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Sample GSM989776 Query DataSets for GSM989776
Status Public on Aug 23, 2012
Title PC 252T
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 252T2
Organism Homo sapiens
Characteristics ethnicity: Caucasian
age: 73
pre-operation treatment: None
individual: PC 248T
disease free survival: 3.00
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/2008-08/81101.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 37057 28927 154 125 36902 28801 40452 32461 209 147 40298 32335 0 0 10915 12406 560 124 100 100 100 100 65703 72633 1.281 .78 .802 .672 .821 1.702 32 236 .819 .95 70 1780 6890 33 40 22 29 0 26346 114 26232 .711 29565 29450 1.407 .731 -.492 -.452
2 28316 20633 176 155 28140 20478 31865 23653 233 184 31689 23497 0 0 14055 11791 584 147 100 100 100 96 48618 55186 1.374 .728 .741 .588 .713 2.027 32 230 .747 .96 70 1930 6890 33 40 37 44 0 18792 141 18651 .663 21543 21401 1.509 .675 -.593 -.566
3 30779 45385 166 153 30613 45231 33277 56921 183 174 33111 56768 0 21 14826 20467 80 100 100 100 100 100 75844 89879 .677 1.478 1.714 1.492 1.623 1.869 32 233 1.489 .94 70 2080 6890 33 40 52 59 -100 41336 139 41196 1.346 51843 51704 .743 1.562 .428 .643
4 46508 35112 152 131 46356 34980 52314 40771 168 151 52162 40640 0 0 15476 12587 77 90 100 100 100 100 81336 92802 1.325 .755 .779 .739 .785 1.442 32 223 .749 .95 70 2230 6890 33 40 67 74 0 31980 119 31859 .687 37134 37015 1.455 .71 -.541 -.495
5 2391 1002 167 162 2223 840 2594 1073 199 193 2426 910 0 0 698 315 92 126 100 96 100 93 3063 3336 2.646 .378 .375 .361 .392 1.647 32 202 .386 .84 70 2380 6890 33 40 82 89 0 913 148 765 .344 977 829 2.906 .342 -1.539 -1.549
6 12204 15557 248 250 11956 15306 1933 1907 299 296 1684 1656 0 0 14822 19996 183 178 100 100 100 100 27262 3340 .781 1.28 .983 1.101 1.08 1.517 120 536 1.351 .96 120 2540 6870 29 41 96 108 0 14169 228 13941 1.166 1737 1508 .858 .896 .222 -.159
7 818 439 199 188 619 250 831 431 218 210 632 242 0 0 156 122 97 122 100 87 100 50 869 874 2.476 .404 .383 .33 .388 2.113 32 203 .507 .6 70 2690 6890 33 40 113 120 0 400 171 228 .368 393 220 2.719 .349 -1.443 -1.52
8 47217 53392 159 134 47057 53257 52832 62514 165 144 52672 62379 0 59 16171 17514 55 72 100 100 100 100 100314 115051 .884 1.132 1.184 1.138 1.122 1.382 32 230 1.175 .95 70 2840 6890 33 40 128 135 -100 48629 122 48506 1.031 56937 56814 .97 1.079 .044 .109
9 371 759 138 116 232 642 339 753 147 144 201 637 0 0 110 128 54 96 100 100 91 100 874 838 .361 2.767 3.169 2.992 3.425 1.515 12 104 2.692 .76 50 2980 6880 33 38 143 148 0 691 106 585 2.52 686 580 .397 2.886 1.334 1.529
10 391 475 116 100 274 374 383 492 122 115 267 392 0 0 67 98 38 62 100 100 100 96 648 659 .733 1.365 1.468 1.348 1.33 1.326 32 201 1.481 .83 70 3140 6890 33 40 158 165 0 433 91 341 1.243 448 357 .804 1.337 .314 .419
11 1452 2518 131 110 1321 2407 1620 2667 143 125 1489 2556 0 0 582 848 59 77 100 100 93 100 3728 4045 .549 1.822 1.717 2.037 1.938 1.444 32 218 1.802 .95 70 3290 6890 33 40 173 180 0 2293 100 2192 1.66 2429 2328 .603 1.563 .731 .645
12 1114 2289 140 132 973 2156 1136 2290 152 151 995 2157 0 0 229 379 55 83 100 100 100 100 3129 3152 .451 2.216 2.168 2.244 2.262 1.278 32 232 1.008 .47 70 3440 6880 32 39 188 195 0 2085 120 1964 2.018 2086 1965 .496 1.974 1.013 .981
13 1079 837 122 104 957 732 1083 864 126 121 961 759 0 0 184 162 37 64 100 100 100 100 1689 1720 1.307 .765 .79 .762 .754 1.171 32 216 .788 .93 70 3590 6880 32 39 203 210 0 762 95 667 .697 787 691 1.435 .719 -.521 -.475
14 354 510 126 117 227 393 360 499 135 140 233 382 0 0 208 353 49 94 73 63 65 57 620 615 .578 1.731 1.639 1.747 1.848 2.99 52 304 1.166 .63 90 3740 6870 30 39 217 226 -50 465 107 358 1.577 454 348 .634 1.493 .657 .578
15 121 88 122 127 -1 -39 120 75 135 148 -2 -52 0 0 33 47 58 97 5 1 0 0 -40 -54 null null null 2.428 2.382 4.108 52 309 7.361 .25 90 3890 6870 30 39 232 241 -50 80 116 -36 null 68 -47 null null null null
16 4300 4634 121 120 4178 4513 5000 4806 143 150 4878 4686 0 0 2866 2878 104 119 88 96 84 88 8691 9564 .926 1.08 .961 1.271 1.024 3.115 52 253 1.057 .97 80 4040 6880 32 40 248 256 0 4221 109 4110 .984 4377 4268 1.016 .875 -.024 -.193
17 224 398 124 107 99 290 221 406 134 130 96 298 0 0 66 144 54 87 75 96 40 75 389 394 .341 2.929 3.104 3.068 2.855 2.098 32 169 3.011 .78 60 4190 6880 33 39 264 270 0 362 97 264 2.668 370 271 .375 2.827 1.416 1.499
18 111 80 126 113 -15 -33 107 77 142 146 -18 -36 0 0 31 35 67 127 1 0 0 0 -48 -54 null null null 1.167 1.14 3.663 52 325 2.81 .53 90 4340 6880 31 40 277 286 -50 73 103 -30 null 70 -33 null null null null
19 1502 2122 124 115 1377 2007 1633 2194 150 166 1508 2079 0 0 458 566 82 159 100 100 100 100 3384 3587 .686 1.458 1.379 1.507 1.422 1.381 32 226 1.503 .91 70 4500 6880 32 39 294 301 0 1933 105 1828 1.327 1998 1894 .753 1.256 .409 .328
20 5875 25827 121 118 5754 25708 7544 29775 137 144 7423 29657 0 0 3330 11043 62 102 93 100 93 100 31462 37080 .224 4.468 3.995 6.329 4.429 2.261 32 214 4.227 .94 70 4640 6880 32 39 308 315 0 23523 107 23415 4.069 27119 27011 .246 3.639 2.025 1.863

Total number of rows: 44544

Table truncated, full table size 9583 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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