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Sample GSM989788 Query DataSets for GSM989788
Status Public on Aug 23, 2012
Title PC 604N
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 604N2
Organism Homo sapiens
Characteristics individual: PC 604N
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/2008-08/81150.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 16391 24573 130 210 16261 24362 19097 26860 137 223 18967 26649 0 0 6698 7623 36 80 100 100 100 100 40623 45616 .667 1.498 1.405 1.704 1.448 1.991 52 298 1.437 .99 80 2140 7160 24 32 50 58 0 23146 198 22948 1.411 25301 25102 .709 1.323 .497 .404
2 16833 24945 135 206 16697 24739 19408 28557 140 214 19272 28350 0 0 7834 10483 36 69 100 100 100 100 41436 47622 .675 1.482 1.471 1.621 1.481 1.822 52 268 1.451 .99 80 2290 7150 23 31 65 73 0 23497 194 23303 1.396 26899 26704 .717 1.386 .481 .471
3 35390 42712 146 216 35244 42495 41627 47806 154 225 41480 47589 0 0 15854 15089 47 88 100 100 100 100 77739 89069 .829 1.206 1.147 1.367 1.18 1.853 52 273 1.147 .99 90 2440 7160 23 32 79 88 0 40232 203 40028 1.136 45030 44826 .88 1.081 .184 .112
4 20377 30666 142 219 20235 30446 21778 31574 149 235 21636 31354 0 0 5010 5333 49 106 100 100 100 100 50681 52990 .665 1.505 1.449 1.555 1.478 1.566 52 282 1.48 .99 90 2590 7160 23 32 94 103 0 28886 206 28678 1.417 29741 29534 .706 1.365 .503 .449
5 978 393 142 215 836 177 975 397 158 257 833 182 0 0 140 83 116 209 100 40 100 0 1013 1015 4.723 .212 .218 .18 .214 2.636 32 210 .194 .59 70 2740 7150 23 30 110 117 0 370 203 167 .199 374 171 5.014 .206 -2.326 -2.281
6 15680 21004 184 179 15496 20825 20457 25363 208 207 20272 25183 0 0 8457 10148 110 165 100 100 100 100 36321 45455 .744 1.344 1.242 1.579 1.326 2.378 80 415 1.311 .99 100 2890 7160 23 33 124 134 0 19785 169 19616 1.266 23890 23721 .79 1.17 .34 .227
7 411 226 149 147 261 79 406 209 157 155 256 62 0 0 67 62 49 55 100 56 100 28 340 318 3.304 .303 .242 .262 .287 2.976 32 215 .279 .47 70 3050 7170 25 32 141 148 0 213 138 74 .285 197 58 3.507 .228 -1.81 -2.132
8 43238 45431 130 143 43107 45287 55006 53538 136 168 54876 53394 23 0 18113 16247 48 148 100 100 100 100 88394 108270 .952 1.051 .973 1.105 1.028 1.741 52 268 1.02 .99 80 3200 7150 23 31 156 164 -100 42793 135 42658 .99 50430 50294 1.011 .917 -.015 -.126
9 392 546 132 160 260 385 391 565 142 199 259 404 0 0 116 140 76 206 92 88 78 48 645 663 .675 1.481 1.56 1.502 1.423 2.256 52 243 1.597 .82 80 3350 7150 23 31 171 179 0 514 151 363 1.395 532 381 .717 1.469 .48 .555
10 489 851 117 146 372 705 497 907 125 167 380 761 0 0 125 221 41 88 98 98 96 98 1077 1141 .528 1.895 2.003 1.932 1.882 1.802 52 275 1.945 .93 80 3490 7140 22 30 185 193 0 802 138 664 1.785 854 717 .56 1.886 .836 .916
11 2242 3522 118 139 2124 3383 2306 3655 121 153 2187 3516 0 0 555 621 32 81 100 100 100 100 5507 5703 .628 1.593 1.608 1.64 1.567 1.587 32 230 1.594 .97 70 3640 7140 22 29 200 207 0 3318 131 3187 1.5 3443 3312 .667 1.514 .585 .599
12 1401 2638 112 124 1289 2514 1482 2616 115 140 1370 2491 0 0 343 477 29 78 100 100 100 100 3803 3861 .513 1.95 1.818 2.052 1.858 1.897 52 314 1.968 .95 90 3800 7160 23 32 215 224 0 2485 117 2368 1.837 2464 2346 .544 1.713 .877 .776
13 954 875 113 140 840 734 1071 898 116 157 957 758 0 0 330 264 31 72 98 96 98 94 1574 1715 1.144 .874 .792 .904 .843 1.958 52 292 .846 .94 80 3950 7140 22 30 231 239 0 824 132 691 .823 846 714 1.215 .746 -.281 -.423
14 562 765 113 137 449 627 576 771 121 148 463 634 0 0 63 111 37 70 100 100 100 100 1076 1097 .716 1.396 1.369 1.392 1.43 1.618 32 213 1.45 .93 70 4090 7150 23 30 245 252 0 721 129 591 1.315 726 597 .76 1.29 .395 .367
15 82 78 112 130 -29 -52 81 64 115 147 -30 -65 0 0 22 48 29 83 1 1 1 0 -81 -95 null null null 1.958 2.12 3.056 52 312 3.888 .44 90 4240 7150 22 31 259 268 -50 73 122 -49 null 60 -61 null null null null
16 4780 5101 117 133 4663 4968 5222 5215 119 151 5105 5081 0 0 1435 970 32 83 100 100 100 100 9631 10186 .939 1.065 .995 1.139 1.017 1.8 52 302 1.02 .98 90 4390 7160 23 32 274 283 0 4805 125 4680 1.004 4912 4786 .996 .938 .005 -.093
17 252 338 112 133 139 205 243 318 119 146 130 184 0 0 39 83 34 68 100 100 100 75 344 314 .678 1.475 1.415 1.417 1.357 2.091 32 209 1.873 .74 70 4550 7160 24 31 291 298 0 318 125 193 1.389 300 173 .72 1.333 .474 .415
18 82 66 117 137 -34 -70 77 65 121 153 -39 -71 0 0 22 27 36 71 1 0 0 0 -104 -110 null null null 2 1.842 2.629 52 329 3.645 .39 90 4700 7150 22 31 305 314 -50 62 129 -66 null 61 -67 null null null null
19 1677 1483 116 141 1561 1342 1709 1463 124 159 1593 1321 0 0 289 308 37 94 100 100 100 100 2903 2914 1.163 .86 .829 .853 .858 1.626 52 274 .85 .96 80 4850 7150 23 31 321 329 0 1397 133 1264 .81 1378 1244 1.235 .781 -.304 -.356
20 6198 18534 125 148 6073 18386 7038 19886 131 172 6913 19737 0 0 2111 4277 44 124 100 100 100 100 24459 26650 .33 3.027 2.855 3.298 2.906 1.808 52 265 2.932 .98 80 5000 7150 23 31 336 344 0 17458 139 17319 2.852 18731 18591 .351 2.689 1.512 1.427

Total number of rows: 44544

Table truncated, full table size 9818 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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