NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM989785 Query DataSets for GSM989785
Status Public on Aug 23, 2012
Title PC 351T
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 351T2
Organism Homo sapiens
Characteristics ethnicity: Caucasian
age: 69
pre-operation treatment: None
individual: PC 92T
disease free survival: 74.47
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/2008-08/81203.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 GPL15971
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 7020 3379 50 50 6970 3328 5988 3254 53 54 5938 3203 0 0 6106 3030 13 25 90 79 84 72 10298 9141 2.094 .477 .539 .478 .491 5.048 120 609 .476 .97 120 1870 7230 69 81 17 29 0 3553 53 3500 .502 3422 3368 1.992 .567 -.994 -.818
2 7697 3612 56 54 7640 3558 4618 1735 65 61 4561 1680 0 0 7646 3681 30 32 84 70 78 64 11198 6241 2.147 .466 .368 .43 .473 5.998 120 413 .462 .97 120 2020 7230 69 81 32 44 0 3798 57 3741 .49 1824 1767 2.042 .387 -1.03 -1.368
3 13965 13322 61 57 13903 13265 17365 16567 71 62 17303 16510 0 0 12261 12183 35 31 91 80 82 74 27168 33813 1.048 .954 .954 .758 .96 4.594 120 389 .967 .98 120 2170 7230 69 81 47 59 0 14009 60 13949 1.003 17421 17361 .997 1.003 .005 .005
4 12717 6006 58 51 12658 5954 17099 7200 66 55 17041 7149 0 0 10047 4928 27 25 97 83 94 80 18612 24190 2.126 .47 .42 .383 .486 3.954 120 361 .469 .97 120 2320 7230 69 81 62 74 0 6316 54 6261 .495 7571 7517 2.022 .441 -1.016 -1.181
5 931 249 78 62 852 187 946 255 97 73 867 192 0 0 156 81 55 50 100 98 100 86 1039 1059 4.556 .219 .221 .208 .22 2.714 52 231 .209 .83 90 2470 7230 70 79 78 87 0 262 65 197 .231 268 202 4.333 .233 -2.115 -2.102
6 4961 5791 69 59 4891 5731 5905 7100 84 69 5835 7040 0 0 2374 3003 44 38 100 100 100 100 10622 12875 .853 1.172 1.207 1.067 1.169 3.02 120 370 1.191 .97 120 2630 7240 70 82 93 105 0 6089 62 6026 1.232 7466 7403 .812 1.269 .301 .343
7 320 183 61 48 258 134 329 187 63 52 268 138 0 0 69 62 16 21 100 96 100 91 392 406 1.925 .519 .515 .472 .507 3.423 80 188 .495 .8 100 2780 7240 71 81 109 119 0 192 50 141 .546 197 145 1.831 .541 -.873 -.885
8 14275 18503 61 52 14213 18450 9258 20232 71 58 9196 20179 0 0 13782 17225 49 29 80 83 75 77 32663 29375 .77 1.298 2.194 1.17 1.251 4.338 120 305 1.236 .97 120 2910 7240 70 82 121 133 0 19457 55 19401 1.365 21275 21219 .733 2.307 .449 1.206
9 192 135 55 50 136 85 191 126 66 58 135 76 0 0 94 85 49 38 78 61 60 48 221 211 1.6 .625 .563 .558 .644 5.014 156 586 .376 .73 150 3080 7230 67 82 136 151 0 142 53 89 .657 132 80 1.522 .592 -.606 -.756
10 235 293 57 50 178 243 235 291 61 54 178 241 0 0 61 122 16 21 100 96 98 95 421 419 .733 1.365 1.354 1.242 1.333 3.126 80 261 1.462 .85 100 3230 7230 70 80 154 164 0 308 53 256 1.436 306 253 .697 1.424 .522 .51
11 1009 868 58 50 950 818 1093 954 61 54 1035 904 0 0 338 331 16 21 100 98 100 98 1768 1939 1.161 .861 .873 .834 .834 2.971 80 301 .851 .95 100 3390 7230 70 80 170 180 0 913 53 860 .905 1003 951 1.104 .918 -.143 -.123
12 560 716 56 50 503 666 606 754 57 54 549 704 0 0 167 266 13 21 100 100 100 96 1169 1253 .755 1.324 1.282 1.239 1.297 2.803 80 281 1.351 .94 100 3540 7230 70 80 185 195 0 753 53 700 1.392 793 740 .718 1.348 .477 .431
13 687 401 58 48 629 352 685 393 59 52 626 344 0 0 155 100 15 21 100 100 100 100 981 970 1.787 .56 .55 .555 .534 2.563 52 249 .541 .92 90 3680 7240 71 80 199 208 0 422 50 370 .588 413 362 1.699 .578 -.765 -.791
14 272 286 54 47 218 238 272 289 56 54 218 241 0 0 40 84 15 28 100 98 100 98 456 459 .916 1.092 1.106 1.024 1.147 2.937 80 345 1.108 .87 110 3840 7230 69 80 214 225 0 301 49 250 1.148 304 253 .871 1.162 .199 .217
15 81 77 55 46 25 31 73 70 57 52 17 24 0 0 25 35 13 23 57 50 33 27 56 41 .806 1.24 1.412 1.531 1.433 7.905 80 275 .684 .25 100 3990 7240 71 81 230 240 0 81 48 33 1.304 74 25 .767 1.485 .383 .57
16 2443 1959 55 48 2388 1910 2840 2242 57 52 2785 2193 0 0 902 779 14 23 100 98 100 98 4298 4978 1.25 .8 .787 .767 .786 2.921 80 262 .789 .96 100 4150 7230 70 80 246 256 0 2060 50 2008 .841 2358 2306 1.189 .828 -.25 -.272
17 116 134 58 52 58 81 117 130 61 58 59 77 0 0 20 61 16 25 98 82 86 66 139 136 .716 1.397 1.305 1.288 1.574 4.692 80 300 1.616 .48 100 4300 7230 70 80 261 271 0 141 55 85 1.469 137 81 .681 1.372 .554 .457
18 78 67 69 51 8 16 74 59 72 58 4 8 0 0 25 28 19 25 37 28 12 9 24 12 .5 2 2 .846 1.106 6.765 32 162 .549 .18 70 4440 7260 74 81 276 283 0 70 54 17 2.103 62 8 .475 2.103 1.073 1.073
19 699 606 59 48 640 557 726 609 62 54 666 560 0 0 187 160 16 24 100 100 100 100 1197 1226 1.149 .87 .841 .889 .87 2.582 80 372 .841 .94 110 4590 7230 69 80 289 300 0 637 50 586 .915 640 589 1.093 .884 -.128 -.178
20 5489 6638 56 50 5433 6588 5947 7521 59 57 5891 7471 0 0 1734 2546 15 25 100 100 100 98 12021 13362 .825 1.213 1.268 1.055 1.239 3.605 80 321 1.239 .97 100 4750 7220 69 79 306 316 0 6980 53 6928 1.275 7909 7856 .784 1.334 .351 .415

Total number of rows: 44544

Table truncated, full table size 9542 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap