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Sample GSM989689 Query DataSets for GSM989689
Status Public on Aug 23, 2012
Title PC 248T
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 248T2
Organism Homo sapiens
Characteristics ethnicity: Asian
age: 65
pre-operation treatment: None
individual: PC 547T
disease free survival: 3.20
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/2008-08/81166.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) [email protected]
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 20670 11165 168 118 20502 11046 23898 14066 209 140 23729 13947 0 0 8356 5647 147 92 100 96 100 93 31548 37676 1.856 .539 .588 .411 .538 3.215 32 236 .549 .91 70 1780 7090 45 52 26 33 0 9956 105 9849 .48 12542 12436 2.082 .524 -1.058 -.932
2 19470 12228 174 127 19295 12100 24736 14979 205 150 24561 14851 0 0 9951 5942 184 97 94 100 88 100 31395 39412 1.595 .627 .605 .858 .641 3.142 52 309 .61 .96 80 1940 7090 45 53 42 50 0 10903 113 10789 .559 13356 13242 1.788 .539 -.839 -.891
3 7422 17986 177 175 7245 17810 8251 24213 195 184 8074 24037 0 0 5194 11748 104 95 100 100 93 93 25055 32111 .407 2.458 2.977 2.233 2.178 2.824 32 176 2.538 .91 60 2100 7080 45 51 59 65 0 16038 156 15881 2.192 21590 21433 .456 2.655 1.132 1.408
4 12431 6374 166 117 12265 6256 15718 2889 189 142 15552 2771 0 0 10967 6409 95 113 92 78 86 71 18521 18323 1.961 .51 .178 .386 .527 2.568 52 359 .551 .93 90 2250 7080 43 52 72 81 0 5684 104 5578 .455 2576 2471 2.199 .159 -1.137 -2.654
5 1120 332 120 95 1000 236 1091 325 132 115 971 230 0 0 217 98 63 125 100 90 100 37 1236 1201 4.237 .236 .237 .224 .212 1.581 32 217 .261 .56 70 2400 7080 44 51 88 95 0 296 85 210 .21 290 205 4.752 .211 -2.249 -2.243
6 8778 7778 140 113 8638 7665 4453 4984 154 131 4313 4871 0 0 8254 7214 72 88 100 100 100 97 16303 9184 1.127 .887 1.129 .857 .857 1.614 120 522 .878 .98 120 2560 7080 42 54 102 114 0 6935 101 6835 .791 4444 4343 1.264 1.007 -.338 .01
7 284 148 144 138 140 9 280 132 167 184 136 -5 0 0 98 64 83 162 63 3 38 0 149 131 15.556 .064 null .411 .411 4.415 52 292 2.923 .39 90 2700 7080 43 52 117 126 -50 132 123 8 .057 118 -4 17.445 null -4.125 null
8 7762 17320 165 197 7597 17123 9277 14026 185 286 9112 13829 0 0 6441 15999 100 582 84 73 78 63 24720 22941 .444 2.254 1.518 1.885 2.25 2.159 52 332 2.495 .97 90 2850 7080 43 52 132 141 0 15444 176 15268 2.01 12507 12331 .498 1.353 1.007 .436
9 150 163 117 115 33 47 146 157 131 140 29 41 0 0 53 98 64 93 21 23 7 5 80 70 .702 1.424 1.414 1.561 1.54 2.735 52 342 2.512 .5 90 3000 7070 42 51 147 156 -50 145 103 42 1.27 140 37 .787 1.261 .345 .334
10 131 118 101 94 29 24 121 107 135 159 19 12 0 0 45 63 153 237 1 0 0 0 53 31 1.208 .828 .632 1.386 1.106 4.187 52 336 13.92 .23 90 3150 7070 42 51 162 171 -50 105 84 21 .738 95 11 1.355 .563 -.438 -.828
11 508 868 129 165 379 702 520 929 229 296 391 764 0 0 189 348 273 357 71 82 17 57 1081 1155 .54 1.852 1.954 1.64 1.887 2.051 52 277 2.156 .73 80 3310 7080 44 52 179 187 0 774 147 626 1.652 828 681 .605 1.742 .724 .801
12 334 496 132 173 202 323 341 573 212 325 209 399 0 0 159 339 247 437 40 42 1 3 525 608 .625 1.599 1.909 1.561 1.73 2.098 52 326 1.773 .51 90 3460 7070 42 51 193 202 -50 442 154 288 1.426 511 356 .701 1.702 .512 .767
13 297 236 133 166 164 70 293 217 198 306 160 50 0 0 110 113 200 366 36 0 0 0 234 210 2.343 .427 .313 .498 .575 3.092 52 326 1.659 .48 90 3610 7070 42 51 208 217 -50 210 148 62 .381 193 45 2.627 .279 -1.394 -1.843
14 195 201 135 159 60 41 181 158 223 319 46 0 0 0 73 173 255 382 1 5 0 1 101 46 1.463 .683 null 1.471 1.43 4.212 52 326 1.834 .51 90 3760 7070 42 51 223 232 -50 179 142 37 .609 141 0 1.641 null -.715 null
15 147 127 131 152 16 -24 131 67 212 271 0 -85 0 0 102 220 271 302 1 5 1 1 -8 -85 null null null 3.205 2.468 4.373 52 337 1.965 .55 90 3910 7070 42 51 238 247 -50 113 136 -21 null 60 -76 null null null null
16 2065 1355 122 155 1943 1199 2419 1467 205 282 2297 1311 0 0 990 589 233 322 88 84 86 80 3142 3608 1.621 .617 .571 .607 .64 1.764 52 254 .618 .88 80 4070 7090 45 53 255 263 0 1208 138 1069 .55 1308 1169 1.817 .509 -.862 -.974
17 134 105 138 178 -4 -73 129 97 206 351 -9 -81 0 0 46 45 204 468 0 0 0 0 -77 -90 null null null 2.393 1.966 4.287 52 320 3.535 .62 90 4210 7070 42 51 268 277 -50 94 159 -65 null 86 -72 null null null null
18 129 97 143 178 -14 -81 104 58 218 319 -38 -119 0 0 127 150 261 416 1 1 1 0 -95 -157 null null null 3.159 2.728 2.842 52 347 2.694 .32 90 4360 7070 42 51 283 292 -50 86 159 -72 null 52 -106 null null null null
19 525 493 146 176 379 317 512 478 197 294 366 302 0 0 118 223 182 320 93 40 53 3 696 668 1.196 .836 .825 .741 .689 1.663 32 227 1.574 .62 70 4520 7080 44 51 300 307 0 440 157 283 .746 426 269 1.341 .736 -.423 -.443
20 2027 6464 134 163 1893 6301 2400 7808 199 306 2266 7644 0 0 967 2768 197 388 86 100 86 96 8194 9910 .3 3.329 3.373 4.219 3.276 2.895 52 276 3.347 .95 80 4670 7070 43 51 315 323 0 5764 145 5618 2.968 6962 6816 .337 3.008 1.57 1.589

Total number of rows: 44544

Table truncated, full table size 9657 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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