NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM989723 Query DataSets for GSM989723
Status Public on Aug 23, 2012
Title PC 19N
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 19N2
Organism Homo sapiens
Characteristics individual: PC 19N
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/2008-08/81098.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 5009 5226 119 174 4889 5052 6983 6404 129 204 6863 6230 0 0 3545 3567 55 122 94 92 92 90 9941 13093 .968 1.033 .908 1.127 1.047 6.375 52 318 .989 .95 80 1990 6950 68 76 47 55 0 4908 163 4744 .97 6014 5851 1.031 .852 -.043 -.23
2 7188 7597 162 205 7026 7392 9319 9305 180 238 9156 9099 0 0 3665 3726 85 178 96 100 93 96 14418 18255 .95 1.052 .994 1.302 1.065 6.751 32 174 1.016 .93 60 2140 6960 70 76 63 69 0 7134 193 6942 .988 8738 8545 1.012 .933 -.017 -.1
3 12547 9206 189 230 12357 8976 16032 9953 223 270 15843 9723 0 0 7190 4791 118 148 100 100 100 100 21333 25566 1.377 .726 .614 .819 .732 4.17 32 217 .676 .94 70 2290 6960 69 76 77 84 0 8645 216 8429 .682 9347 9131 1.466 .576 -.552 -.795
4 7205 8166 182 215 7023 7951 8885 9863 218 255 8703 9648 0 0 5146 5850 124 164 96 96 90 88 14974 18351 .883 1.132 1.109 1.16 1.156 4.945 52 317 1.111 .95 90 2440 6950 67 76 91 100 0 7669 202 7467 1.063 9262 9060 .941 1.041 .088 .058
5 707 263 196 197 510 65 756 242 216 235 559 45 0 0 153 117 92 149 100 16 100 8 575 604 7.846 .127 .081 .169 .173 4.319 12 104 .077 .11 50 2590 6940 68 73 108 113 0 247 185 61 .12 227 42 8.355 .076 -3.063 -3.726
6 7430 5385 237 234 7192 5151 7747 6113 261 309 7509 5879 0 0 1630 1924 127 271 100 96 100 93 12343 13388 1.396 .716 .783 .615 .762 3.373 32 212 .739 .94 70 2740 6940 67 74 122 129 0 5057 220 4837 .673 5741 5521 1.487 .735 -.572 -.444
7 253 192 164 198 88 -6 248 181 184 238 84 -17 0 0 91 117 102 193 46 3 9 1 82 67 null null null 1.068 1.225 9.404 52 296 1.012 .22 90 2880 6940 66 75 135 144 -50 180 186 -6 null 170 -16 null null null null
8 9466 6100 150 185 9316 5915 10887 7424 196 222 10737 7239 0 0 7208 5141 188 148 86 80 82 76 15231 17976 1.575 .635 .674 .513 .623 6.028 52 292 .647 .94 90 3030 6940 66 75 150 159 -100 5728 174 5555 .596 6972 6798 1.677 .633 -.746 -.659
9 220 294 161 187 59 106 168 216 204 229 6 28 0 0 142 315 187 154 19 25 7 11 165 34 .557 1.797 4.667 1.402 1.478 7.452 52 292 .262 .22 90 3180 6940 66 75 165 174 -50 276 176 100 1.687 203 26 .593 4.382 .755 2.132
10 166 288 147 194 19 93 135 223 173 270 -11 28 0 0 113 241 109 253 11 13 5 3 112 17 .204 4.895 null 1.614 1.603 7.681 52 297 2.404 .46 90 3330 6940 66 75 180 189 -50 270 182 87 4.597 209 26 .218 null 2.201 null
11 255 429 126 215 128 213 269 423 150 260 142 208 0 0 136 240 86 189 61 51 36 21 341 350 .601 1.664 1.465 1.818 1.523 5.54 52 311 1.925 .59 90 3480 6940 66 75 195 204 -50 403 202 200 1.563 397 195 .64 1.376 .644 .46
12 191 282 128 220 63 61 178 245 157 271 50 24 0 0 73 139 134 201 13 19 1 1 124 74 1.033 .968 .48 1.45 1.976 9.043 52 306 1.154 .44 90 3630 6940 66 75 210 219 -50 265 207 57 .909 230 23 1.1 .451 -.137 -1.15
13 199 154 134 231 64 -76 205 124 170 308 70 -106 0 0 59 117 104 272 25 1 1 0 -12 -36 null null null 2.883 1.463 13.92 52 272 4.602 .32 90 3780 6940 66 75 225 234 -50 145 217 -71 null 116 -100 null null null null
14 211 293 137 227 74 65 214 278 162 304 77 50 0 0 76 134 104 253 28 5 7 0 139 127 1.138 .878 .649 1.268 1.581 8.207 52 282 2.295 .44 90 3930 6940 66 75 240 249 -50 275 213 61 .825 261 47 1.212 .61 -.278 -.714
15 124 149 148 237 -23 -87 120 122 172 325 -27 -115 0 0 51 94 101 323 1 0 1 0 -110 -142 null null null 2.68 2.726 7.568 52 296 7.772 .34 90 4090 6940 66 75 256 265 -50 140 223 -82 null 115 -108 null null null null
16 2100 722 158 263 1941 459 2221 718 189 326 2062 455 0 0 462 218 123 246 100 87 100 43 2400 2517 4.229 .236 .221 .2 .242 4.853 32 168 .23 .68 60 4240 6940 68 74 273 279 0 678 247 431 .222 674 427 4.503 .207 -2.171 -2.271
17 215 327 146 268 68 58 155 244 182 371 8 -24 0 0 211 329 146 617 13 7 9 1 126 -16 1.172 .853 null 2.243 2.586 8.03 52 286 15.066 .31 90 4390 6940 66 75 286 295 -50 307 252 54 .801 229 -23 1.248 null -.32 null
18 129 238 126 189 2 49 113 128 152 270 -12 -60 0 0 70 315 126 272 3 9 1 5 51 -72 .041 24.5 null 3.651 3.247 5.419 52 286 4.441 .58 90 4540 6930 65 74 301 310 -50 224 177 46 23.008 120 -56 .043 null 4.524 null
19 227 325 138 242 88 82 225 312 168 329 86 69 0 0 83 179 153 312 21 12 0 3 170 155 1.073 .932 .802 1.432 1.912 9.798 32 159 .675 .42 60 4670 6940 68 74 316 322 0 305 227 77 .875 293 65 1.143 .753 -.193 -.408
20 1247 2223 145 238 1102 1984 1350 2623 177 312 1205 2384 0 0 420 991 109 229 93 90 93 84 3086 3589 .555 1.8 1.978 1.662 1.964 3.319 32 214 1.943 .88 70 4840 6940 67 74 332 339 0 2088 224 1863 1.691 2463 2239 .591 1.858 .758 .894

Total number of rows: 44544

Table truncated, full table size 9705 Kbytes.




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