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Sample GSM989818 Query DataSets for GSM989818
Status Public on Aug 23, 2012
Title PC 2364T
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 PT 2364
Organism Homo sapiens
Characteristics individual: PC 2364T
disease state: Tumor
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/2008-11/81788.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 GPL15972
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 7045 6460 69 131 6975 6328 7808 7378 74 146 7738 7247 0 0 2080 2369 21 66 100 100 100 100 13303 14985 1.102 .907 .937 .838 .898 1.825 52 304 .927 .98 80 1740 7180 22 30 54 62 0 5779 117 5661 .812 6600 6483 1.232 .838 -.301 -.255
2 8980 8306 86 182 8894 8124 10636 9475 95 209 10550 9293 0 0 3350 2917 37 109 100 100 100 100 17018 19843 1.095 .913 .881 .939 .894 2.394 52 221 .891 .97 80 1890 7190 23 31 69 77 0 7431 163 7268 .817 8477 8314 1.224 .788 -.291 -.344
3 11431 25097 91 210 11340 24887 14134 30435 109 247 14043 30225 0 0 8427 17701 50 138 95 100 92 98 36227 44268 .456 2.195 2.152 2.605 2.144 3.262 80 322 2.175 .98 100 2040 7190 22 32 83 93 0 22452 188 22264 1.963 27228 27040 .509 1.926 .973 .945
4 10432 9113 113 216 10318 8896 11837 10362 125 254 11723 10146 0 0 2997 3126 52 147 100 100 100 98 19214 21869 1.16 .862 .865 .794 .87 1.932 52 218 .868 .97 80 2190 7180 22 30 99 107 0 8153 193 7959 .771 9270 9077 1.296 .774 -.375 -.369
5 644 353 110 200 534 152 699 363 120 228 588 162 0 0 204 84 51 104 94 69 92 21 686 750 3.513 .285 .276 .294 .295 4.324 52 176 .203 .43 80 2340 7190 23 31 114 122 0 316 179 136 .255 325 145 3.927 .246 -1.973 -2.02
6 4283 8634 114 224 4168 8410 1952 4378 128 250 1838 4154 0 0 4004 7774 64 117 100 100 100 100 12578 5992 .496 2.018 2.26 2.199 2.034 2.005 120 393 1.984 .98 120 2490 7180 20 32 127 139 0 7724 200 7524 1.805 3917 3716 .554 2.022 .852 1.016
7 178 282 111 245 66 37 173 274 127 265 61 29 0 0 55 80 64 125 48 12 16 1 103 90 1.784 .561 .475 .931 .842 6.625 80 289 .798 .67 100 2640 7180 21 31 143 153 -50 252 219 33 .502 245 26 1.994 .425 -.996 -1.233
8 12493 27624 105 231 12388 27393 16990 35762 118 267 16885 35530 0 0 8963 19467 49 138 100 98 96 97 39781 52415 .452 2.211 2.104 2.547 2.205 2.713 80 349 2.208 .98 110 2790 7180 20 31 157 168 0 24713 207 24506 1.978 31993 31786 .506 1.882 .984 .913
9 163 242 90 186 73 55 152 221 111 226 61 34 0 0 71 105 107 128 18 18 1 3 128 95 1.327 .753 .557 1.066 1.241 3.958 80 324 2.599 .63 100 2940 7180 21 31 173 183 -50 216 166 49 .674 198 30 1.484 .499 -.569 -1.004
10 216 228 83 157 133 70 214 219 99 171 130 61 0 0 37 65 135 70 43 43 0 15 203 191 1.9 .526 .469 .426 .589 4.493 32 172 .252 .52 70 3100 7190 23 30 190 197 0 204 140 63 .471 196 55 2.124 .42 -1.087 -1.252
11 1067 2434 74 134 992 2299 1077 2455 79 144 1003 2320 0 0 209 471 29 55 100 100 100 100 3291 3323 .431 2.318 2.313 2.304 2.374 1.687 52 248 2.333 .97 80 3250 7180 22 30 205 213 0 2177 120 2057 2.073 2196 2076 .482 2.069 1.052 1.049
12 790 1442 67 119 723 1322 818 1477 87 134 751 1357 0 0 163 268 220 91 100 100 90 98 2045 2108 .547 1.828 1.807 1.823 1.764 1.841 52 262 1.497 .82 80 3400 7180 22 30 220 228 0 1290 106 1183 1.636 1321 1214 .611 1.617 .71 .693
13 332 321 63 111 268 210 352 329 66 121 289 218 0 0 99 90 17 62 100 94 98 82 478 507 1.276 .784 .754 .833 .779 2.419 52 249 .831 .73 80 3550 7180 22 30 235 243 0 287 99 188 .701 294 195 1.427 .675 -.513 -.567
14 214 307 61 102 153 205 223 308 63 112 162 206 0 0 63 95 15 61 96 90 96 82 358 368 .746 1.34 1.272 1.278 1.34 2.867 52 216 1.442 .81 80 3710 7180 22 30 251 259 0 275 91 183 1.199 276 184 .834 1.138 .261 .186
15 60 85 61 108 -1 -22 60 80 65 120 -1 -27 0 0 10 38 24 84 0 1 0 0 -23 -28 null null null 3.628 4.89 5.574 80 308 1.065 .59 100 3860 7180 21 31 265 275 -50 76 97 -20 null 72 -24 null null null null
16 1583 3282 64 117 1518 3165 1684 3455 71 137 1620 3338 0 0 305 716 32 103 100 100 100 100 4683 4958 .48 2.085 2.06 2.041 2.099 1.716 52 223 2.128 .98 80 4010 7180 22 30 281 289 0 2936 105 2831 1.865 3091 2986 .536 1.843 .899 .882
17 210 279 67 112 142 167 215 284 76 131 148 171 0 0 34 73 33 74 100 88 98 55 309 319 .85 1.176 1.155 1.072 1.14 2.501 52 233 .401 .39 90 4160 7180 21 30 295 304 0 250 100 149 1.052 254 153 .95 1.034 .073 .048
18 76 124 71 132 5 -8 71 102 92 184 0 -30 0 0 20 70 112 358 0 0 0 0 -3 -30 null null null 4.293 4.177 5.024 80 281 3.647 .95 100 4310 7180 21 31 310 320 -50 111 118 -7 null 91 -27 null null null null
19 586 953 80 167 505 786 601 953 88 181 520 786 0 0 96 126 34 92 100 100 100 100 1291 1306 .642 1.556 1.512 1.571 1.513 1.829 52 222 1.567 .92 80 4460 7180 22 30 326 334 0 853 149 703 1.392 853 703 .718 1.352 .478 .435
20 2018 11460 74 170 1944 11289 2192 12115 81 186 2118 11944 0 0 639 2089 31 89 98 100 98 100 13233 14062 .172 5.807 5.639 6.597 5.575 2.461 52 279 5.651 .97 90 4610 7180 21 30 340 349 0 10252 152 10099 5.195 10838 10685 .192 5.045 2.377 2.335

Total number of rows: 44544

Table truncated, full table size 9508 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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