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Sample GSM989691 Query DataSets for GSM989691
Status Public on Aug 23, 2012
Title PC 405N
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 405N2
Organism Homo sapiens
Characteristics individual: PC 405N
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/2008-08/81135.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) [email protected]
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
1 133 156 107 109 25 46 126 103 125 137 19 -6 0 0 55 143 176 146 3 15 0 7 71 13 .543 1.84 null 2.054 2.105 4.721 52 359 10.272 .15 90 1880 6870 30 39 19 28 -50 140 98 41 1.648 92 -5 .607 null .721 null
2 6633 24487 108 105 6524 24382 7893 27851 113 120 7785 27745 0 0 3451 8348 44 82 96 100 94 100 30906 35530 .268 3.737 3.564 4.689 3.325 3.189 52 303 3.646 .92 90 2040 6870 30 39 35 44 0 21934 94 21840 3.348 24947 24852 .299 3.192 1.743 1.675
3 5702 19547 106 109 5596 19437 6925 23130 113 132 6818 23020 0 0 3289 10059 39 92 100 98 100 98 25033 29838 .288 3.473 3.376 3.248 3.05 4.044 52 281 3.658 .89 80 2190 6860 30 38 51 59 0 17509 98 17410 3.111 20718 20620 .321 3.024 1.637 1.597
4 8426 14961 114 129 8311 14832 10413 16897 122 141 10298 16768 0 0 4107 5794 41 91 100 100 100 100 23143 27066 .56 1.785 1.628 1.999 1.708 2.745 52 266 1.742 .93 80 2340 6860 30 38 66 74 0 13401 116 13286 1.599 15135 15020 .626 1.459 .677 .544
5 6962 28536 123 117 6839 28418 7916 31057 127 130 7793 30940 0 0 2419 7374 45 82 100 100 100 100 35257 38733 .241 4.155 3.97 4.34 3.914 2.176 52 291 4.222 .94 90 2490 6860 29 38 80 89 0 25561 105 25455 3.722 27819 27714 .269 3.556 1.896 1.83
6 355 240 124 126 231 114 330 224 135 146 205 97 0 0 142 163 55 82 94 55 84 25 345 302 2.026 .494 .473 .471 .567 3.863 52 261 .605 .37 80 2640 6860 30 38 96 104 0 215 113 102 .442 201 87 2.262 .424 -1.178 -1.238
7 3668 8889 142 143 3525 8746 3284 8728 153 158 3142 8585 0 0 3444 1674 70 98 100 100 100 100 12271 11727 .403 2.481 2.732 2.765 2.783 1.671 52 297 1.869 .61 90 2800 6860 29 38 111 120 0 7962 128 7834 2.222 7818 7690 .45 2.447 1.152 1.291
8 252 131 114 106 137 25 247 117 145 129 132 10 0 0 72 80 184 110 26 15 0 1 162 142 5.48 .182 .076 .595 .534 3.61 52 256 .265 .07 80 2950 6850 29 37 127 135 0 117 95 22 .163 105 9 6.118 .068 -2.613 -3.881
9 11366 11689 113 107 11253 11582 12788 13153 140 134 12675 13046 0 0 4225 4867 169 106 100 100 100 100 22835 25721 .972 1.029 1.029 .967 .991 1.792 52 313 1.089 .9 90 3100 6850 28 37 141 150 0 10470 96 10374 .922 11782 11686 1.085 .922 -.117 -.117
10 220 314 119 94 101 219 203 312 122 105 83 217 0 0 72 134 43 66 78 84 46 75 320 300 .461 2.168 2.614 2.32 2.228 3.682 32 215 3.319 .34 70 3240 6860 30 37 156 163 0 281 84 196 1.942 279 194 .515 2.342 .958 1.228
11 196 282 115 100 80 182 189 259 122 118 73 159 0 0 50 115 45 79 80 84 36 50 262 232 .44 2.275 2.178 2.044 2.44 3.739 52 321 4.362 .31 90 3400 6860 29 38 171 180 -50 253 90 163 2.038 232 142 .491 1.951 1.027 .964
12 512 735 110 106 402 628 547 772 118 125 436 665 0 0 281 402 45 81 86 90 76 83 1030 1101 .64 1.562 1.525 1.704 1.502 2.726 80 340 1.543 .83 100 3560 6870 30 40 187 197 0 658 95 563 1.399 692 596 .715 1.366 .485 .45
13 320 701 113 106 206 594 324 705 125 127 210 599 0 0 80 274 49 92 98 100 88 94 800 809 .347 2.883 2.852 2.829 2.593 2.308 52 273 4.124 .67 90 3700 6870 30 39 201 210 0 628 95 532 2.583 631 537 .387 2.555 1.369 1.353
14 308 351 111 124 197 227 317 336 121 145 205 212 0 0 82 141 45 103 98 73 88 51 424 417 .868 1.152 1.034 1.094 1.371 3.031 52 259 1.647 .58 80 3860 6860 30 38 218 226 0 314 111 203 1.032 301 190 .969 .926 .046 -.11
15 205 194 106 107 99 87 208 174 116 127 102 66 0 0 76 103 44 81 75 48 53 17 186 168 1.138 .879 .647 .829 .757 4.101 52 279 2.516 .22 90 4000 6860 29 38 231 240 -50 174 96 78 .787 156 59 1.27 .58 -.345 -.787
16 172 106 113 102 59 4 170 96 136 132 57 -5 0 0 56 77 159 158 3 1 0 1 63 52 14.75 .068 null .607 .644 3.241 52 302 .897 .7 90 4150 6860 29 38 246 255 -50 95 91 4 .061 86 -4 16.467 null -4.041 null
17 1083 591 127 122 956 468 1061 546 154 162 934 423 0 0 394 318 166 200 100 82 94 55 1424 1357 2.043 .49 .453 .423 .404 2.341 52 292 .518 .68 90 4300 6860 29 38 261 270 0 529 109 419 .438 489 379 2.281 .406 -1.189 -1.302
18 213 174 124 122 89 51 193 147 130 139 69 25 0 0 74 97 49 88 69 28 36 15 140 94 1.745 .573 .362 .683 .68 5.257 52 291 1.899 .21 90 4450 6860 29 38 276 285 -50 156 109 46 .513 132 22 1.948 .325 -.962 -1.624
19 174 115 125 112 48 3 177 93 129 124 51 -18 0 0 53 69 44 83 53 11 21 3 51 33 16 .063 null 1.6 1.756 6.493 52 301 -9.852 -.09 90 4600 6860 29 38 291 300 -50 103 100 3 .056 83 -16 17.862 null -4.159 null
20 410 385 125 128 284 256 420 381 132 147 294 253 0 0 106 155 46 88 100 84 92 65 540 547 1.109 .901 .861 .815 .804 3.068 52 315 1.417 .41 90 4760 6860 29 38 307 316 0 345 115 229 .807 341 227 1.239 .771 -.309 -.376

Total number of rows: 44544

Table truncated, full table size 9665 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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