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Sample GSM989709 Query DataSets for GSM989709
Status Public on Aug 23, 2012
Title PC 26T2
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 26T2.1
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/2008-09/81251.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 7229 7463 30 69 7199 7394 8267 8689 31 80 8237 8620 0 0 2697 3198 5 46 100 100 100 100 14593 16857 .974 1.027 1.046 .971 1.047 2.808 80 441 1.041 .98 100 1990 6570 28 38 30 40 0 6646 61 6585 .915 7738 7677 1.093 .932 -.129 -.102
2 7370 8529 33 78 7336 8450 7495 8743 35 113 7461 8665 0 0 860 1075 13 176 100 100 100 100 15786 16126 .868 1.152 1.161 1.15 1.178 2.159 52 277 1.121 .97 90 2140 6570 28 37 45 54 0 7596 69 7525 1.026 7786 7717 .975 1.034 .037 .049
3 6920 17142 34 91 6886 17050 7831 19346 36 124 7797 19255 0 0 2301 7226 12 171 100 98 100 97 23936 27052 .404 2.476 2.47 2.122 2.571 3.639 80 364 2.612 .97 100 2310 6560 27 37 62 72 0 15266 81 15184 2.205 17229 17148 .453 2.199 1.141 1.137
4 6700 8380 32 80 6667 8300 7053 9193 34 88 7020 9112 0 0 1350 2794 6 46 100 100 100 98 14967 16132 .803 1.245 1.298 1.12 1.293 3.335 80 308 1.3 .97 100 2450 6560 27 37 76 86 0 7463 71 7392 1.109 8187 8115 .902 1.156 .149 .209
5 475 265 33 89 442 175 498 259 105 210 465 170 0 0 90 105 481 739 31 0 0 0 617 635 2.526 .396 .366 .328 .355 3.777 80 301 .391 .74 100 2600 6570 28 38 91 101 0 236 79 156 .353 231 151 2.836 .326 -1.504 -1.619
6 2431 4431 34 88 2397 4342 2632 4974 66 146 2598 4886 0 0 1056 2251 313 485 88 87 87 84 6739 7484 .552 1.811 1.881 1.608 1.822 3.415 156 715 1.882 .95 150 2750 6560 24 39 103 118 0 3946 78 3867 1.613 4430 4351 .62 1.675 .69 .744
7 140 158 35 88 104 70 139 157 38 106 104 69 0 0 18 64 15 129 100 15 100 1 174 173 1.486 .673 .663 .602 .787 4.197 52 241 5.874 .28 90 2910 6570 28 37 122 131 0 141 78 62 .599 140 61 1.668 .591 -.738 -.759
8 6979 10936 33 89 6946 10846 7022 11139 66 139 6988 11049 0 0 489 2041 317 374 100 100 100 100 17792 18037 .64 1.561 1.581 1.516 1.548 2.557 52 303 1.562 .97 90 3050 6550 26 35 136 145 0 9739 79 9659 1.391 9920 9840 .719 1.408 .476 .494
9 49 76 30 84 19 -8 49 69 54 111 19 -15 0 0 14 38 264 301 0 0 0 0 11 4 null null null 1.766 1.672 8.075 120 439 1.127 .98 120 3200 6560 26 38 150 162 -50 68 75 -7 null 61 -13 null null null null
10 39 73 28 73 10 0 40 64 29 84 11 -8 0 0 7 37 3 45 80 13 65 2 10 3 null null null 2.534 2.406 6.843 120 383 -1 -1 120 3350 6560 26 38 165 177 -50 65 65 0 null 57 -7 null null null null
11 350 790 28 81 321 709 344 822 29 89 315 740 0 0 68 269 4 42 100 98 100 97 1030 1055 .453 2.209 2.349 1.969 2.265 3.441 80 268 2.433 .91 100 3500 6560 27 37 181 191 0 704 72 631 1.967 732 659 .508 2.092 .976 1.065
12 131 655 28 73 102 581 145 700 29 82 116 627 0 0 52 367 4 49 95 86 91 84 683 743 .176 5.696 5.405 5.342 5.283 3.597 120 424 6.521 .91 120 3650 6560 26 38 195 207 0 583 65 517 5.073 623 558 .197 4.814 2.343 2.267
13 132 150 28 76 103 74 133 121 29 87 104 45 0 0 18 116 5 52 100 48 100 26 177 149 1.392 .718 .433 .557 .7 6.505 52 257 1.17 .34 90 3800 6570 28 37 211 220 0 134 68 66 .64 108 40 1.563 .385 -.644 -1.376
14 59 161 28 80 30 81 60 158 29 88 31 78 0 0 8 74 5 46 100 60 100 40 111 109 .37 2.7 2.516 2.442 3.111 5.085 80 339 8.876 .44 110 3950 6560 26 37 225 236 0 143 71 72 2.405 141 69 .416 2.241 1.266 1.164
15 32 62 28 73 3 -11 32 55 29 82 3 -17 0 0 4 37 3 48 45 9 15 1 -8 -14 null null null 9.559 10.189 7.302 120 373 -121.648 -.08 120 4100 6560 26 38 240 252 -50 55 65 -10 null 49 -15 null null null null
16 779 945 30 78 748 866 813 949 30 91 783 870 0 0 200 308 4 52 100 98 98 98 1614 1653 .864 1.158 1.111 1.143 1.149 2.999 80 343 1.128 .93 110 4260 6570 27 38 256 267 0 842 69 771 1.031 845 775 .97 .99 .044 -.015
17 39 80 29 80 9 0 38 67 30 89 8 -12 0 0 8 44 4 51 65 10 49 3 9 -4 null null null 4.452 4.955 6.776 120 424 -126.987 -.04 120 4400 6560 26 38 270 282 -50 71 71 0 null 60 -11 null null null null
18 31 70 30 82 0 -12 30 60 31 91 0 -22 0 0 4 40 5 52 11 8 2 1 -12 -22 null null null 12.236 14.329 6.149 120 394 87.538 .13 120 4560 6560 26 38 286 298 -100 62 73 -11 null 53 -20 null null null null
19 251 327 29 80 221 247 245 316 31 88 216 236 0 0 47 120 5 42 100 98 100 93 468 452 .895 1.118 1.093 1.005 1.103 3.271 80 250 1.124 .78 110 4710 6570 27 38 301 312 0 291 71 220 .995 281 210 1.005 .973 -.007 -.039
20 1174 3463 29 76 1144 3387 1325 4105 30 82 1295 4029 0 0 447 1655 4 41 100 100 100 97 4531 5324 .338 2.961 3.111 2.512 3.111 3.419 120 360 3.162 .97 120 4860 6570 27 39 316 328 0 3084 68 3016 2.637 3656 3588 .379 2.771 1.399 1.47

Total number of rows: 44544

Table truncated, full table size 9131 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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