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Sample GSM989820 Query DataSets for GSM989820
Status Public on Aug 23, 2012
Title PC 563N
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 563N2
Organism Homo sapiens
Characteristics individual: PC 563N
disease state: Normal
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/2008-08/81162.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 11241 15771 65 113 11176 15657 12504 17149 85 189 12438 17035 0 0 3620 4089 131 558 100 100 100 100 26833 29473 .714 1.401 1.37 1.482 1.367 2.11 52 306 1.365 .97 80 1800 7250 33 41 28 36 0 13807 99 13707 1.226 15013 14913 .815 1.199 .294 .262
2 11452 15175 66 119 11385 15055 13536 18246 83 231 13470 18127 0 0 4736 7118 101 697 100 90 100 90 26440 31597 .756 1.322 1.346 1.027 1.346 3.832 52 329 1.356 .98 90 1950 7240 31 40 42 51 0 13285 104 13180 1.158 15973 15869 .864 1.178 .211 .236
3 14917 11244 65 108 14851 11135 15229 12338 77 165 15163 12229 0 0 2529 2904 80 285 100 100 100 100 25986 27392 1.334 .75 .807 .721 .784 1.908 52 288 .755 .98 90 2110 7260 33 42 58 67 0 9844 95 9748 .656 10801 10706 1.523 .706 -.607 -.502
4 14477 19281 69 129 14408 19152 14868 19224 80 182 14799 19094 0 0 2092 2462 78 268 100 100 100 100 33560 33893 .752 1.329 1.29 1.335 1.298 1.622 52 289 1.311 .97 90 2260 7250 32 41 73 82 0 16879 113 16767 1.164 16830 16716 .859 1.13 .219 .176
5 542 173 75 150 466 22 591 159 85 196 515 8 0 0 208 64 42 206 96 1 92 0 488 523 21.182 .047 .016 .144 .124 6.144 52 272 .422 .13 80 2400 7240 32 40 88 96 0 151 131 19 .041 139 7 24.195 .014 -4.597 -6.2
6 8757 8462 146 207 8611 8255 8995 8844 167 256 8848 8637 0 0 1875 2342 107 313 100 98 100 98 16866 17485 1.043 .959 .976 .909 .97 1.978 52 273 .941 .95 90 2560 7260 33 42 103 112 0 7408 181 7227 .839 7742 7561 1.192 .855 -.253 -.227
7 168 123 98 170 70 -46 151 119 128 233 52 -50 0 0 60 53 109 305 28 0 0 0 24 2 null null null .814 1.066 7.594 52 318 3.213 .33 90 2700 7240 31 40 117 126 -50 108 149 -40 null 104 -44 null null null null
8 15674 11299 75 153 15598 11146 16533 12160 84 185 16457 12007 0 0 2933 3018 68 210 100 100 100 100 26744 28464 1.399 .715 .73 .678 .731 2.052 52 288 .723 .98 90 2870 7250 32 41 134 143 0 9892 134 9758 .626 10645 10511 1.599 .639 -.677 -.647
9 96 106 71 147 24 -40 91 98 79 188 19 -49 0 0 29 58 45 244 21 0 0 0 -16 -30 null null null 3.96 8.668 9.12 52 286 6.675 .65 90 3000 7240 31 40 147 156 -50 93 129 -35 null 86 -43 null null null null
10 91 155 63 123 28 32 92 162 69 150 29 39 0 0 25 56 41 197 30 0 1 0 60 68 .875 1.143 1.345 2.017 2.065 3.719 52 310 6.974 .64 90 3150 7240 31 40 162 171 -50 136 108 28 1.001 142 34 .999 1.177 .001 .236
11 390 627 64 129 326 498 401 658 71 168 337 529 0 0 108 203 47 214 100 88 96 69 824 866 .655 1.528 1.57 1.443 1.531 2.463 52 270 2.108 .77 80 3310 7240 32 40 179 187 0 549 113 436 1.337 576 463 .748 1.374 .419 .459
12 172 663 68 150 104 512 172 692 74 197 104 541 0 0 60 283 33 279 88 75 77 48 616 645 .203 4.923 5.202 4.876 4.672 3.363 80 336 5.7 .81 100 3460 7250 32 42 193 203 0 580 131 448 4.31 606 474 .232 4.554 2.108 2.187
13 146 158 67 159 79 -1 151 143 75 206 83 -15 0 0 45 64 35 263 82 0 57 0 78 68 null null null .695 .569 6.154 52 267 19.366 .24 90 3600 7240 31 40 207 216 -50 138 139 -1 null 125 -13 null null null null
14 126 159 66 168 59 -9 124 137 76 209 57 -31 0 0 43 87 45 210 69 3 23 1 50 26 null null null 1.492 1.393 9.136 52 291 7.156 .54 90 3750 7240 31 40 222 231 -50 139 147 -8 null 120 -27 null null null null
15 79 76 69 158 10 -81 72 64 75 195 3 -93 0 0 23 45 41 196 11 0 1 0 -71 -90 null null null 11.032 8.488 4.666 52 301 11.748 .38 90 3900 7240 31 40 237 246 -50 67 138 -71 null 56 -81 null null null null
16 1351 825 71 161 1279 663 1357 846 77 186 1285 685 0 0 242 269 33 128 100 96 100 90 1942 1970 1.929 .518 .533 .483 .539 2.284 52 301 .531 .87 90 4060 7240 31 40 253 262 0 722 141 580 .454 741 600 2.204 .467 -1.14 -1.1
17 104 142 70 161 33 -19 101 134 82 247 30 -27 0 0 29 52 97 330 3 0 0 0 14 3 null null null 1.412 1.421 6.902 52 291 7.085 .27 90 4210 7240 31 40 268 277 -50 124 141 -17 null 117 -24 null null null null
18 82 65 67 154 15 -88 80 62 80 234 12 -92 0 0 22 31 97 353 0 0 0 0 -73 -80 null null null 13.329 8.593 4.545 52 291 8.723 .29 90 4360 7240 31 40 283 292 -50 57 135 -77 null 54 -81 null null null null
19 336 229 62 135 273 94 326 219 71 176 263 83 0 0 77 59 32 220 100 1 100 0 367 346 2.904 .344 .316 .321 .388 3.029 52 272 3.872 .21 90 4510 7250 32 41 298 307 0 200 118 82 .301 192 73 3.317 .276 -1.73 -1.856
20 1080 2264 65 134 1014 2130 1131 2312 75 173 1065 2178 0 0 308 452 40 250 100 100 100 100 3144 3243 .476 2.101 2.045 2.178 2.2 1.972 52 269 2.163 .92 80 4660 7250 33 41 314 322 0 1982 117 1865 1.839 2024 1907 .544 1.79 .879 .84

Total number of rows: 44544

Table truncated, full table size 9797 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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