302 226 105 3.307 .206 -1.726 -2.278
18 96 212 77 177 18 34 91 170 82 221 13 -7 0 0 39 173 34 180 30 21 15 3 52 6 .529 1.889 null 3.969 5.723 7.966 52 292 84.158 .06 90 4520 6760 19 28 299 308 -50 152 127 24 1.352 122 -5 .739 null .436 null
19 87 153 75 195 12 -41 80 124 81 248 5 -70 0 0 31 89 31 276 30 0 7 0 -29 -65 null null null 6.636 6.282 6.676 52 308 92.608 .03 90 4670 6760 19 28 314 323 -50 110 140 -29 null 89 -50 null null null null
20 149 224 71 180 78 43 144 177 78 227 72 -2 0 0 66 149 30 183 73 13 53 5 121 70 1.814 .551 null 1.869 2.396 8.72 52 302 8.462 .14 90 4830 6760 19 28 330 339 -50 160 129 31 .395 127 -1 2.533 null -1.341 null

Total number of rows: 44544

Table truncated, full table size 9476 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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