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Sample GSM989682 Query DataSets for GSM989682
Status Public on Aug 23, 2012
Title PC 103T
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 PT 103
Organism Homo sapiens
Characteristics ethnicity: Caucasian
age: 57
disease state: Tumor
pre-operation treatment: None
individual: PC 19T
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/2008-11/81778.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 GPL15972
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 11640 6496 71 228 11568 6267 12719 6740 77 232 12647 6511 0 0 3186 1460 29 68 100 100 100 100 17835 19158 1.846 .542 .515 .56 .54 2.054 52 294 .524 .97 80 1860 7980 26 34 50 58 0 5869 206 5662 .489 6089 5882 2.043 .465 -1.031 -1.104
2 11241 6504 71 228 11169 6275 12696 7171 75 233 12624 6943 0 0 4100 2038 23 69 100 100 100 100 17444 19567 1.78 .562 .55 .598 .554 2.158 52 297 .546 .98 90 2010 7980 25 34 64 73 0 5876 206 5669 .508 6479 6273 1.97 .497 -.978 -1.009
3 18733 40919 74 241 18659 40677 21796 46314 75 246 21722 46072 0 0 7698 12716 14 85 100 100 100 100 59336 67794 .459 2.18 2.121 2.538 2.132 2.311 52 258 2.092 .98 80 2160 7980 26 34 80 88 0 36968 218 36749 1.97 41842 41623 .508 1.916 .978 .938
4 11842 6505 75 252 11766 6253 12762 6868 76 256 12686 6616 0 0 2989 1257 15 68 100 100 100 100 18019 19302 1.882 .531 .522 .548 .517 1.922 52 274 .515 .98 80 2310 7980 26 34 95 103 0 5877 228 5649 .48 6205 5977 2.083 .471 -1.059 -1.086
5 1050 432 75 250 975 182 1071 426 76 256 996 176 0 0 146 87 19 69 100 90 100 69 1157 1172 5.357 .187 .177 .168 .178 2.673 52 261 .196 .76 80 2470 7980 26 34 111 119 0 390 226 164 .169 385 159 5.93 .16 -2.568 -2.647
6 6485 6737 87 273 6398 6464 5584 7797 121 292 5497 7523 0 0 5305 5266 97 114 100 99 98 97 12862 13020 .99 1.01 1.369 .973 1.004 2.372 120 489 .995 .97 130 2620 7980 23 36 123 136 0 6086 247 5840 .913 7044 6797 1.096 1.236 -.132 .306
7 245 364 81 263 163 100 248 331 115 283 166 68 0 0 147 140 102 118 58 29 36 13 263 234 1.63 .613 .41 .855 .768 6.385 120 406 .359 .89 130 2740 7990 24 37 135 148 0 329 238 90 .554 299 61 1.804 .37 -.851 -1.434
8 20693 44445 75 245 20617 44200 23873 48757 80 265 23797 48511 0 0 8069 13553 25 129 100 100 100 100 64817 72308 .466 2.144 2.039 2.435 2.064 2.313 52 279 2.062 .98 90 2910 7980 25 34 154 163 0 40153 221 39932 1.937 44049 43826 .516 1.842 .954 .881
9 340 276 73 233 267 43 342 264 78 255 268 31 0 0 70 59 27 134 100 9 100 0 310 299 6.209 .161 .116 .166 .168 4.873 52 234 .072 .06 80 3070 7980 26 34 171 179 0 249 211 39 .145 239 28 6.873 .105 -2.781 -3.258
10 379 352 66 210 313 141 368 337 70 220 301 126 0 0 65 70 23 76 100 84 100 34 454 427 2.22 .45 .419 .402 .393 2.618 32 187 2.234 .45 70 3210 7980 26 33 185 192 0 318 190 127 .407 304 114 2.457 .378 -1.297 -1.403
11 1377 2049 65 213 1312 1836 1391 1972 66 223 1326 1759 0 0 394 662 14 69 100 100 100 100 3148 3085 .715 1.399 1.327 1.353 1.449 2.016 52 302 1.449 .96 90 3370 7970 24 33 200 209 0 1851 192 1659 1.264 1782 1589 .791 1.198 .338 .261
12 1001 1607 65 208 935 1398 1003 1669 65 221 938 1461 0 0 251 455 13 70 100 100 100 100 2333 2399 .669 1.495 1.558 1.447 1.528 1.951 52 284 1.543 .96 90 3520 7980 25 34 215 224 0 1452 188 1263 1.351 1508 1320 .74 1.407 .434 .493
13 737 433 64 209 672 223 750 428 67 226 686 219 0 0 173 106 24 100 100 90 100 55 895 905 3.013 .332 .319 .294 .327 3.009 52 231 .343 .83 80 3670 7980 26 34 231 239 0 391 189 201 .3 387 198 3.336 .288 -1.738 -1.794
14 348 492 64 211 283 280 351 485 65 228 287 273 0 0 70 101 25 110 100 96 100 71 563 560 1.011 .989 .951 .974 .929 2.161 52 203 1.06 .84 80 3820 7980 26 34 246 254 0 444 191 253 .894 438 247 1.119 .859 -.162 -.219
15 64 134 61 213 2 -79 60 128 62 219 0 -85 0 0 10 63 11 67 16 1 5 0 -77 -85 null null null 14.919 14.751 4.479 80 306 103.708 .06 100 3970 7980 25 35 260 270 -50 121 192 -71 null 116 -77 null null null null
16 3323 6143 63 211 3259 5931 3323 6152 65 221 3260 5940 0 0 819 1082 14 67 100 100 100 100 9190 9200 .549 1.82 1.822 1.865 1.848 1.797 52 226 1.789 .97 80 4120 7980 26 34 276 284 0 5550 191 5358 1.644 5558 5366 .608 1.646 .717 .719
17 160 208 63 207 96 1 162 196 66 215 99 -10 0 0 23 53 15 71 100 9 100 0 97 89 96 .01 null .343 .518 4.3 32 145 .604 .05 60 4280 7980 27 33 293 299 0 188 187 1 .009 177 -9 106.261 null -6.731 null
18 65 150 64 208 0 -57 62 130 66 214 -1 -77 0 0 19 146 15 61 8 8 3 2 -57 -78 null null null 8.739 9.535 4.725 80 336 19.677 .29 100 4420 7970 24 34 305 315 -50 136 188 -51 null 117 -70 null null null null
19 962 1164 69 206 893 958 912 1137 74 214 843 931 0 0 248 286 26 73 100 100 100 100 1851 1774 .932 1.073 1.104 1.064 1.067 1.773 52 284 1.079 .94 90 4570 7970 24 33 320 329 0 1052 186 865 .969 1027 841 1.032 .998 -.045 -.003
20 4385 16782 63 198 4321 16583 4518 16614 65 208 4455 16415 0 0 994 3503 15 63 100 100 100 100 20904 20870 .261 3.838 3.685 3.888 3.884 1.767 52 293 3.847 .98 90 4720 7970 24 33 335 344 0 15161 179 14982 3.467 15010 14830 .288 3.329 1.794 1.735

Total number of rows: 44544

Table truncated, full table size 9587 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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