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Sample GSM989779 Query DataSets for GSM989779
Status Public on Aug 23, 2012
Title PC 351T2
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 351T2.1
Organism Homo sapiens
Characteristics ethnicity: Caucasian
age: 62
pre-operation treatment: None
individual: PC 351T
disease free survival: 62.30
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/2008-08/81239.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 17919 15523 43 90 17876 15433 18190 17954 58 109 18147 17864 0 0 3468 6631 46 65 100 98 100 98 33309 36011 1.158 .863 .984 .702 .94 5.797 52 332 .939 .92 90 1980 6800 55 64 37 46 0 16861 98 16764 .938 19502 19404 1.066 1.069 -.093 .097
2 18074 16643 45 96 18029 16546 19324 18182 52 109 19278 18085 0 0 4598 5993 23 65 100 100 100 98 34575 37363 1.09 .918 .938 .737 .919 7.531 52 268 .901 .93 90 2120 6810 56 65 51 60 0 18078 104 17973 .997 19750 19644 1.003 1.019 -.005 .027
3 15370 11297 50 104 15319 11192 15871 12520 60 118 15820 12415 0 0 2766 3813 45 67 100 100 100 100 26511 28235 1.369 .731 .785 .636 .761 5.236 52 284 .732 .91 90 2280 6800 55 64 67 76 0 12271 113 12157 .794 13599 13485 1.26 .852 -.334 -.23
4 15187 15672 47 101 15139 15571 18200 18297 53 116 18152 18195 0 0 7387 8236 25 68 100 97 100 96 30710 36347 .972 1.029 1.002 .953 1.023 9.578 80 391 .968 .9 100 2430 6800 55 65 82 92 0 17023 110 16914 1.117 19875 19764 .895 1.089 .16 .123
5 1162 281 43 98 1118 183 1215 280 53 111 1171 181 0 0 181 96 29 67 100 86 100 67 1301 1352 6.109 .164 .155 .137 .158 6.134 52 233 .132 .6 90 2580 6800 55 64 97 106 0 305 106 199 .178 304 197 5.624 .168 -2.492 -2.574
6 3461 3801 45 101 3415 3700 611 634 51 111 566 532 0 0 3999 4519 22 60 95 92 92 81 7115 1098 .923 1.083 .94 .994 1.102 6.982 208 813 1.086 .96 160 2710 6800 52 68 107 123 0 4129 110 4019 1.177 689 578 .85 1.021 .235 .03
7 260 162 44 100 215 62 261 154 47 119 216 54 0 0 60 72 15 119 100 19 98 0 277 270 3.468 .288 .25 .367 .418 6.691 52 233 .265 .16 90 2890 6800 55 64 128 137 0 176 109 67 .313 167 59 3.192 .272 -1.675 -1.881
8 15896 10352 51 109 15844 10242 16345 11354 60 137 16294 11244 0 0 2733 3518 51 150 100 98 100 94 26086 27538 1.547 .646 .69 .506 .665 7.241 52 261 .639 .92 80 3030 6790 55 63 143 151 0 11245 118 11125 .702 12333 12213 1.424 .75 -.51 -.416
9 240 142 40 98 200 44 234 122 52 114 193 24 0 0 67 83 50 109 98 21 94 5 244 217 4.545 .22 .124 .323 .33 8.206 52 275 .15 .19 90 3190 6790 54 63 158 167 0 154 106 48 .239 133 26 4.185 .135 -2.065 -2.888
10 200 326 37 93 162 232 195 324 39 101 157 231 0 0 38 139 10 52 100 88 100 78 394 388 .698 1.432 1.471 1.222 1.523 5.774 52 213 1.553 .7 90 3340 6800 55 64 173 182 0 354 101 252 1.556 352 251 .643 1.598 .637 .676
11 844 1113 38 91 805 1021 849 1231 40 103 811 1139 0 0 162 409 10 57 100 94 100 94 1826 1950 .788 1.268 1.404 1.087 1.329 6.826 52 277 1.26 .85 90 3490 6790 54 63 188 197 0 1209 99 1109 1.378 1337 1237 .726 1.526 .462 .609
12 564 1065 38 96 525 968 558 1060 40 103 519 963 0 0 89 363 10 55 100 96 100 96 1493 1482 .542 1.844 1.855 1.518 1.999 7.848 52 304 1.796 .84 90 3630 6790 54 63 202 211 0 1157 104 1051 2.003 1151 1046 .499 2.015 1.002 1.011
13 399 257 39 96 360 160 400 262 39 104 361 165 0 0 64 121 9 55 100 82 100 63 520 526 2.25 .444 .457 .443 .496 5.172 52 288 .457 .63 90 3790 6790 54 63 218 227 0 279 104 174 .483 285 179 2.071 .496 -1.051 -1.01
14 119 180 37 95 82 85 126 157 39 103 89 62 0 0 43 98 9 54 87 55 86 33 167 151 .965 1.037 .697 1.067 1.022 10.649 80 261 1.104 .43 100 3940 6800 55 65 233 243 0 196 103 92 1.126 171 67 .888 .757 .171 -.402
15 51 80 39 96 12 -16 48 73 40 104 9 -22 0 0 15 40 12 55 42 7 18 0 -4 -13 null null null 4.367 4.778 10.389 120 384 -11.178 -.13 120 4090 6800 54 66 247 259 -50 87 104 -17 null 79 -24 null null null null
16 775 463 40 93 735 370 898 463 43 101 858 370 0 0 337 239 14 57 97 86 96 82 1105 1228 1.986 .503 .431 .544 .512 8.741 80 245 .447 .78 100 4250 6800 55 65 264 274 0 503 101 402 .547 503 402 1.829 .468 -.871 -1.094
17 114 178 38 81 76 96 114 177 40 91 76 95 0 0 26 86 10 47 100 67 98 48 172 171 .792 1.263 1.25 1.172 1.476 6.873 52 160 1.303 .45 80 4390 6790 55 63 279 287 0 193 88 104 1.372 192 103 .729 1.358 .456 .441
18 50 85 40 91 9 -6 48 73 43 101 7 -18 0 0 15 49 13 50 35 11 12 3 3 -11 null null null 4.504 4.166 9.331 120 422 10.844 .07 120 4540 6790 53 65 292 304 -50 92 99 -7 null 79 -20 null null null null
19 594 324 44 96 549 227 586 304 48 109 541 208 0 0 115 116 17 55 100 98 100 84 776 749 2.419 .413 .384 .362 .368 5.09 52 265 .357 .66 90 4700 6800 55 64 309 318 0 352 104 247 .449 330 226 2.227 .418 -1.155 -1.26
20 2951 6157 43 106 2907 6051 2957 6549 48 136 2913 6442 0 0 352 1867 26 200 100 100 100 98 8958 9355 .48 2.082 2.211 1.847 2.196 5.332 52 270 2.143 .88 90 4850 6790 54 63 324 333 0 6688 115 6573 2.261 7114 6997 .442 2.402 1.177 1.264

Total number of rows: 44544

Table truncated, full table size 9445 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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