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Sample GSM989799 Query DataSets for GSM989799
Status Public on Aug 23, 2012
Title PC 457T
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 457T2
Organism Homo sapiens
Characteristics ethnicity: Caucasian
age: 71
individual: PC 453T
disease state: Tumor
pre-operation treatment: None
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/2008-08/81185.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 GPL9497
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 6686 10464 71 260 6614 10203 7092 11608 83 330 7020 11348 0 0 1849 3429 40 239 100 100 100 100 16817 18368 .648 1.543 1.617 1.484 1.608 3.834 52 378 1.541 .97 90 1680 6900 17 26 27 36 0 8097 201 7895 1.194 8982 8781 .838 1.251 .255 .323
2 5918 8903 69 239 5848 8663 6576 9938 81 288 6506 9698 0 0 1923 3455 49 190 100 98 100 98 14511 16204 .675 1.481 1.491 1.374 1.533 4.018 52 278 1.501 .97 80 1830 6900 18 26 43 51 0 6889 185 6703 1.146 7690 7504 .872 1.153 .197 .206
3 9190 8707 66 220 9124 8487 10425 10324 75 266 10358 10103 0 0 2578 3358 38 185 100 100 100 98 17611 20461 1.075 .93 .975 .826 .978 4.174 52 253 .95 .97 80 1980 6910 19 27 58 66 0 6737 170 6567 .72 7988 7817 1.389 .755 -.474 -.406
4 6682 10457 65 208 6617 10249 7672 11977 75 254 7607 11769 0 0 2473 4164 44 195 100 98 100 98 16866 19376 .646 1.549 1.547 1.518 1.598 4.109 52 288 1.533 .97 90 2130 6900 17 26 72 81 0 8091 161 7930 1.198 9267 9106 .834 1.197 .261 .26
5 348 263 68 217 280 46 362 252 78 277 294 34 0 0 105 139 45 185 94 13 94 3 326 328 6.087 .164 .116 .312 .322 7.567 52 221 1.152 .07 80 2280 6910 19 27 88 96 0 203 168 36 .127 195 26 7.867 .089 -2.976 -3.482
6 3134 2972 85 233 3048 2739 3231 3101 98 284 3145 2867 0 0 603 760 44 176 100 100 100 100 5787 6012 1.113 .899 .912 .869 .898 3.248 52 264 .891 .95 90 2440 6900 17 26 103 112 0 2300 180 2119 .695 2399 2218 1.438 .705 -.524 -.504
7 136 222 73 214 63 7 141 184 82 254 68 -30 0 0 59 144 40 165 65 11 42 5 70 38 9 .111 null 2.025 1.626 14.95 80 305 9.957 .17 100 2590 6900 17 27 118 128 -50 172 166 5 .086 142 -23 11.632 null -3.54 null
8 10318 9943 61 193 10256 9749 11119 11094 66 225 11058 10900 0 0 2312 2955 29 142 100 100 100 100 20005 21958 1.052 .951 .986 .924 1.002 3.546 52 276 .943 .96 90 2740 6900 17 26 133 142 0 7693 149 7543 .736 8584 8434 1.36 .763 -.443 -.391
9 129 168 59 173 69 -4 125 150 59 209 66 -22 0 0 22 92 17 166 100 8 91 0 65 44 null null null .649 .413 10.318 12 68 14.988 .19 40 2890 6900 20 24 151 155 0 130 134 -3 null 116 -17 null null null null
10 107 198 59 190 48 7 103 168 68 236 44 -22 0 0 54 114 37 171 55 5 28 2 55 22 6.857 .146 null 1.719 2.311 9.011 80 319 6.281 .31 100 3040 6900 17 27 163 173 -50 153 147 5 .113 130 -17 8.862 null -3.148 null
11 177 423 59 212 117 211 177 363 68 255 117 150 0 0 86 281 35 182 78 42 66 17 328 267 .555 1.803 1.282 1.777 1.527 7.911 80 366 4.62 .48 110 3190 6900 16 27 177 188 0 327 164 163 1.395 281 116 .717 .992 .481 -.012
12 219 568 59 184 159 384 222 544 70 238 162 360 0 0 68 196 42 182 92 82 86 50 543 522 .414 2.415 2.222 2.366 2.27 4.959 52 265 3.238 .6 90 3340 6900 17 26 193 202 0 439 142 297 1.869 421 279 .535 1.719 .902 .782
13 132 249 64 225 67 23 137 203 79 281 73 -22 0 0 55 130 49 252 60 8 32 0 90 51 2.913 .343 null 2.019 2.477 8.817 80 312 5.529 .31 100 3490 6890 16 26 208 218 -50 193 174 18 .266 157 -17 3.765 null -1.913 null
14 112 214 79 293 32 -79 115 196 95 371 35 -96 0 0 47 131 62 296 31 1 2 1 -47 -61 null null null 5.844 4.646 10.917 80 296 11.174 .35 100 3640 6890 16 26 223 233 -50 166 227 -61 null 152 -74 null null null null
15 83 168 76 284 6 -115 76 122 90 344 0 -161 0 0 36 206 60 233 6 5 2 1 -109 -161 null null null 11.409 9.647 9.026 80 324 7.894 .49 100 3790 6890 16 26 238 248 -50 130 220 -89 null 94 -125 null null null null
16 682 967 75 298 607 668 720 973 91 355 644 674 0 0 153 241 51 230 100 94 100 84 1275 1318 .909 1.1 1.047 1.038 1.127 4.193 52 211 1.096 .8 80 3950 6900 18 26 255 263 0 748 231 517 .852 753 522 1.174 .81 -.232 -.304
17 115 258 77 292 37 -33 116 217 89 331 39 -74 0 0 66 174 47 208 42 8 6 2 4 -35 null null null 3.506 3.689 7.579 80 314 5.094 .4 100 4090 6890 16 26 268 278 -50 200 226 -26 null 168 -57 null null null null
18 76 188 74 269 1 -80 67 122 86 338 -6 -147 0 0 47 282 45 235 5 5 2 3 -79 -153 null null null 9.603 8.965 7.256 80 310 9.352 .5 100 4250 6890 16 26 284 294 -50 145 208 -62 null 94 -114 null null null null
19 139 214 75 285 63 -71 146 187 90 352 70 -98 0 0 49 109 53 230 65 2 11 0 -8 -28 null null null 2.261 2.451 11.759 80 344 9.84 .29 100 4400 6890 16 26 299 309 -50 166 221 -55 null 145 -76 null null null null
20 576 1556 73 273 503 1282 609 1675 90 354 536 1402 0 0 172 693 54 277 98 86 96 82 1785 1938 .392 2.549 2.616 2.267 2.602 4.816 52 254 3.002 .85 90 4560 6900 17 26 315 324 0 1204 211 992 1.972 1296 1085 .507 2.024 .98 1.017

Total number of rows: 44544

Table truncated, full table size 9530 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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