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Sample GSM989747 Query DataSets for GSM989747
Status Public on Aug 23, 2012
Title PC 480N
Sample type RNA
 
Channel 1
Source name Human 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 480N RNA
Organism Homo sapiens
Characteristics individual: PC 480N
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/2008-08/80964.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 GPL9497
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 3139 5186 46 49 3093 5137 3242 5330 48 58 3196 5281 0 0 734 1166 13 59 100 100 100 100 8230 8477 .602 1.661 1.652 1.685 1.627 1.604 52 364 1.73 .92 90 1550 6590 26 35 22 31 0 4623 44 4579 1.481 4751 4708 .675 1.473 .566 .559
2 3763 5936 47 50 3716 5886 4055 6680 47 53 4008 6630 0 0 818 2508 6 19 100 100 100 100 9602 10638 .631 1.584 1.654 1.279 1.647 2.273 52 274 1.787 .92 90 1700 6590 26 35 37 46 0 5291 45 5247 1.412 5955 5910 .708 1.475 .498 .56
3 13894 18013 48 55 13846 17958 16618 20538 50 60 16570 20483 0 0 5640 6800 8 24 100 100 100 100 31804 37053 .771 1.297 1.236 1.303 1.237 2.243 52 304 1.307 .91 90 1840 6590 26 35 51 60 0 16057 49 16008 1.156 18308 18259 .865 1.102 .209 .14
4 5487 8900 49 57 5438 8843 6160 9605 50 61 6111 9548 0 0 1820 2920 8 26 100 100 100 100 14281 15659 .615 1.626 1.562 1.624 1.584 2.063 52 309 1.7 .93 90 2010 6590 26 35 68 77 0 7934 51 7883 1.45 8562 8511 .69 1.393 .536 .478
5 322 119 48 53 274 66 331 113 49 59 283 60 0 0 72 46 7 25 100 76 100 57 340 343 4.152 .241 .212 .21 .218 2.13 52 221 .24 .68 80 2160 6590 27 35 84 92 0 106 47 59 .215 101 53 4.657 .189 -2.219 -2.404
6 3724 5314 54 64 3670 5250 4567 6338 57 71 4513 6274 0 0 2027 2677 15 48 100 98 97 98 8920 10787 .699 1.431 1.39 1.687 1.418 2.455 80 321 1.425 .94 100 2300 6590 26 36 97 107 0 4737 57 4680 1.275 5650 5593 .784 1.239 .351 .309
7 132 91 53 61 79 30 133 86 57 67 80 25 0 0 28 36 17 47 96 25 92 5 109 105 2.633 .38 .313 .377 .458 2.819 52 271 .628 .47 80 2460 6580 26 34 114 122 0 81 54 27 .339 77 22 2.954 .279 -1.563 -1.844
8 23678 28985 51 60 23627 28925 25322 29644 52 63 25271 29584 0 0 4806 5778 9 24 100 100 100 100 52552 54855 .817 1.224 1.171 1.238 1.191 1.507 52 297 1.241 .94 90 2610 6590 26 35 128 137 0 25838 53 25784 1.091 26425 26372 .916 1.044 .126 .062
9 118 113 48 55 70 58 120 114 50 58 72 59 0 0 26 36 8 24 98 86 96 61 128 131 1.207 .829 .819 .835 .796 2.403 52 250 1.446 .55 80 2760 6590 27 35 144 152 0 101 49 52 .739 102 53 1.354 .73 -.437 -.453
10 145 286 47 51 98 235 151 291 49 55 104 240 0 0 34 83 9 26 100 100 96 98 333 344 .417 2.398 2.308 2.445 2.505 2.02 52 220 2.803 .84 80 2910 6590 27 35 159 167 0 255 45 209 2.138 259 214 .468 2.057 1.096 1.041
11 233 570 47 49 186 521 257 547 48 54 210 498 0 0 79 183 8 24 98 100 98 100 707 708 .357 2.801 2.371 3.063 2.574 1.898 52 254 2.905 .89 90 3060 6590 26 35 173 182 0 508 44 464 2.497 488 444 .4 2.114 1.32 1.08
12 255 5319 47 51 208 5268 261 5374 48 57 214 5323 0 0 78 1491 8 24 100 100 100 100 5476 5537 .039 25.327 24.874 26.375 24.951 1.466 52 323 28.269 .89 90 3210 6580 25 34 188 197 0 4741 45 4696 22.577 4790 4745 .044 22.173 4.497 4.471
13 257 281 46 50 211 231 283 290 47 53 237 240 0 0 75 82 8 21 98 100 96 100 442 477 .913 1.095 1.013 1.193 1.048 2.056 52 302 1.118 .88 90 3370 6590 26 35 204 213 0 250 45 206 .976 259 214 1.025 .903 -.035 -.148
14 221 331 47 50 174 281 224 335 47 54 177 285 0 0 38 113 6 21 100 100 100 100 455 462 .619 1.615 1.61 1.501 1.653 1.483 52 257 1.89 .9 90 3520 6580 25 34 219 228 0 295 45 250 1.44 299 254 .695 1.435 .526 .521
15 49 43 46 50 3 -7 49 38 48 53 3 -12 0 0 6 22 8 22 16 7 2 6 -4 -9 null null null 2.942 3.55 2.927 80 317 15.132 .2 100 3670 6580 25 35 234 244 -50 38 45 -6 null 34 -11 null null null null
16 1375 1713 46 49 1329 1664 1423 1715 48 54 1377 1666 0 0 305 443 9 23 100 100 100 100 2993 3043 .799 1.252 1.21 1.245 1.222 1.37 52 263 1.309 .93 90 3820 6580 25 34 249 258 0 1527 44 1483 1.116 1529 1485 .896 1.078 .158 .109
17 74 121 46 42 28 79 75 121 46 46 29 79 0 0 17 42 7 20 88 94 73 80 107 108 .354 2.821 2.724 2.868 2.821 2.892 52 181 5.054 .5 80 3970 6590 27 35 265 273 0 108 37 70 2.515 108 70 .398 2.428 1.331 1.28
18 47 40 45 44 2 -4 46 38 48 53 1 -6 0 0 7 16 17 46 3 2 0 0 -2 -5 null null null 1.812 2 3.528 80 281 20.126 .17 100 4120 6580 25 35 279 289 -50 36 39 -4 null 34 -5 null null null null
19 262 201 45 50 217 151 276 200 48 56 231 150 0 0 50 58 15 41 100 96 100 88 368 381 1.437 .696 .649 .657 .637 1.741 52 230 .745 .78 80 4270 6580 26 34 295 303 0 179 45 135 .62 178 134 1.612 .579 -.689 -.789
20 1438 5654 48 53 1390 5601 1455 5975 49 58 1407 5922 0 0 200 1543 10 30 100 100 100 100 6991 7329 .248 4.029 4.209 3.838 4.098 1.448 52 277 4.5 .94 90 4430 6580 25 34 310 319 0 5040 47 4993 3.592 5326 5279 .278 3.752 1.845 1.908

Total number of rows: 44544

Table truncated, full table size 9353 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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