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Sample GSM989775 Query DataSets for GSM989775
Status Public on Aug 23, 2012
Title PC 544T
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 544T2
Organism Homo sapiens
Characteristics ethnicity: Caucasian
age: 58
pre-operation treatment: None
individual: PC 582T
disease free survival: 19.73
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/2008-08/81205.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 10258 4818 43 47 10214 4771 12477 5730 45 51 12433 5683 0 0 4457 2331 9 21 100 98 100 95 14985 18116 2.141 .467 .457 .391 .487 5.233 80 349 .458 .95 100 1960 7050 4 14 19 29 0 5035 49 4985 .488 5988 5938 2.049 .478 -1.035 -1.066
2 14050 6577 49 53 14000 6523 13970 6976 50 57 13920 6923 0 0 902 1768 14 25 100 100 100 100 20523 20843 2.146 .466 .497 .43 .498 3.325 52 210 .467 .94 90 2120 7060 5 14 35 44 0 6873 55 6816 .487 7290 7234 2.054 .52 -1.038 -.944
3 26666 16430 49 50 26617 16379 30967 19448 49 54 30917 19398 0 0 10022 7308 10 28 100 98 100 97 42996 50315 1.625 .615 .627 .473 .623 5.45 80 190 .612 .96 100 2270 7040 3 13 50 60 0 17168 52 17115 .643 20322 20270 1.555 .656 -.637 -.609
4 13739 6459 48 46 13691 6413 15464 7525 49 51 15416 7479 0 0 4628 2687 12 23 100 100 100 100 20104 22895 2.135 .468 .485 .446 .499 4.566 80 141 .457 .93 100 2420 7050 4 14 65 75 0 6749 48 6701 .489 7863 7815 2.043 .507 -1.031 -.98
5 820 270 50 50 770 219 825 277 54 60 775 226 0 0 120 105 28 44 100 94 100 86 989 1001 3.516 .284 .292 .244 .309 4.395 52 150 .26 .82 90 2560 7040 3 12 79 88 0 282 52 229 .297 289 236 3.365 .305 -1.751 -1.714
6 10488 7775 54 51 10433 7723 11663 8969 57 61 11609 8917 0 0 3546 3288 29 44 100 100 100 98 18156 20526 1.351 .74 .768 .691 .795 4.87 80 147 .73 .93 110 2730 7050 3 14 95 106 0 8124 53 8070 .774 9372 9318 1.293 .803 -.37 -.317
7 164 98 50 57 114 40 167 89 64 74 116 32 0 0 101 60 77 81 53 25 44 4 154 148 2.85 .351 .276 .572 .422 7.225 120 112 .476 .65 120 2870 7040 2 14 109 121 0 102 60 42 .367 93 33 2.727 .288 -1.448 -1.795
8 34591 19416 52 65 34539 19350 34375 20615 161 123 34322 20549 0 0 1822 5199 563 368 100 100 100 100 53889 54871 1.785 .56 .599 .502 .582 3.663 52 108 .557 .92 80 3020 7040 4 12 126 134 0 20289 68 20220 .585 21542 21473 1.708 .626 -.772 -.677
9 157 170 46 49 110 121 177 162 125 91 131 113 0 0 89 112 506 327 0 4 0 0 231 244 .909 1.1 .863 1.11 1.131 4.872 120 133 .62 .89 120 3170 7040 2 14 139 151 0 178 51 126 1.149 169 118 .87 .901 .201 -.15
10 159 151 43 47 116 103 184 142 47 53 141 95 0 0 85 92 19 25 76 68 68 61 219 236 1.126 .888 .674 .959 .952 4.696 120 140 .858 .77 120 3320 7040 2 14 154 166 0 158 49 108 .928 148 99 1.078 .704 -.108 -.506
11 1690 1621 46 51 1644 1569 1600 1635 52 60 1553 1583 0 0 304 393 34 39 100 100 100 100 3213 3136 1.048 .954 1.019 .933 .967 2.672 52 161 .931 .93 90 3470 7040 3 12 170 179 0 1694 53 1640 .997 1708 1654 1.003 1.065 -.004 .091
12 776 2237 43 46 732 2191 820 2431 51 56 776 2384 0 0 272 882 34 36 96 97 93 97 2923 3160 .334 2.993 3.072 3.05 3.15 3.882 80 158 3.153 .93 100 3620 7040 3 13 185 195 0 2338 48 2289 3.128 2540 2491 .32 3.21 1.645 1.683
13 593 320 42 46 550 274 626 350 45 53 583 304 0 0 214 138 9 22 100 90 96 88 824 887 2.007 .498 .521 .495 .505 4.739 80 155 .477 .89 100 3770 7040 3 13 200 210 0 334 48 286 .521 366 318 1.921 .545 -.942 -.876
14 371 365 43 49 328 316 380 375 45 53 336 326 0 0 83 119 9 21 98 100 98 100 644 662 1.038 .963 .97 .968 .973 3.805 80 159 .955 .89 110 3930 7040 2 13 215 226 0 381 51 330 1.007 392 341 .993 1.014 .01 .02
15 74 91 43 44 31 46 74 85 45 50 31 40 0 0 20 47 9 21 85 62 68 48 77 71 .674 1.484 1.29 1.32 1.473 6.584 80 92 1.983 .49 100 4090 7030 2 12 232 242 0 95 46 48 1.551 89 42 .645 1.348 .633 .431
16 3690 1883 44 46 3646 1836 3984 2006 44 56 3940 1960 0 0 1268 687 9 26 100 100 98 100 5482 5900 1.986 .504 .497 .515 .51 4.048 80 92 .482 .94 100 4230 7040 3 13 246 256 0 1968 48 1919 .526 2096 2048 1.9 .52 -.926 -.944
17 130 273 44 51 86 221 143 291 45 56 99 239 0 0 64 186 10 23 78 75 70 68 307 338 .389 2.57 2.414 2.489 2.849 4.872 120 194 2.972 .8 120 4380 7020 0 12 260 272 0 285 53 231 2.685 304 250 .372 2.523 1.425 1.335
18 56 65 44 49 11 16 52 60 47 53 7 11 0 0 14 29 12 22 42 42 17 15 27 18 .688 1.455 1.571 1.977 2.086 7.403 52 130 .701 .09 80 4530 7000 0 8 277 285 0 68 51 17 1.52 63 11 .658 1.642 .604 .716
19 1146 770 47 46 1099 724 1111 791 49 53 1064 745 0 0 343 246 16 23 100 100 98 100 1823 1809 1.518 .659 .7 .64 .643 3.241 80 178 .625 .93 110 4680 7040 2 13 290 301 0 805 48 757 .688 827 778 1.453 .732 -.539 -.451
20 4604 9090 47 53 4556 9037 4416 9508 64 82 4369 9455 0 0 477 1618 112 179 100 100 100 100 13593 13824 .504 1.984 2.164 1.946 2.04 2.499 52 189 2.039 .94 90 4830 7030 2 11 306 315 0 9499 55 9443 2.073 9935 9880 .482 2.261 1.052 1.177

Total number of rows: 44544

Table truncated, full table size 9515 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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