NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM989795 Query DataSets for GSM989795
Status Public on Aug 23, 2012
Title PC 579T
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 579T RNA
Organism Homo sapiens
Characteristics ethnicity: Caucasian
age: 60
pre-operation treatment: None
individual: PC 621T
disease free survival: 16.77
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/2008-08/80847.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 5040 6238 136 184 4904 6054 6717 8330 157 219 6581 8146 0 0 4348 5108 112 157 87 78 71 65 10958 14727 .81 1.235 1.238 1.182 1.146 1.761 32 176 1.229 .97 60 1760 6890 6 12 25 31 0 8571 253 8319 1.696 11446 11193 .59 1.701 .762 .766
2 5897 6833 139 233 5758 6600 6749 7311 154 249 6610 7078 0 0 5476 6172 74 163 84 68 84 68 12358 13688 .872 1.146 1.071 1.106 1.065 2.621 32 176 1.133 .98 60 1910 6890 6 12 40 46 0 9389 320 9069 1.575 10046 9726 .635 1.471 .655 .557
3 5633 16253 154 273 5479 15980 4178 16840 186 310 4024 16567 0 0 5083 14583 102 201 87 93 78 81 21459 20591 .343 2.917 4.117 2.98 2.771 2.855 32 176 2.969 .98 60 2060 6890 6 12 55 61 0 22333 375 21958 4.008 23139 22764 .25 5.657 2.003 2.5
4 8056 10033 138 220 7918 9813 10282 12227 160 250 10144 12007 0 0 6139 7210 89 163 90 84 87 81 17731 22151 .807 1.239 1.184 1.639 1.268 2.215 32 213 1.209 .97 70 2210 6890 5 12 69 76 0 13786 302 13484 1.703 16801 16498 .587 1.626 .768 .702
5 974 1993 144 217 830 1776 1048 1802 173 256 904 1585 0 0 465 1031 106 213 100 91 83 83 2606 2489 .467 2.14 1.753 2.052 1.951 1.543 12 104 2.202 .89 50 2360 6890 6 11 85 90 0 2739 298 2440 2.94 2476 2178 .34 2.409 1.556 1.269
6 3307 4093 163 223 3144 3870 3556 4623 196 263 3393 4400 0 0 2785 3590 118 192 86 82 71 67 7014 7793 .812 1.231 1.297 1.079 1.297 2.355 52 281 1.309 .96 90 2510 6880 3 12 98 107 0 5624 306 5318 1.691 6352 6046 .591 1.782 .758 .833
7 350 815 118 228 232 587 382 754 144 251 264 526 0 0 136 496 115 166 83 75 58 58 819 790 .395 2.53 1.992 3.638 3.986 2.575 12 104 2.563 .63 50 2660 6880 5 10 115 120 0 1120 313 807 3.477 1036 723 .288 2.738 1.798 1.453
8 7664 18671 125 203 7539 18468 10840 24241 137 235 10715 24038 0 0 6233 14876 66 174 90 90 84 75 26007 34753 .408 2.45 2.243 2.429 2.381 1.78 32 170 2.514 .97 60 2810 6880 5 11 130 136 0 25655 279 25376 3.366 33309 33030 .297 3.083 1.751 1.624
9 432 718 104 189 328 529 459 638 120 201 355 449 0 0 171 411 50 122 91 75 91 66 857 804 .62 1.613 1.265 1.36 1.364 1.922 12 104 2.551 .73 50 2960 6880 5 10 145 150 0 987 260 727 2.216 877 617 .451 1.738 1.148 .797
10 359 963 112 195 247 768 396 1081 125 257 284 886 0 0 169 474 81 534 78 71 68 25 1015 1170 .322 3.109 3.12 3.534 2.979 2.338 32 210 3.277 .87 70 3110 6890 5 12 159 166 0 1323 268 1055 4.272 1485 1217 .234 4.287 2.095 2.1
11 981 2730 99 155 882 2575 962 2459 104 184 863 2304 0 0 681 2002 31 122 81 90 78 84 3457 3167 .343 2.92 2.67 2.501 2.658 2.634 32 170 3.047 .93 60 3260 6880 5 11 175 181 0 3751 213 3538 4.012 3379 3166 .249 3.668 2.004 1.875
12 625 1575 106 166 519 1409 697 1436 110 193 591 1270 0 0 315 1003 36 130 87 84 87 81 1928 1861 .368 2.715 2.149 2.715 2.496 1.7 32 218 3.127 .89 70 3410 6880 4 11 189 196 0 2164 228 1936 3.73 1973 1745 .268 2.953 1.899 1.562
13 546 1411 106 165 440 1246 620 1561 114 184 514 1396 0 0 296 965 43 128 84 81 78 71 1686 1910 .353 2.832 2.716 2.449 2.992 2.739 32 168 3.353 .85 60 3560 6880 5 11 205 211 0 1939 227 1712 3.891 2145 1918 .257 3.732 1.96 1.9
14 351 1077 112 205 239 872 310 922 132 265 198 717 0 0 215 937 84 285 58 50 50 50 1111 915 .274 3.649 3.621 4.499 4.468 1.982 12 104 3.903 .84 50 3700 6880 5 10 219 224 0 1480 282 1198 5.013 1267 985 .199 4.976 2.326 2.315
15 309 751 103 190 206 561 271 631 117 233 168 441 0 0 207 647 67 203 59 55 50 51 767 609 .367 2.723 2.625 2.57 3.136 3.3 52 261 3.473 .87 90 3850 6880 3 12 232 241 -50 1032 261 771 3.742 867 606 .267 3.607 1.904 1.851
16 745 1468 96 155 649 1313 594 922 104 179 498 767 0 0 611 1356 35 114 69 71 69 61 1962 1265 .494 2.023 1.54 2.289 2.108 1.81 52 235 2.182 .9 80 4010 6880 4 12 249 257 0 2017 213 1804 2.78 1267 1054 .36 2.116 1.475 1.082
17 465 2079 105 174 360 1905 501 2362 123 250 396 2188 0 0 238 1157 86 352 75 83 75 83 2265 2584 .189 5.292 5.525 4.998 5.102 2.103 12 104 5.691 .66 50 4160 6880 5 10 265 270 0 2857 239 2618 7.271 3246 3006 .138 7.592 2.862 2.924
18 164 531 102 183 62 348 107 301 116 221 5 118 0 0 118 581 67 240 28 34 21 26 410 123 .178 5.613 23.6 4.639 5.349 3.013 52 255 5.499 .73 90 4310 6870 2 11 278 287 -50 730 251 478 7.713 414 162 .13 32.428 2.947 5.019
19 828 2516 97 189 731 2327 892 2512 108 197 795 2323 0 0 462 1740 45 110 90 93 90 84 3058 3118 .314 3.183 2.922 3.079 2.919 2.604 32 206 3.392 .91 70 4470 6870 3 10 295 302 0 3457 260 3197 4.374 3452 3192 .229 4.015 2.129 2.005
20 1979 5227 101 164 1878 5063 2573 5871 111 181 2472 5707 0 0 1160 3347 52 115 96 93 87 87 6941 8179 .371 2.696 2.309 2.797 2.55 1.377 32 165 2.792 .97 60 4620 6880 5 11 311 317 0 7182 225 6957 3.704 8067 7842 .27 3.172 1.889 1.666

Total number of rows: 44544

Table truncated, full table size 9725 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap