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Sample GSM989748 Query DataSets for GSM989748
Status Public on Aug 23, 2012
Title PC 180T
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 PT 180
Organism Homo sapiens
Characteristics individual: PC 180T
disease state: Tumor
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/2008-11/81780.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 GPL15972
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 10930 9808 51 87 10878 9721 11364 10141 52 91 11313 10054 0 0 2893 2755 10 35 100 100 100 100 20599 21367 1.119 .894 .889 .883 .89 1.813 52 327 .913 .97 90 1620 7890 28 37 25 34 0 8247 73 8174 .751 8527 8454 1.331 .747 -.412 -.42
2 10720 10072 54 94 10666 9978 10803 10028 57 101 10749 9934 0 0 2069 1479 15 45 100 100 100 100 20644 20683 1.069 .935 .924 .947 .898 1.806 52 280 .91 .97 90 1760 7880 27 36 39 48 0 8469 79 8390 .787 8432 8353 1.271 .777 -.346 -.364
3 12608 20136 57 93 12550 20043 13039 20543 59 100 12981 20450 0 0 3043 4462 16 41 100 100 100 100 32593 33431 .626 1.597 1.575 1.626 1.583 1.963 52 260 1.649 .96 90 1920 7880 27 36 55 64 0 16931 78 16853 1.343 17273 17195 .745 1.325 .425 .406
4 7960 7741 57 84 7902 7657 10568 9377 61 93 10510 9293 0 0 5029 4069 19 50 100 97 97 97 15559 19803 1.032 .969 .884 1.419 .924 3.813 80 315 .902 .97 100 2060 7880 27 37 69 79 0 6509 71 6438 .815 7885 7814 1.227 .743 -.296 -.428
5 633 309 60 87 573 222 614 278 64 99 554 191 0 0 90 107 18 60 100 98 100 84 795 745 2.581 .387 .345 .35 .358 2.313 52 188 .401 .69 80 2220 7880 28 36 86 94 0 260 73 187 .326 234 161 3.07 .29 -1.618 -1.786
6 3091 6062 63 107 3027 5954 2068 5894 68 116 2004 5786 0 0 2872 4915 22 50 100 100 100 100 8981 7790 .508 1.967 2.887 2.442 1.916 2.695 120 362 1.835 .96 120 2370 7880 26 38 99 111 0 5097 90 5006 1.654 4956 4865 .605 2.428 .726 1.28
7 194 205 60 102 133 102 195 215 65 118 135 112 0 0 36 66 21 59 100 69 98 48 235 247 1.304 .767 .83 .68 .833 3.588 52 200 .939 .54 80 2520 7880 28 36 116 124 0 172 86 86 .645 181 94 1.551 .698 -.633 -.52
8 10886 19075 58 99 10827 18976 14372 23413 59 110 14314 23314 0 0 6557 9380 14 55 100 100 100 100 29803 37628 .571 1.753 1.629 2.239 1.654 3.521 80 315 1.653 .97 100 2670 7880 27 37 130 140 0 16039 83 15956 1.474 19687 19603 .679 1.37 .559 .454
9 171 135 56 85 115 49 170 135 58 91 114 49 0 0 31 42 15 41 100 51 100 23 164 163 2.347 .426 .43 .43 .475 3.108 52 189 .472 .53 80 2820 7880 28 36 146 154 0 114 71 41 .358 114 41 2.791 .361 -1.481 -1.468
10 194 203 58 85 135 117 206 189 65 94 147 104 0 0 52 68 67 52 86 86 59 50 252 251 1.154 .867 .707 .82 .853 2.772 52 198 .979 .68 80 2960 7880 28 36 160 168 0 171 71 98 .729 159 87 1.372 .595 -.457 -.749
11 696 1510 65 94 631 1415 689 1469 69 110 623 1374 0 0 195 361 57 129 100 100 98 100 2046 1997 .446 2.242 2.205 2.33 2.184 2.135 52 279 2.333 .91 90 3120 7870 26 35 175 184 0 1270 79 1190 1.886 1235 1155 .53 1.854 .915 .891
12 616 1108 61 84 554 1023 599 1104 63 101 537 1020 0 0 134 217 13 125 100 100 100 100 1577 1557 .542 1.847 1.899 1.873 1.815 1.918 52 296 1.902 .95 90 3270 7870 26 35 190 199 0 932 71 860 1.553 928 858 .644 1.597 .635 .675
13 349 229 59 82 290 147 352 225 61 85 292 142 0 0 60 70 12 42 100 98 100 78 437 434 1.973 .507 .486 .48 .487 2.378 52 227 .526 .8 80 3420 7870 27 35 206 214 0 193 69 124 .426 189 119 2.346 .409 -1.23 -1.29
14 223 394 59 91 164 302 218 392 62 98 159 300 0 0 46 78 37 52 100 100 98 100 466 459 .543 1.841 1.887 1.858 1.786 2.144 52 202 1.807 .8 80 3570 7870 27 35 221 229 0 331 77 254 1.548 330 252 .646 1.586 .631 .666
15 69 53 58 89 10 -36 66 47 61 98 8 -42 0 0 25 30 31 50 10 2 2 1 -26 -34 null null null 3.278 4.027 6.022 80 305 45.996 .03 100 3720 7870 26 36 235 245 -50 45 75 -30 null 40 -35 null null null null
16 1287 2100 58 87 1228 2013 1255 2070 60 93 1196 1983 0 0 248 367 13 37 100 100 100 100 3241 3179 .61 1.639 1.658 1.648 1.631 1.752 52 240 1.645 .97 90 3870 7870 26 35 250 259 0 1766 73 1693 1.378 1741 1667 .726 1.394 .463 .479
17 190 256 55 100 135 156 188 266 79 117 133 165 0 0 36 68 211 85 3 86 0 42 291 298 .865 1.156 1.241 1.056 1.091 2.491 52 202 1.265 .75 80 4020 7870 27 35 266 274 0 215 84 131 .972 224 139 1.029 1.043 -.042 .061
18 61 58 52 94 8 -36 60 55 54 99 7 -38 0 0 14 27 20 37 16 2 5 0 -28 -31 null null null 3.016 3.514 5.874 80 327 .248 .61 100 4170 7860 25 35 280 290 -50 49 79 -30 null 46 -32 null null null null
19 435 602 52 90 383 511 416 603 58 99 364 513 0 0 99 156 63 76 100 100 100 100 894 877 .75 1.334 1.409 1.313 1.272 1.98 52 283 1.356 .93 90 4320 7850 24 33 295 304 0 506 76 430 1.122 507 431 .891 1.185 .166 .245
20 1421 7479 48 90 1372 7388 1673 8417 59 112 1624 8326 0 0 756 3309 94 169 87 97 83 95 8760 9950 .186 5.385 5.127 6.775 5.224 2.882 80 363 5.231 .97 100 4470 7870 26 36 310 320 0 6289 76 6212 4.528 7077 7001 .221 4.311 2.179 2.108

Total number of rows: 44544

Table truncated, full table size 9324 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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