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Sample GSM989814 Query DataSets for GSM989814
Status Public on Aug 23, 2012
Title PC 527T2
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 527T2
Organism Homo sapiens
Characteristics individual: PC 527T
disease state: Tumor
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/2008-09/81293.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
1 815 775 30 96 785 678 906 794 31 126 875 697 0 0 529 514 5 96 96 78 96 73 1463 1572 1.158 .864 .797 .848 .85 7.016 80 436 .799 .84 100 1790 6770 20 30 34 44 0 647 80 566 .721 663 582 1.387 .665 -.472 -.588
2 2123 1970 32 98 2091 1872 2002 1771 34 126 1969 1672 0 0 676 842 7 96 100 100 100 100 3963 3641 1.117 .895 .849 .857 .89 2.85 52 233 .906 .95 90 1940 6780 21 30 49 58 0 1645 82 1563 .747 1479 1396 1.338 .709 -.42 -.496
3 5262 6887 35 136 5227 6751 5087 6373 107 239 5052 6237 0 0 1414 2214 731 823 100 100 100 100 11978 11289 .774 1.292 1.235 1.267 1.319 2.585 52 339 1.257 .96 90 2080 6740 17 26 63 72 0 5750 114 5637 1.078 5321 5207 .927 1.031 .109 .044
4 4901 5311 37 173 4864 5138 5055 5099 113 268 5017 4925 0 0 1687 1841 749 841 93 96 92 95 10002 9942 .947 1.056 .982 1.133 1.033 4.342 80 323 1.06 .95 100 2240 6770 20 30 79 89 0 4434 144 4290 .882 4257 4112 1.134 .82 -.181 -.287
5 384 232 40 174 343 57 371 221 48 195 330 46 0 0 82 136 21 121 100 30 100 9 400 376 6.018 .166 .139 .368 .395 4.652 52 234 .148 .18 90 2390 6770 20 29 94 103 0 194 145 48 .139 185 38 7.207 .116 -2.849 -3.103
6 3992 3932 55 173 3937 3759 3658 3623 61 198 3602 3449 0 0 1143 1368 26 136 100 100 100 100 7696 7051 1.047 .955 .958 .93 .948 2.66 80 310 1.018 .94 110 2540 6770 19 30 108 119 0 3283 144 3138 .797 3025 2880 1.254 .799 -.327 -.323
7 110 201 42 180 68 20 123 187 53 211 80 7 0 0 55 130 29 142 65 15 58 4 88 87 3.4 .294 .088 1.891 1.445 14.02 120 420 12.732 .07 120 2690 6770 19 31 123 135 -50 168 150 17 .246 156 6 4.072 .073 -2.026 -3.775
8 10043 13434 38 155 10005 13279 10787 14089 45 190 10748 13934 0 0 3659 4539 23 138 100 100 100 100 23284 24682 .753 1.327 1.296 1.425 1.308 3.945 80 398 1.316 .96 110 2840 6770 19 30 138 149 0 11216 129 11087 1.108 11763 11634 .902 1.082 .148 .114
9 113 149 54 143 59 5 113 149 63 168 59 5 0 0 19 85 30 118 91 8 50 0 64 64 11.8 .085 .085 1.034 1.501 4.306 12 89 -4.54 -.27 50 3000 6800 25 30 157 162 0 124 119 4 .071 124 4 14.133 .071 -3.821 -3.821
10 132 151 37 155 95 -4 132 114 47 174 94 -41 0 0 29 116 27 118 100 12 90 3 91 53 null null null 1.021 .892 4.807 32 130 -6.263 -.18 60 3160 6780 23 29 173 179 0 126 129 -3 null 95 -34 null null null null
11 367 665 34 158 333 506 345 632 35 187 311 474 0 0 167 361 7 124 97 85 96 72 839 785 .658 1.52 1.524 1.42 1.475 6.713 80 277 1.6 .81 100 3300 6770 20 30 185 195 0 555 132 422 1.269 528 396 .788 1.273 .343 .348
12 264 538 34 149 230 389 247 541 34 171 213 392 0 0 74 259 6 113 100 87 100 71 619 605 .591 1.691 1.84 1.457 1.652 4.508 80 287 2.152 .7 110 3440 6770 19 30 198 209 0 449 124 325 1.412 452 327 .708 1.537 .498 .62
13 219 185 34 187 185 -2 214 171 35 229 180 -16 0 0 48 108 7 160 100 2 100 1 183 164 null null null .346 .399 5.953 80 224 -.09 -.04 100 3590 6770 20 30 214 224 0 154 156 -2 null 143 -13 null null null null
14 139 330 33 165 106 164 142 292 34 201 108 126 0 0 28 164 6 133 100 47 100 26 270 234 .646 1.547 1.167 1.265 1.426 6.079 80 236 4.554 .37 110 3730 6770 19 30 227 238 0 276 138 137 1.292 244 105 .774 .974 .369 -.038
15 41 104 34 165 6 -61 40 67 39 195 6 -98 0 0 8 86 23 142 3 2 0 0 -55 -92 null null null 12.302 17.524 8.289 120 420 -69.925 -.09 120 3880 6760 18 30 242 254 -100 87 138 -51 null 56 -82 null null null null
16 723 1528 34 157 689 1371 731 1436 39 187 696 1279 0 0 268 561 23 149 98 98 98 96 2060 1975 .503 1.99 1.838 2.089 2.009 3.627 80 314 1.989 .92 110 4040 6760 18 29 258 269 0 1276 131 1145 1.661 1199 1068 .602 1.534 .732 .618
17 74 135 34 157 40 -22 74 96 34 182 40 -60 0 0 25 117 6 118 88 12 80 5 18 -20 null null null 2.934 3.52 10.919 120 314 -21.53 -.2 120 4190 6760 18 30 273 285 -50 113 131 -18 null 80 -50 null null null null
18 38 121 36 161 2 -39 37 93 40 190 1 -67 0 0 6 98 18 129 0 7 0 0 -37 -66 null null null 20.65 23.417 5.692 120 400 -1 -1 120 4340 6760 18 30 288 300 -100 101 134 -33 null 78 -56 null null null null
19 307 378 38 179 268 199 294 340 61 218 256 161 0 0 105 211 115 220 97 41 61 13 467 417 1.347 .743 .629 .652 .881 5.317 80 355 .92 .51 100 4500 6770 20 30 305 315 0 316 149 166 .62 284 134 1.613 .525 -.69 -.929
20 1302 6574 36 179 1265 6395 1226 6218 55 215 1189 6038 0 0 328 1641 115 220 100 100 100 100 7660 7227 .198 5.055 5.078 5.08 4.998 2.623 80 358 5.248 .95 110 4640 6760 18 29 318 329 0 5489 149 5339 4.221 5192 5041 .237 4.24 2.078 2.084

Total number of rows: 44544

Table truncated, full table size 9620 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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