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Sample GSM989708 Query DataSets for GSM989708
Status Public on Aug 23, 2012
Title PC 366T
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 366T2
Organism Homo sapiens
Characteristics ethnicity: Caucasian
age: 58
pre-operation treatment: None
individual: PC 167T
disease free survival: 54.93
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/2008-08/81108.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) [email protected]
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 29789 43776 65 105 29724 43671 32906 47734 70 121 32841 47629 0 0 9647 14164 25 84 100 100 100 100 73395 80470 .681 1.469 1.45 1.479 1.463 2.202 32 234 1.463 .99 70 1780 7270 7 14 26 33 0 35595 85 35510 1.195 38813 38728 .837 1.179 .257 .238
2 30937 42289 84 150 30853 42138 36613 50284 90 166 36529 50133 3 0 13349 18373 31 83 100 100 100 100 72991 86662 .732 1.366 1.372 1.388 1.342 2.71 32 236 1.364 .99 70 1930 7260 6 13 41 48 0 34386 122 34263 1.111 40887 40764 .9 1.116 .151 .158
3 15741 33144 99 171 15641 32972 19061 38881 105 195 18961 38709 0 0 7205 14923 41 102 100 100 100 100 48613 57670 .474 2.108 2.042 2.028 2.104 2.806 32 230 2.073 .99 70 2080 7250 5 12 56 63 0 26950 139 26810 1.714 31615 31475 .583 1.66 .777 .731
4 38190 56435 127 196 38063 56238 40833 61237 132 220 40705 61040 6 0 8841 17456 44 112 100 100 100 100 94301 101745 .677 1.477 1.5 1.395 1.505 2.533 32 226 1.496 .99 70 2230 7250 5 12 71 78 0 45888 159 45728 1.201 49793 49633 .832 1.219 .265 .286
5 1158 524 169 272 989 251 1233 538 168 290 1064 265 0 0 286 116 48 119 100 90 100 53 1240 1329 3.94 .254 .249 .233 .268 3.438 32 169 .223 .67 60 2380 7260 7 13 87 93 0 426 221 204 .206 437 215 4.846 .203 -2.277 -2.304
6 13205 28649 278 470 12927 28178 18019 38496 320 560 17740 38025 0 0 7778 16764 198 383 96 98 86 90 41105 55765 .459 2.18 2.143 2.218 2.162 2.561 52 290 2.164 .99 90 2530 7250 4 13 100 109 0 23295 382 22912 1.772 31302 30919 .564 1.743 .826 .801
7 413 373 192 361 220 12 455 348 214 384 262 -12 0 0 130 132 100 159 83 8 75 8 232 250 18.333 .055 null .203 .219 8.708 12 104 -.055 -.04 50 2680 7240 5 10 117 122 0 303 294 10 .044 283 -10 22.547 null -4.495 null
8 13205 30577 71 163 13133 30414 15986 35387 78 193 15914 35223 0 0 9587 22184 31 155 100 100 98 98 43547 51137 .432 2.316 2.213 2.688 2.342 3.163 52 274 2.319 .99 80 2840 7260 6 14 132 140 0 24863 133 24730 1.883 28774 28640 .531 1.8 .913 .848
9 264 405 56 130 208 275 283 409 61 156 226 279 0 0 65 127 21 127 100 84 100 56 483 505 .756 1.322 1.235 1.155 1.269 4.698 32 175 1.538 .77 60 2990 7250 6 12 148 154 0 329 106 224 1.075 333 227 .93 1.004 .104 .005
10 241 494 51 128 190 365 234 485 54 153 182 357 0 0 35 117 14 113 100 100 100 84 555 539 .521 1.921 1.962 1.845 1.847 2.745 32 214 2.635 .83 70 3140 7260 6 13 162 169 0 402 104 297 1.562 394 290 .64 1.595 .643 .674
11 892 2559 49 112 842 2447 909 2648 52 127 860 2536 0 0 148 413 14 76 100 100 100 100 3289 3396 .344 2.906 2.949 2.904 2.872 2.302 32 227 2.921 .98 70 3290 7250 5 12 177 184 0 2081 91 1990 2.363 2153 2062 .423 2.398 1.241 1.262
12 941 2234 50 116 891 2118 963 2230 52 139 913 2113 0 0 136 415 14 89 100 100 100 100 3009 3026 .421 2.377 2.314 2.355 2.257 2.248 32 230 2.372 .97 70 3440 7250 5 12 192 199 0 1817 94 1722 1.933 1813 1718 .517 1.882 .951 .912
13 522 438 49 116 473 322 531 436 52 143 482 319 0 0 91 130 16 137 100 90 100 68 795 801 1.469 .681 .662 .632 .644 2.758 32 230 .681 .83 70 3590 7250 5 12 207 214 0 356 94 262 .554 355 259 1.807 .538 -.853 -.894
14 176 251 46 105 129 146 176 242 49 116 130 137 0 0 44 71 13 59 100 93 96 59 275 267 .884 1.132 1.054 1.094 1.275 3.079 32 221 1.526 .64 70 3740 7250 5 12 222 229 0 204 85 119 .92 197 111 1.087 .857 -.12 -.223
15 46 55 46 103 0 -48 44 47 49 114 -1 -56 0 0 7 26 15 66 3 0 0 0 -48 -57 null null null 9.44 11.179 5.249 52 272 7.244 .59 90 3890 7250 4 13 236 245 -50 45 84 -39 null 38 -46 null null null null
16 1084 1448 47 99 1037 1348 1340 1828 48 114 1293 1729 0 0 536 762 13 74 100 96 98 92 2385 3022 .769 1.3 1.337 1.234 1.305 3.039 52 238 1.323 .98 80 4050 7250 5 13 253 261 0 1177 80 1096 1.057 1486 1406 .946 1.087 .08 .121
17 120 221 46 109 74 112 117 213 49 131 70 103 0 0 22 81 15 91 100 56 100 18 186 173 .661 1.514 1.471 1.389 1.552 4.183 32 197 3.762 .49 70 4200 7250 5 12 268 275 0 180 89 91 1.231 173 84 .813 1.196 .299 .259
18 44 89 45 113 -1 -23 41 70 49 138 -3 -42 0 0 9 71 18 110 5 5 0 1 -24 -45 null null null 7.782 7.803 5.871 52 242 9.861 .58 90 4350 7240 3 12 282 291 -50 72 92 -19 null 57 -34 null null null null
19 678 815 47 113 630 701 673 844 51 132 625 730 0 0 119 156 13 89 100 100 100 100 1331 1355 .899 1.113 1.168 1.104 1.135 2.432 32 211 1.094 .93 70 4500 7240 4 11 298 305 0 663 92 570 .905 686 594 1.105 .95 -.144 -.074
20 3866 13568 52 127 3814 13440 4451 15301 55 148 4399 15174 0 0 1368 4387 16 107 100 100 100 100 17254 19573 .284 3.524 3.449 3.7 3.554 2.377 32 214 3.463 .99 70 4650 7240 4 11 313 320 0 11032 103 10928 2.865 12442 12338 .349 2.805 1.519 1.488

Total number of rows: 44544

Table truncated, full table size 9059 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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