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Sample GSM989734 Query DataSets for GSM989734
Status Public on Aug 23, 2012
Title PC 367N
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 367N2
Organism Homo sapiens
Characteristics individual: PC 367N
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/2008-08/81082.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 8166 9618 92 66 8073 9552 4599 5928 119 91 4506 5861 0 0 8258 9437 113 99 80 90 75 78 17625 10367 .845 1.183 1.301 1.147 1.08 3.348 52 292 1.168 .95 80 2010 7020 50 58 89 97 0 9669 66 9603 1.189 5959 5892 .841 1.308 .25 .387
2 12034 14653 87 68 11946 14584 13609 16427 111 96 13521 16359 0 0 9293 9711 77 167 100 100 100 93 26530 29880 .819 1.221 1.21 1.314 1.197 3.555 32 205 1.156 .95 70 2160 7020 50 57 104 111 0 14731 68 14661 1.227 16514 16446 .815 1.216 .295 .283
3 3234 4234 90 61 3143 4172 1187 1102 117 92 1096 1040 0 0 3692 4861 155 94 59 71 53 65 7315 2136 .753 1.327 .949 1.424 1.382 3.502 52 301 1.335 .96 80 2310 7010 49 57 119 127 0 4256 61 4194 1.334 1108 1046 .749 .954 .416 -.068
4 14635 17346 102 70 14532 17275 17865 19908 118 88 17763 19837 0 0 8675 10133 66 87 100 96 100 96 31807 37600 .841 1.189 1.117 1.05 1.136 2.618 32 225 1.196 .95 70 2460 7010 49 56 134 141 0 17438 70 17367 1.195 20014 19942 .837 1.123 .257 .167
5 546 206 94 70 452 135 577 180 138 128 482 109 0 0 249 132 204 275 78 3 62 3 587 591 3.348 .299 .226 .344 .3 3.046 32 158 .517 .24 60 2620 7020 51 57 151 157 0 207 70 136 .3 181 110 3.33 .227 -1.736 -2.137
6 4397 4981 94 66 4302 4914 5292 5727 124 112 5197 5660 0 0 2682 3017 134 229 96 88 92 84 9216 10857 .875 1.142 1.089 1.044 1.057 2.533 52 276 1.144 .93 80 2770 7010 49 57 165 173 0 5007 66 4940 1.148 5757 5690 .871 1.095 .2 .131
7 259 131 92 73 166 57 254 126 130 99 161 52 0 0 121 66 124 92 62 28 15 9 223 213 2.912 .343 .323 .371 .385 5.724 32 212 21.841 .09 70 2920 7020 50 57 180 187 0 132 73 57 .345 127 52 2.897 .325 -1.535 -1.623
8 6575 8017 105 85 6470 7932 7686 8736 149 119 7580 8651 0 0 3306 4293 149 181 100 93 96 87 14402 16231 .816 1.226 1.141 1 1.144 2.008 32 202 1.261 .95 70 3070 7010 49 56 195 202 0 8060 85 7974 1.232 8782 8697 .811 1.147 .302 .198
9 132 96 98 75 33 20 113 82 148 113 14 6 0 0 97 55 168 168 5 0 1 0 53 20 1.65 .606 .429 1.211 1.168 5.014 52 300 .937 .46 90 3210 7010 48 57 208 217 -50 97 75 20 .609 82 6 1.641 .431 -.715 -1.215
10 122 168 86 61 35 106 117 162 103 72 30 100 0 0 41 72 94 46 8 75 0 50 141 130 .33 3.029 3.333 3.117 2.788 6.482 12 102 3.042 .34 50 3360 7020 51 56 225 230 0 169 61 107 3.045 163 101 .328 3.351 1.606 1.745
11 259 465 94 89 164 376 261 439 139 113 166 350 0 0 52 137 116 108 83 100 16 91 540 516 .436 2.293 2.108 2.267 1.934 1.814 12 103 2.848 .64 50 3510 7010 50 55 240 245 0 467 89 378 2.305 441 352 .434 2.12 1.205 1.084
12 274 1375 100 64 173 1310 293 1419 140 96 192 1354 0 0 93 537 216 150 34 100 0 96 1483 1546 .132 7.572 7.052 9.636 7.681 2.659 32 199 8.433 .6 70 3680 7020 50 57 256 263 0 1382 64 1317 7.612 1427 1361 .131 7.09 2.928 2.826
13 188 170 91 72 96 97 144 138 140 117 52 65 0 0 159 116 216 181 11 21 3 1 193 117 .99 1.01 1.25 1.23 1.264 3.561 52 234 .593 .58 80 3810 7020 50 58 269 277 0 171 72 98 1.016 139 65 .984 1.257 .023 .33
14 164 131 90 60 74 70 156 129 122 93 66 68 0 0 77 66 108 164 25 9 3 0 144 134 1.057 .946 1.03 .933 1.061 4.884 32 158 .469 .38 60 3970 7020 51 57 286 292 0 132 60 70 .951 130 68 1.052 1.036 -.073 .051
15 98 85 98 70 0 14 84 54 143 102 -13 -16 0 0 35 109 214 115 0 7 0 3 14 -29 null null null 1.584 1.529 2.523 52 298 2.257 .96 90 4120 7020 49 58 299 308 -50 85 70 14 null 54 -16 null null null null
16 708 388 96 70 612 318 738 412 122 104 641 341 0 0 485 259 82 100 76 69 67 63 930 982 1.925 .52 .532 .551 .471 2.42 52 202 .513 .81 80 4280 7020 50 58 316 324 0 390 70 320 .522 414 343 1.914 .535 -.937 -.903
17 126 139 92 76 33 62 107 117 139 117 14 40 0 0 84 124 174 167 5 7 3 5 95 54 .532 1.879 2.857 2.231 1.811 4.139 52 273 4.93 .14 90 4420 7010 48 57 329 338 -50 140 76 62 1.889 118 40 .529 2.872 .917 1.522
18 98 68 98 80 0 -11 89 49 197 172 -8 -30 0 0 56 65 692 545 0 0 0 0 -11 -38 null null null 2.158 1.854 4.104 52 309 1.079 .4 90 4580 7010 48 57 345 354 -50 68 80 -11 null 49 -30 null null null null
19 375 264 90 73 284 190 298 220 127 123 207 146 0 0 391 233 234 256 37 12 6 6 474 353 1.495 .669 .705 .736 .707 2.108 32 219 .736 .72 70 4740 7010 49 56 362 369 0 265 73 191 .673 221 147 1.487 .709 -.572 -.496
20 1882 3552 92 69 1789 3482 2263 4177 141 117 2170 4107 0 0 1011 1925 246 259 84 93 84 87 5271 6277 .514 1.946 1.893 2.034 1.924 1.831 32 210 1.963 .96 70 4880 7020 50 57 376 383 0 3571 69 3500 1.957 4199 4129 .511 1.903 .968 .928

Total number of rows: 44544

Table truncated, full table size 9356 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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