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Sample GSM989817 Query DataSets for GSM989817
Status Public on Aug 23, 2012
Title PC 619T
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 619T2
Organism Homo sapiens
Characteristics ethnicity: Caucasian
age: 65
pre-operation treatment: None
individual: PC 163T
disease free survival: 62.70
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/2008-08/81075.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 3234 4266 96 236 3138 4030 3319 4115 109 328 3222 3879 0 0 2029 2844 59 327 96 84 90 81 7168 7101 .779 1.284 1.204 1.265 1.377 17.904 32 176 1.111 .79 60 1860 7110 36 42 59 65 0 3287 182 3105 .989 3171 2989 1.011 .928 -.015 -.108
2 2514 3105 104 256 2410 2849 2248 3664 127 366 2144 3408 0 0 2028 2501 113 469 87 75 78 59 5259 5552 .846 1.182 1.59 1.229 1.189 17.714 32 176 .921 .71 60 2010 7110 36 42 74 80 0 2392 197 2195 .911 2823 2626 1.098 1.225 -.135 .292
3 2751 5614 93 241 2657 5372 2005 5018 105 302 1911 4777 0 0 2226 4658 52 225 87 84 81 81 8029 6688 .495 2.022 2.5 2.46 2.035 28.369 32 176 1.835 .78 60 2160 7110 36 42 89 95 0 4325 186 4139 1.558 3866 3681 .642 1.926 .639 .946
4 4085 4851 87 254 3998 4597 3965 5248 109 380 3878 4994 0 0 2484 3248 85 554 100 84 100 81 8595 8872 .87 1.15 1.288 .774 1.12 17.528 32 171 1.036 .82 60 2310 7110 36 42 104 110 0 3738 196 3542 .886 4043 3848 1.129 .992 -.175 -.011
5 160 343 91 240 69 103 136 300 114 369 44 60 0 0 96 282 123 576 25 5 3 1 172 104 .67 1.493 1.364 3.203 1.524 19.537 52 286 1.961 .5 90 2460 7110 34 43 117 126 -50 264 185 79 1.15 231 46 .869 1.051 .202 .071
6 1349 1975 93 225 1255 1749 1369 1945 105 311 1275 1719 0 0 291 789 63 494 100 90 100 84 3004 2994 .718 1.394 1.348 1.227 1.413 6.274 32 190 1.322 .8 70 2610 7110 35 42 133 140 0 1522 173 1348 1.074 1499 1324 .931 1.039 .103 .055
7 127 350 96 225 30 124 105 188 137 348 8 -37 0 0 70 592 264 798 0 1 0 1 154 -29 .242 4.133 null 4.028 4.142 18 52 305 -1 -1 90 2750 7100 33 42 146 155 -50 270 173 96 3.185 145 -29 .314 null 1.671 null
8 2373 4469 99 215 2274 4254 517 659 107 277 417 444 0 0 2616 5667 55 225 61 51 59 50 6528 861 .535 1.871 1.065 1.495 1.952 12.89 52 301 2.077 .83 90 2910 7100 33 42 162 171 0 3443 166 3278 1.441 508 342 .694 .82 .527 -.286
9 134 444 97 238 37 206 129 268 109 291 32 30 0 0 64 428 54 238 32 36 13 21 243 62 .18 5.568 .938 4.428 2.999 19.841 52 296 29.264 .1 90 3060 7100 33 42 177 186 -50 342 183 159 4.29 206 23 .233 .722 2.101 -.469
10 146 259 92 220 53 39 150 241 106 300 58 21 0 0 66 160 54 272 51 9 19 1 92 79 1.359 .736 .362 1.295 1.533 16.563 52 291 59.702 .05 90 3210 7100 33 42 192 201 -50 200 170 30 .567 186 16 1.764 .279 -.819 -1.842
11 159 350 96 240 62 110 152 305 111 339 56 65 0 0 81 241 69 510 40 7 9 1 172 121 .564 1.774 1.161 1.832 1.969 8.955 52 337 -1 -1 90 3360 7100 33 42 207 216 -50 270 185 85 1.367 235 50 .732 .894 .451 -.161
12 297 533 91 259 206 273 315 545 95 321 224 286 0 0 112 190 37 236 91 66 83 16 479 510 .755 1.325 1.277 1.533 1.348 14.346 12 104 1.27 .2 50 3520 7110 36 41 225 230 0 411 200 210 1.021 420 220 .979 .984 .03 -.024
13 147 250 89 256 58 -5 135 227 107 362 46 -28 0 0 61 151 71 485 40 0 11 0 53 18 null null null 2.301 1.086 18.01 52 306 77.413 .06 90 3660 7100 33 42 237 246 -50 193 197 -4 null 175 -22 null null null null
14 138 243 92 241 45 1 126 183 103 312 33 -58 0 0 68 163 56 346 36 5 17 0 46 -25 45 .022 null 3.18 2.229 21.253 52 291 5.009 .14 90 3810 7100 33 42 252 261 -50 187 186 1 .017 141 -45 58.405 null -5.868 null
15 118 273 86 227 32 46 119 206 100 289 33 -21 0 0 46 222 59 248 17 11 7 5 78 12 .696 1.438 null 2.954 3.908 15.822 52 311 8.66 .21 90 3960 7100 33 42 267 276 -50 210 175 35 1.108 159 -16 .903 null .147 null
16 320 540 93 224 226 316 303 446 106 305 209 222 0 0 161 312 56 296 78 43 75 21 542 431 .715 1.398 1.062 1.329 1.625 18.487 32 175 1.037 .28 60 4120 7100 35 41 285 291 0 416 173 243 1.077 344 171 .928 .818 .107 -.289
17 173 400 98 236 75 163 185 387 115 401 86 151 0 0 63 234 63 801 66 0 33 0 238 237 .46 2.173 1.756 2.694 2.947 6.919 12 68 11.279 .17 40 4250 7100 36 40 299 303 0 308 182 126 1.675 298 116 .597 1.353 .744 .436
18 95 199 81 204 13 -5 85 163 91 254 3 -40 0 0 38 163 47 204 21 7 1 3 8 -37 null null null 4.069 3.99 12.115 52 329 66.241 .04 90 4410 7100 33 42 312 321 -50 153 157 -4 null 126 -31 null null null null
19 123 220 79 225 43 -5 118 215 91 286 39 -10 0 0 51 128 52 332 42 1 11 0 38 29 null null null 2.569 1.838 17.009 52 340 9.187 .11 90 4570 7100 33 42 328 337 -50 170 173 -4 null 166 -8 null null null null
20 714 2035 83 240 631 1795 763 2321 103 341 680 2081 0 0 389 1125 66 448 84 87 84 65 2426 2761 .352 2.845 3.06 2.858 3.049 8.766 32 161 2.851 .82 60 4730 7110 36 42 346 352 0 1568 185 1383 2.192 1788 1603 .456 2.358 1.132 1.238

Total number of rows: 44544

Table truncated, full table size 9643 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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