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Sample GSM989743 Query DataSets for GSM989743
Status Public on Aug 23, 2012
Title PC 629T
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 629T2
Organism Homo sapiens
Characteristics ethnicity: Caucasian
age: 72
pre-operation treatment: None
individual: PC 361T
disease free survival: 24.40
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/2008-08/81072.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 18480 28199 87 202 18392 27997 16623 34468 99 251 16536 34265 0 0 18057 22472 58 188 90 96 81 87 46389 50801 .657 1.522 2.072 2.836 1.355 11.688 32 221 1.333 .91 70 1700 6940 18 25 42 49 0 25161 180 24981 1.358 30754 30573 .736 1.849 .442 .887
2 17415 26362 96 174 17318 26188 9118 20971 98 209 9021 20797 0 0 17632 22120 32 122 100 100 96 100 43506 29818 .661 1.512 2.305 2.733 1.345 7.63 32 158 1.332 .92 60 1860 6940 19 25 59 65 0 23522 155 23367 1.349 18712 18556 .741 2.057 .432 1.041
3 7104 16653 83 174 7020 16479 3470 11534 96 224 3386 11360 0 0 7639 14900 52 206 87 93 81 84 23499 14746 .426 2.347 3.355 3.577 2.079 9.833 32 169 2.129 .92 60 2010 6940 19 25 74 80 0 14859 155 14704 2.095 10291 10136 .477 2.994 1.067 1.582
4 24422 36852 97 174 24325 36678 21017 38329 104 202 20919 38155 21 0 19196 24038 42 132 100 100 100 100 61003 59074 .663 1.508 1.824 2.459 1.367 8.303 32 169 1.371 .94 60 2160 6940 19 25 89 95 -100 32882 155 32726 1.345 34199 34044 .743 1.627 .428 .703
5 1227 506 77 154 1150 351 1246 489 87 205 1168 334 0 0 320 192 61 223 100 83 100 25 1501 1502 3.276 .305 .286 .251 .258 4.576 12 104 .285 .7 50 2310 6930 18 23 104 109 0 451 137 313 .272 436 298 3.672 .255 -1.877 -1.971
6 4346 7745 84 172 4261 7572 562 3438 94 198 478 3266 0 0 5309 8326 53 121 91 82 80 73 11833 3744 .563 1.777 6.833 2.003 1.596 4.906 80 426 1.627 .95 100 2480 6930 16 26 119 129 0 6911 153 6756 1.586 3068 2914 .631 6.096 .665 2.608
7 362 264 78 160 283 104 358 248 93 175 280 87 0 0 51 75 76 107 100 41 100 8 387 367 2.721 .367 .311 .229 .395 7.214 12 104 .479 .37 50 2620 6930 18 23 135 140 0 236 143 93 .328 221 78 3.05 .277 -1.609 -1.851
8 9491 21751 79 154 9411 21596 8090 25463 86 174 8011 25308 0 0 8349 15591 38 96 90 100 87 100 31007 33319 .436 2.295 3.159 4.39 2.314 7.336 32 176 2.094 .95 60 2770 6930 18 24 150 156 0 19408 137 19269 2.048 22720 22581 .488 2.819 1.034 1.495
9 243 370 69 153 174 217 235 343 77 179 165 189 0 0 59 179 30 115 100 66 100 41 391 354 .802 1.247 1.145 .64 1.102 11.744 12 68 2.364 .53 40 2910 6910 17 21 165 169 0 330 137 194 1.113 306 169 .899 1.022 .154 .031
10 143 238 65 138 77 100 91 165 78 168 25 27 0 0 126 184 47 122 38 34 28 13 177 52 .77 1.299 1.08 1.668 1.262 7.281 52 315 2.035 .67 90 3060 6920 15 24 177 186 -50 212 123 89 1.159 147 24 .863 .964 .213 -.053
11 509 1310 71 152 437 1158 588 1377 78 177 517 1225 0 0 278 518 32 105 90 93 78 93 1595 1742 .377 2.65 2.369 3.244 2.531 5.764 32 169 2.479 .87 60 3220 6930 18 24 195 201 0 1169 136 1033 2.364 1229 1093 .423 2.114 1.241 1.08
12 699 1666 75 158 624 1507 758 1679 86 211 683 1520 0 0 209 471 50 168 100 100 100 100 2131 2203 .414 2.415 2.225 2.435 2.305 2.663 12 104 2.892 .9 50 3370 6920 17 22 210 215 0 1487 141 1345 2.155 1498 1356 .464 1.986 1.108 .99
13 402 276 74 165 328 110 382 273 91 242 307 107 0 0 84 37 59 304 100 0 100 0 438 414 2.982 .335 .349 .323 .313 3.011 12 104 .514 .48 50 3520 6920 17 22 225 230 0 246 147 98 .299 244 95 3.342 .311 -1.741 -1.685
14 110 217 74 160 35 57 86 217 79 185 11 57 0 0 56 118 27 132 44 25 30 7 92 68 .614 1.629 5.182 2.993 3.056 6.583 52 300 5.996 .4 90 3670 6920 15 24 238 247 -50 194 143 51 1.453 194 51 .688 4.624 .539 2.209
15 68 153 73 164 -4 -11 66 125 79 193 -6 -39 0 0 18 96 31 147 3 3 1 1 -15 -45 null null null 3.99 4.584 7.793 52 292 9.724 .38 90 3820 6920 15 24 253 262 -50 137 146 -10 null 112 -35 null null null null
16 658 1144 73 160 584 984 683 1197 76 186 609 1037 0 0 440 602 24 117 93 90 87 87 1568 1646 .593 1.685 1.703 2.222 1.702 5.687 32 163 1.523 .91 60 3980 6920 17 23 271 277 0 1021 143 878 1.503 1068 925 .665 1.519 .588 .603
17 125 251 78 175 46 75 107 228 84 206 28 52 0 0 63 139 42 168 42 21 34 3 121 80 .613 1.63 1.857 2.595 2.709 9.192 52 276 4.868 .58 90 4120 6920 15 24 283 292 -50 224 156 67 1.455 203 46 .687 1.657 .541 .729
18 76 178 71 175 5 2 74 142 83 211 2 -33 0 0 25 128 57 179 3 9 0 3 7 -31 2.5 .4 null 4.662 4.894 8.639 52 300 8.111 .26 90 4270 6920 15 24 298 307 -50 159 156 2 .357 127 -29 2.802 null -1.486 null
19 440 662 65 131 375 531 468 624 70 157 403 493 0 0 140 273 22 112 100 90 100 84 906 896 .706 1.416 1.223 1.326 1.241 3.473 32 176 1.495 .83 60 4440 6910 16 22 317 323 0 591 117 474 1.263 557 440 .791 1.092 .337 .126
20 2004 8321 70 164 1933 8156 1535 6982 76 192 1464 6818 0 0 1684 6682 25 104 81 96 81 96 10089 8282 .237 4.219 4.657 5.65 4.458 4.648 32 165 4.142 .98 60 4580 6920 17 23 331 337 0 7425 146 7277 3.765 6230 6083 .266 4.155 1.913 2.055

Total number of rows: 44544

Table truncated, full table size 9508 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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