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Sample GSM989720 Query DataSets for GSM989720
Status Public on Aug 23, 2012
Title PC 21T4
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 21T2.2
Organism Homo sapiens
Characteristics ethnicity: Caucasian
age: 62
pre-operation treatment: None
individual: PC 26T
disease free survival: 60.30
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/2008-09/81263.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 32866 35988 46 62 32820 35926 32957 35921 52 76 32910 35859 3 0 5398 6564 25 49 100 100 100 100 68746 68769 .914 1.095 1.09 1.091 1.083 2.991 52 366 1.063 .96 90 1980 7050 23 32 26 35 0 34027 59 33968 1.035 33964 33905 .966 1.03 .05 .043
2 33443 34369 52 69 33390 34299 32463 33725 63 88 32410 33655 9 0 6389 8660 38 60 100 100 100 100 67689 66065 .973 1.027 1.038 1.014 1.021 3.535 52 294 1.023 .96 90 2140 7050 23 32 42 51 0 32496 65 32430 .971 31887 31821 1.03 .982 -.042 -.026
3 28891 32304 53 80 28837 32223 32764 36880 68 102 32710 36799 10 0 12785 14982 51 80 100 100 100 100 61060 69509 .895 1.117 1.125 1.096 1.124 4.819 80 342 1.106 .97 100 2300 7050 23 33 58 68 0 30544 76 30467 1.057 34870 34794 .946 1.064 .079 .089
4 30069 31944 49 74 30019 31869 30277 31526 63 99 30227 31452 7 0 9262 9993 48 82 100 100 100 100 61888 61679 .942 1.062 1.041 1.108 1.049 3.445 80 356 1.039 .97 110 2440 7050 22 33 71 82 0 30203 70 30133 1.004 29808 29738 .996 .984 .005 -.024
5 1500 710 56 86 1444 623 1518 684 107 161 1462 597 0 0 543 313 156 201 96 91 91 77 2067 2059 2.318 .431 .408 .43 .419 4.403 80 336 .423 .85 100 2590 7050 23 33 87 97 0 671 81 589 .408 647 564 2.451 .386 -1.294 -1.373
6 17215 14978 101 136 17114 14841 16675 14611 164 217 16574 14475 0 0 3388 3142 183 211 100 100 100 100 31955 31049 1.153 .867 .873 .863 .858 3.012 80 395 .835 .97 110 2730 7050 22 33 100 111 0 14162 129 14032 .82 13815 13686 1.22 .826 -.286 -.276
7 512 580 70 103 442 476 565 606 119 158 494 502 0 0 184 231 138 190 91 86 81 71 918 996 .929 1.077 1.016 1.149 1.105 4.49 80 316 1.043 .81 100 2890 7060 24 34 117 127 0 548 97 450 1.018 573 475 .982 .961 .026 -.058
8 32963 37667 64 94 32899 37572 33724 37602 81 178 33660 37507 0 0 6270 6585 88 521 100 100 100 100 70471 71167 .876 1.142 1.114 1.154 1.125 3.2 52 277 1.101 .96 90 3050 7050 23 32 133 142 0 35615 89 35525 1.08 35553 35463 .926 1.054 .111 .075
9 306 243 44 68 261 175 316 223 57 96 271 155 0 0 111 110 69 166 91 42 85 11 436 426 1.491 .67 .572 .67 .597 6.717 80 319 .604 .71 110 3200 7060 23 34 147 158 0 230 64 165 .634 211 147 1.577 .541 -.658 -.887
10 335 437 40 49 295 387 369 432 43 62 329 383 0 0 111 166 14 35 96 98 96 97 682 712 .762 1.312 1.164 1.357 1.336 4.458 80 300 1.242 .87 100 3340 7050 23 33 162 172 0 413 46 366 1.24 408 362 .806 1.101 .311 .138
11 1047 1384 40 55 1007 1328 1042 1427 43 68 1001 1371 0 0 333 453 15 45 98 100 98 100 2335 2372 .758 1.319 1.37 1.339 1.308 3.983 80 325 1.27 .94 110 3490 7050 22 33 176 187 0 1309 52 1256 1.247 1349 1296 .802 1.295 .318 .373
12 1022 2759 40 55 981 2703 1015 2655 43 69 974 2599 0 0 306 955 13 45 98 100 97 100 3684 3573 .363 2.755 2.668 2.865 2.712 3.817 80 322 2.823 .94 110 3640 7050 22 33 191 202 0 2609 52 2556 2.605 2510 2457 .384 2.523 1.381 1.335
13 638 782 39 54 598 727 689 772 41 65 649 718 0 0 216 344 11 37 100 98 97 96 1325 1367 .823 1.216 1.106 1.227 1.184 4.22 80 338 1.181 .89 110 3790 7050 22 33 206 217 0 739 51 687 1.149 730 679 .87 1.046 .201 .065
14 458 577 39 52 418 524 471 552 41 62 431 499 0 0 93 186 12 32 100 100 100 100 942 930 .798 1.254 1.158 1.213 1.25 3.579 80 294 1.212 .87 110 3940 7050 22 33 221 232 0 546 49 495 1.185 522 472 .844 1.095 .245 .131
15 66 62 36 54 29 7 65 54 39 63 28 0 0 0 26 29 12 32 70 19 52 3 36 28 4.143 .241 null .889 .89 10.757 120 373 .273 .11 120 4090 7050 22 34 236 248 -100 59 51 7 .228 51 0 4.382 null -2.131 null
16 2125 2757 37 60 2087 2697 2040 2749 38 66 2002 2689 0 0 559 836 10 35 100 100 100 100 4784 4691 .774 1.292 1.343 1.273 1.29 3.489 80 270 1.266 .95 110 4250 7060 23 34 252 263 0 2607 57 2550 1.222 2599 2542 .818 1.27 .289 .345
17 237 299 37 51 200 248 247 287 39 63 210 235 0 0 78 127 12 35 96 96 95 91 448 445 .806 1.24 1.119 1.24 1.227 5.348 80 296 1.191 .84 110 4400 7060 23 34 267 278 0 283 48 234 1.172 271 222 .853 1.058 .23 .081
18 65 79 39 54 26 24 61 69 43 65 22 15 0 0 23 40 16 35 60 25 39 15 50 37 1.083 .923 .682 1.25 1.454 10.317 120 411 .345 .1 120 4550 7060 23 35 282 294 -100 75 51 23 .873 65 14 1.146 .645 -.196 -.633
19 899 817 41 63 858 754 851 747 44 69 810 684 0 0 242 268 14 35 100 100 100 100 1612 1494 1.138 .879 .844 .853 .909 3.406 80 258 .839 .9 110 4700 7060 23 34 297 308 0 772 60 713 .831 706 647 1.204 .798 -.267 -.325
20 3731 13370 39 65 3692 13305 4308 15321 41 76 4269 15255 0 0 1997 7301 13 41 99 99 95 97 16997 19524 .277 3.604 3.573 3.689 3.688 5.173 120 345 3.68 .96 120 4850 7060 23 35 312 324 0 12641 61 12580 3.407 14486 14424 .293 3.379 1.769 1.756

Total number of rows: 44544

Table truncated, full table size 9554 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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