NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM989769 Query DataSets for GSM989769
Status Public on Aug 23, 2012
Title PC 599N
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 599N2
Organism Homo sapiens
Characteristics individual: PC 599N
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/2008-08/81158.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 5079 7058 70 77 5008 6980 5445 7766 75 89 5374 7688 0 0 2185 2960 23 54 100 100 100 100 11988 13062 .717 1.394 1.431 1.359 1.339 2.459 52 316 1.395 .95 80 1740 7400 36 44 14 22 0 6415 70 6344 1.267 7059 6988 .789 1.3 .341 .379
2 5073 6028 77 74 4996 5953 5025 6098 83 101 4948 6023 0 0 923 1273 35 116 100 100 100 100 10949 10971 .839 1.192 1.217 1.179 1.18 1.354 32 226 1.268 .96 70 1890 7390 35 42 29 36 0 5479 67 5411 1.083 5543 5475 .923 1.106 .115 .146
3 8380 8801 82 74 8298 8726 10456 10832 85 100 10374 10757 0 0 4325 4426 25 104 100 100 100 100 17024 21131 .951 1.052 1.037 1.154 1.026 2.664 52 264 1.039 .97 80 2040 7400 36 44 44 52 0 8000 67 7931 .956 9846 9778 1.046 .943 -.065 -.085
4 4248 5423 82 81 4166 5342 4247 5355 85 92 4164 5274 0 0 970 1175 23 58 100 100 100 100 9508 9438 .78 1.282 1.267 1.288 1.242 1.482 52 316 1.276 .98 90 2190 7400 35 44 58 67 0 4929 74 4856 1.166 4867 4794 .858 1.151 .221 .203
5 357 142 86 74 271 67 353 123 87 86 267 48 0 0 79 52 20 51 100 46 100 25 338 315 4.045 .247 .18 .184 .198 3.687 32 220 .229 .29 70 2340 7390 35 42 74 81 0 129 67 61 .225 112 44 4.45 .163 -2.154 -2.613
6 4246 5471 97 78 4149 5393 4224 5503 98 84 4127 5425 0 0 1168 1201 27 44 100 100 100 100 9542 9552 .769 1.3 1.315 1.35 1.276 1.574 52 285 1.273 .98 90 2490 7400 35 44 88 97 0 4973 71 4902 1.181 5002 4931 .846 1.195 .241 .257
7 133 97 85 78 48 18 128 87 88 88 43 8 0 0 38 40 23 55 69 21 46 1 66 51 2.667 .375 .186 .69 .577 5.204 52 303 11.239 .08 90 2640 7400 35 44 103 112 -50 88 71 16 .341 79 7 2.934 .169 -1.553 -2.564
8 7509 7817 83 78 7425 7739 9296 9481 87 90 9213 9403 0 0 3966 3627 24 51 98 100 98 100 15164 18616 .959 1.042 1.021 1.359 1.017 2.571 52 278 1.002 .99 80 2790 7400 36 44 119 127 0 7105 71 7034 .947 8618 8547 1.056 .928 -.078 -.108
9 101 176 78 72 22 103 97 163 81 82 19 90 0 0 24 86 20 45 44 76 17 50 125 109 .214 4.682 4.737 4.318 4.302 5.456 52 310 6.551 .39 90 2940 7390 34 43 133 142 -50 160 65 94 4.256 148 82 .235 4.306 2.089 2.106
10 117 155 78 73 38 81 102 137 84 90 23 63 0 0 76 95 46 87 25 36 5 5 119 86 .469 2.132 2.739 2.057 2.171 4.116 52 267 1.733 .58 80 3100 7390 35 43 150 158 0 141 66 74 1.937 125 57 .516 2.49 .954 1.316
11 334 443 84 73 250 369 321 449 85 82 237 376 0 0 69 99 19 50 100 100 100 100 619 613 .678 1.476 1.586 1.476 1.505 1.745 32 209 1.636 .85 70 3250 7390 35 42 165 172 0 403 66 335 1.342 408 342 .745 1.442 .424 .528
12 233 1864 80 78 153 1786 231 1820 82 88 150 1742 0 0 44 486 19 47 100 100 100 100 1939 1892 .086 11.673 11.613 11.765 11.541 1.624 52 293 13.087 .89 90 3400 7390 34 43 179 188 0 1694 71 1623 10.61 1654 1583 .094 10.556 3.407 3.4
13 195 203 82 83 113 120 189 201 87 94 107 117 0 0 48 68 25 51 96 80 84 55 233 224 .942 1.062 1.093 1.03 1.026 2.701 52 246 1.306 .62 80 3550 7390 35 43 195 203 0 185 75 109 .965 183 106 1.036 .994 -.051 -.009
14 150 164 83 93 67 70 147 143 88 104 64 49 0 0 29 55 47 89 81 43 21 0 137 113 .957 1.045 .766 .774 1.036 3.243 32 202 2.481 .62 70 3700 7390 35 42 210 217 0 149 85 64 .95 130 45 1.053 .696 -.075 -.523
15 72 66 79 86 -7 -19 69 56 86 98 -9 -29 0 0 18 36 30 79 3 1 0 0 -26 -38 null null null 2.661 2.162 3.016 52 311 5.863 .58 90 3850 7390 34 43 224 233 -50 60 78 -17 null 51 -26 null null null null
16 1029 767 84 78 944 689 1083 783 87 89 999 705 0 0 258 239 22 50 100 100 100 100 1633 1704 1.37 .73 .706 .71 .686 1.61 52 256 .734 .94 80 4000 7390 35 43 240 248 0 697 71 626 .663 712 641 1.507 .641 -.592 -.641
17 95 99 83 81 11 17 93 86 86 93 9 4 0 0 26 72 24 62 23 9 7 3 28 13 .647 1.545 .444 1.526 1.831 5.118 52 291 6.354 .36 90 4150 7380 33 42 254 263 -50 90 74 15 1.405 78 4 .712 .404 .49 -1.308
18 63 58 82 81 -19 -23 60 54 84 90 -21 -27 0 0 10 22 19 48 0 0 0 0 -42 -48 null null null 1.328 1.563 3.549 52 301 6.048 .34 90 4300 7380 33 42 269 278 -50 53 74 -21 null 49 -25 null null null null
19 243 196 87 86 156 110 243 184 89 101 156 98 0 0 54 68 27 78 98 69 96 23 266 254 1.418 .705 .628 .609 .662 3.053 52 268 1.025 .56 80 4460 7380 34 42 286 294 0 178 78 100 .641 167 89 1.56 .571 -.642 -.808
20 1379 3258 85 82 1294 3175 1368 3355 91 116 1283 3272 0 0 181 495 48 180 100 100 100 100 4469 4555 .408 2.454 2.55 2.447 2.384 1.394 32 209 2.538 .97 70 4600 7380 34 41 300 307 0 2961 75 2886 2.23 3050 2974 .448 2.318 1.157 1.213

Total number of rows: 44544

Table truncated, full table size 9260 Kbytes.




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