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Sample GSM989825 Query DataSets for GSM989825
Status Public on Aug 23, 2012
Title PC 575N
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 575N2
Organism Homo sapiens
Characteristics individual: PC 575N
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/2008-08/81172.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) [email protected]
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 3624 8973 71 42 3553 8930 4373 8973 78 47 4302 8930 0 0 2136 2439 28 24 94 100 92 100 12483 13232 .398 2.513 2.076 4.307 2.031 6.18 52 305 2.418 .83 80 1760 7310 23 31 44 52 0 8546 40 8505 2.394 8546 8505 .418 1.977 1.259 .983
2 2491 6346 74 40 2416 6305 3160 7062 80 46 3085 7021 0 0 1749 2206 27 31 94 100 84 100 8721 10106 .383 2.61 2.276 4.785 2.165 5.915 52 267 2.379 .85 80 1910 7310 23 31 59 67 0 6044 38 6005 2.485 6726 6687 .402 2.167 1.313 1.116
3 667 6657 74 44 592 6612 794 6921 83 50 719 6876 0 0 360 1614 32 24 94 100 88 100 7204 7595 .09 11.169 9.563 14.536 9.82 3.009 52 243 11.462 .83 80 2060 7310 23 31 74 82 0 6340 42 6297 10.637 6591 6549 .094 9.108 3.411 3.187
4 2840 6517 71 42 2769 6474 3327 6790 76 46 3255 6747 0 0 1668 1714 27 22 90 100 90 100 9243 10002 .428 2.338 2.073 4.17 1.847 6.975 52 230 2.248 .81 80 2210 7310 23 31 89 97 0 6207 40 6166 2.227 6467 6426 .449 1.974 1.155 .981
5 138 101 73 40 64 61 123 98 78 44 49 57 0 0 70 49 27 17 60 80 48 67 125 106 1.049 .953 1.163 .963 .812 3.538 80 350 .537 .47 100 2360 7300 21 31 103 113 -50 96 38 58 .908 93 54 1.102 1.108 -.14 .148
6 440 3862 75 47 364 3814 488 3810 80 51 412 3763 0 0 260 1150 28 22 82 100 78 100 4178 4175 .095 10.478 9.133 15.329 8.697 4.95 52 316 10.957 .76 90 2510 7300 21 30 118 127 0 3678 45 3632 9.979 3629 3584 .1 8.699 3.319 3.121
7 138 84 76 40 61 43 136 80 81 46 59 39 0 0 53 27 29 20 65 71 50 48 104 98 1.419 .705 .661 .691 .554 4.313 52 275 .249 .28 80 2670 7310 23 31 135 143 0 80 38 41 .671 76 37 1.49 .63 -.575 -.668
8 756 7008 75 40 681 6968 860 7240 83 47 784 7199 0 0 372 1923 30 21 88 100 88 100 7649 7983 .098 10.232 9.182 12.649 8.45 3.526 52 298 11.144 .82 90 2820 7310 22 31 149 158 0 6674 38 6636 9.745 6895 6856 .103 8.745 3.285 3.128
9 138 169 71 39 66 129 134 170 77 44 62 130 0 0 56 44 28 17 76 100 51 96 195 192 .512 1.955 2.097 2.192 2.056 3.393 52 295 1.337 .48 90 2970 7300 21 30 164 173 0 161 37 123 1.861 162 124 .537 1.997 .896 .998
10 158 163 71 38 87 125 152 161 75 40 81 123 0 0 52 39 25 12 90 100 71 100 212 204 .696 1.437 1.519 1.541 1.565 2.326 32 215 1.232 .66 70 3110 7300 22 29 179 186 0 155 36 119 1.368 153 117 .731 1.446 .452 .532
11 157 415 68 36 89 378 155 418 73 37 86 382 0 0 56 125 24 13 94 100 73 100 467 468 .235 4.247 4.442 4.568 4.25 2.392 52 308 5.992 .59 90 3270 7310 22 31 194 203 0 395 34 360 4.045 398 364 .247 4.23 2.016 2.081
12 455 1409 69 35 386 1374 494 1471 74 38 425 1436 0 0 228 467 24 14 92 100 90 100 1760 1861 .281 3.56 3.379 4.392 3.031 3.736 52 294 3.971 .77 90 3420 7310 22 31 209 218 0 1342 33 1309 3.39 1401 1368 .295 3.218 1.761 1.686
13 227 193 71 34 156 159 219 200 75 36 148 165 0 0 101 53 22 11 87 100 81 100 315 313 .981 1.019 1.115 1.135 1.068 3.106 32 224 .735 .62 70 3560 7300 22 29 224 231 0 184 32 151 .971 190 157 1.03 1.062 -.043 .086
14 140 128 71 36 69 92 130 122 74 38 59 85 0 0 54 41 22 13 82 98 63 94 161 144 .75 1.333 1.441 1.533 1.437 4.024 52 288 .909 .52 80 3720 7300 22 30 240 248 0 122 34 88 1.27 116 81 .788 1.372 .345 .456
15 124 51 69 35 55 16 109 43 74 38 40 8 0 0 51 21 22 13 73 40 44 26 71 48 3.438 .291 .2 .496 .439 5.181 52 251 .069 .13 80 3870 7310 23 31 255 263 0 49 33 15 .277 41 8 3.609 .19 -1.852 -2.392
16 242 469 71 37 170 432 263 474 77 43 191 436 0 0 99 109 30 31 84 100 84 100 602 627 .394 2.541 2.283 2.48 2.152 2.223 52 271 2.57 .75 80 4020 7300 22 30 270 278 0 447 35 411 2.42 451 415 .413 2.174 1.275 1.12
17 165 108 76 40 88 67 166 101 85 47 89 61 0 0 42 28 56 25 75 96 18 62 155 150 1.313 .761 .685 .734 .737 1.928 32 195 .686 .49 70 4170 7300 22 29 285 292 0 103 38 64 .725 96 58 1.379 .653 -.464 -.615
18 102 40 79 42 23 -2 97 36 96 56 17 -6 0 0 39 18 67 55 11 1 2 0 21 11 null null null .614 .695 4.14 80 339 .379 .45 100 4320 7290 20 30 299 309 -50 38 40 -2 null 34 -6 null null null null
19 155 259 75 39 79 219 145 252 85 48 70 213 0 0 60 66 41 34 71 100 44 100 298 283 .361 2.772 3.043 3.06 2.937 2.807 52 261 2.657 .57 80 4470 7290 21 29 315 323 0 247 37 209 2.64 240 203 .379 2.898 1.401 1.535
20 268 3802 77 43 190 3758 313 4130 83 47 236 4086 0 0 147 1289 28 20 75 100 69 100 3948 4322 .051 19.779 17.314 25.823 15.507 3.696 52 288 19.968 .77 80 4620 7290 21 29 330 338 0 3621 41 3579 18.837 3933 3891 .053 16.489 4.235 4.043

Total number of rows: 44544

Table truncated, full table size 9297 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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