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Sample GSM989686 Query DataSets for GSM989686
Status Public on Aug 23, 2012
Title PC 423N
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 423N2
Organism Homo sapiens
Characteristics individual: PC 423N
disease state: Normal
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/2008-08/81170.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 GPL9497
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 20322 24276 70 92 20251 24183 25135 27546 74 99 25064 27453 0 0 8359 6759 19 47 100 100 100 100 44434 52517 .837 1.194 1.095 1.324 1.114 1.717 52 249 1.132 .96 80 1820 7560 32 40 38 46 0 20692 78 20613 1.018 23480 23400 .982 .934 .026 -.099
2 19644 24120 78 105 19565 24015 25188 29575 80 114 25109 29470 0 0 12022 11413 19 56 100 100 100 100 43580 54579 .815 1.227 1.174 1.685 1.152 2.569 52 206 1.143 .97 80 1960 7560 32 40 52 60 0 20559 89 20470 1.046 25209 25120 .956 1 .065 .001
3 19312 30399 74 96 19237 30302 25627 37911 77 107 25552 37814 0 0 11437 14329 18 56 98 100 96 100 49539 63366 .635 1.575 1.48 2.449 1.464 3.303 52 224 1.498 .96 80 2110 7560 32 40 67 75 0 25911 82 25829 1.343 32314 32232 .745 1.261 .425 .335
4 22083 27684 78 108 22004 27575 28150 32732 81 114 28072 32624 0 0 10758 8981 20 49 100 100 100 100 49579 60696 .798 1.253 1.162 1.51 1.14 2.177 52 227 1.169 .95 80 2270 7560 32 40 83 91 0 23597 92 23504 1.068 27900 27808 .936 .991 .095 -.014
5 1195 610 78 101 1117 508 1429 635 88 112 1351 533 0 0 504 202 32 67 98 96 98 92 1625 1884 2.199 .455 .395 .468 .414 1.733 52 209 .426 .92 80 2420 7560 32 40 98 106 0 520 86 433 .388 541 454 2.58 .336 -1.367 -1.572
6 11760 16561 84 100 11676 16460 15583 20811 88 108 15498 20710 0 0 7637 8824 28 47 100 100 100 100 28136 36208 .709 1.41 1.336 1.926 1.325 2.627 80 314 1.334 .96 100 2570 7560 31 41 112 122 0 14116 85 14030 1.202 17739 17653 .832 1.139 .265 .188
7 481 469 84 103 397 365 482 396 85 110 398 292 0 0 81 288 24 45 100 100 100 100 762 690 1.088 .919 .734 .806 .722 1.757 32 175 1.381 .66 70 2720 7560 32 39 128 135 0 400 88 311 .784 338 249 1.276 .625 -.352 -.677
8 25632 38496 82 107 25549 38389 31350 42754 84 114 31268 42647 0 0 10754 10126 18 45 100 100 100 100 63938 73915 .666 1.503 1.364 1.756 1.361 2.297 52 236 1.431 .94 80 2860 7560 32 40 142 150 0 32813 91 32722 1.281 36442 36351 .781 1.163 .357 .217
9 357 479 77 98 279 380 365 477 80 117 287 378 0 0 75 122 20 112 100 100 100 96 659 665 .734 1.362 1.317 1.361 1.292 1.66 32 215 1.815 .7 70 3020 7550 31 38 158 165 0 408 84 324 1.161 407 322 .861 1.123 .215 .167
10 315 538 72 96 242 441 345 541 73 101 272 444 0 0 104 102 13 45 96 100 93 100 683 716 .549 1.822 1.632 2.351 1.703 3.261 32 222 1.777 .88 70 3170 7550 31 38 173 180 0 459 82 376 1.553 461 378 .644 1.391 .635 .477
11 971 2607 69 87 901 2520 1117 2758 71 96 1047 2671 0 0 420 784 13 47 100 100 98 100 3421 3718 .358 2.797 2.551 3.327 2.586 2.115 52 284 2.778 .92 80 3310 7560 32 40 187 195 0 2222 74 2148 2.384 2351 2277 .419 2.174 1.253 1.121
12 817 11042 72 94 745 10948 963 12251 74 105 890 12156 0 0 351 3505 15 46 92 100 92 100 11693 13046 .068 14.695 13.658 18.009 13.375 2.435 52 296 14.861 .93 90 3470 7550 30 39 202 211 0 9412 80 9332 12.526 10442 10361 .08 11.642 3.647 3.541
13 671 844 77 115 593 728 715 765 83 125 638 650 0 0 170 298 24 60 100 100 100 100 1321 1288 .815 1.228 1.019 1.21 .944 1.929 32 202 1.286 .78 70 3610 7550 31 38 217 224 0 719 98 621 1.046 652 554 .956 .868 .065 -.204
14 309 626 84 120 225 506 297 562 90 141 212 441 0 0 150 382 29 92 94 98 86 92 731 653 .445 2.249 2.08 2.326 2.102 2.097 52 224 2.596 .89 80 3770 7560 32 40 233 241 0 534 102 431 1.917 479 376 .522 1.773 .939 .826
15 94 144 82 123 11 20 89 126 89 155 6 3 0 0 28 62 39 133 10 5 3 0 31 9 .55 1.818 .5 2.884 2.657 4.067 80 311 4.66 .59 100 3920 7550 30 40 247 257 -50 123 105 17 1.55 107 3 .645 .426 .632 -1.23
16 1570 2069 97 180 1473 1889 1863 2227 197 517 1765 2047 0 0 680 591 203 682 88 92 86 82 3362 3812 .78 1.282 1.16 1.372 1.157 2.054 52 204 1.28 .9 80 4070 7550 31 39 263 271 0 1764 153 1610 1.093 1898 1745 .915 .989 .128 -.017
17 168 309 441 1255 -273 -946 144 264 491 1408 -297 -991 0 0 110 277 387 1197 0 0 0 0 -1219 -1288 null null null 3.424 3.272 1.341 80 273 3.258 .95 100 4220 7550 30 40 277 287 -50 263 1070 -806 null 225 -845 null null null null
18 107 231 103 183 3 48 92 157 202 492 -11 -25 0 0 65 207 231 632 2 5 0 0 51 -36 .063 16 null 2.897 2.089 3.249 80 276 3.204 .79 100 4370 7550 30 40 292 302 -50 197 156 41 13.638 134 -21 .073 null 3.77 null
19 237 346 73 116 164 230 240 333 184 363 167 217 0 0 70 158 732 1582 0 0 0 0 394 384 .713 1.402 1.299 1.321 1.221 2.555 52 249 3.99 .55 90 4520 7550 30 39 307 316 0 295 99 196 1.195 284 185 .837 1.108 .258 .147
20 3534 19425 75 119 3459 19306 4256 21839 166 386 4180 21720 0 0 1770 6954 444 1157 86 98 82 98 22765 25900 .179 5.581 5.196 7.448 5.073 2.727 52 227 5.578 .92 90 4670 7550 30 39 322 331 0 16557 101 16456 4.757 18615 18514 .21 4.429 2.25 2.147

Total number of rows: 44544

Table truncated, full table size 9373 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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