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Sample GSM989729 Query DataSets for GSM989729
Status Public on Aug 23, 2012
Title PC 621N
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 621N2
Organism Homo sapiens
Characteristics individual: PC 621N
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/2008-08/81151.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 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 18188 20280 104 108 18083 20172 20504 30423 109 121 20399 30315 0 0 5243 14736 41 66 100 82 100 78 38255 50714 .896 1.116 1.486 .47 1.498 9.847 52 343 1.556 .78 90 2010 6890 24 33 56 65 0 18855 100 18755 1.037 28286 28185 .964 1.382 .053 .466
2 17400 22007 105 112 17294 21895 20755 30672 110 122 20650 30560 0 0 6767 14639 32 56 100 94 100 92 39189 51210 .79 1.266 1.48 .778 1.487 9.273 52 291 1.65 .73 90 2160 6880 23 32 71 80 0 20461 104 20357 1.177 28517 28413 .85 1.376 .235 .46
3 28314 24708 109 120 28205 24588 32536 33899 119 131 32426 33779 0 0 9220 17621 43 61 100 94 100 90 52793 66205 1.147 .872 1.042 .314 1.099 9.582 52 301 1.094 .75 90 2310 6880 23 32 86 95 0 22972 112 22861 .811 31517 31406 1.234 .969 -.303 -.046
4 19332 23632 118 130 19213 23502 20465 30218 134 149 20346 30087 0 0 3704 12552 65 85 100 92 100 88 42715 50433 .818 1.223 1.479 .617 1.529 8.915 52 286 1.535 .81 90 2460 6900 25 34 101 110 0 21972 121 21851 1.137 28095 27973 .879 1.375 .186 .459
5 831 278 124 129 706 149 791 265 136 148 666 136 0 0 154 179 56 68 100 65 100 50 855 802 4.738 .211 .204 .143 .207 3.84 32 222 .225 .29 70 2610 6890 25 32 117 124 0 258 120 139 .196 246 126 5.096 .19 -2.349 -2.397
6 13399 17058 132 134 13266 16923 17012 20876 142 149 16880 20741 0 0 7488 12082 52 77 100 98 100 98 30189 37621 .784 1.276 1.229 .966 1.425 4.614 80 426 1.487 .81 110 2770 6890 23 34 131 142 0 15860 125 15734 1.186 19409 19284 .843 1.142 .246 .192
7 331 160 125 122 205 38 329 157 134 144 203 35 0 0 88 65 49 111 96 11 88 1 243 238 5.395 .185 .172 .315 .279 2.85 52 268 1.661 .09 90 2910 6880 23 32 146 155 -50 149 113 35 .172 146 33 5.802 .16 -2.537 -2.641
8 28291 22969 110 115 28181 22854 34830 33070 118 127 34719 32955 0 0 11898 15829 37 61 100 94 100 90 51035 67674 1.233 .811 .949 .43 .982 8.954 52 314 .924 .74 90 3060 6880 23 32 161 170 0 21355 107 21248 .754 30747 30640 1.326 .883 -.407 -.18
9 173 272 104 118 68 154 162 282 107 130 57 164 0 0 41 86 29 59 84 90 46 62 222 221 .442 2.265 2.877 2.313 2.741 3.095 32 172 5.039 .3 70 3230 6900 26 33 179 186 0 253 110 143 2.106 262 152 .475 2.675 1.074 1.42
10 194 421 106 106 87 315 192 407 109 122 85 301 0 0 52 130 29 60 84 96 73 92 402 386 .276 3.621 3.541 4.376 3.362 2.742 52 212 4.094 .62 80 3360 6890 25 33 192 200 0 391 99 293 3.366 378 280 .297 3.292 1.751 1.719
11 823 1708 107 114 715 1594 967 1999 108 124 859 1884 0 0 377 719 28 57 94 94 90 94 2309 2743 .449 2.229 2.193 2.298 2.288 3.54 52 300 2.382 .79 90 3510 6880 23 32 206 215 0 1588 106 1482 2.073 1859 1752 .482 2.039 1.052 1.028
12 603 6623 102 102 500 6521 651 6844 107 114 549 6742 0 0 206 1648 39 59 90 100 90 100 7021 7291 .077 13.042 12.281 14.693 11.833 2.625 52 291 15.237 .75 90 3670 6890 24 33 222 231 0 6158 95 6063 12.126 6363 6268 .082 11.418 3.6 3.513
13 527 438 109 103 417 335 573 463 110 111 463 360 0 0 183 178 28 53 92 92 90 86 752 823 1.245 .803 .778 .734 .819 3.666 52 284 .721 .63 90 3820 6900 25 34 237 246 0 407 96 311 .747 430 335 1.339 .723 -.421 -.468
14 276 354 99 102 176 252 289 345 102 111 189 243 0 0 91 173 26 48 94 82 90 76 428 432 .698 1.432 1.286 1.515 1.707 3.993 52 256 2.11 .56 80 3970 6890 25 33 253 261 0 329 95 234 1.331 321 226 .751 1.195 .413 .257
15 103 86 98 104 4 -18 102 80 105 118 3 -24 0 0 20 34 35 75 7 0 0 0 -14 -21 null null null 1.874 1.923 3.143 52 263 4.361 .2 90 4120 6890 24 33 267 276 -50 80 97 -17 null 74 -22 null null null null
16 4420 1825 106 107 4314 1718 4708 2311 109 120 4601 2204 0 0 858 1086 30 61 100 84 100 75 6032 6805 2.511 .398 .479 .22 .507 4.94 52 284 .431 .75 90 4270 6890 24 33 282 291 0 1697 99 1597 .37 2149 2049 2.701 .445 -1.433 -1.167
17 147 198 103 114 43 84 145 201 107 122 41 87 0 0 21 50 31 52 75 75 8 50 127 128 .512 1.953 2.122 2.323 2.643 1.827 12 68 5.069 .26 40 4430 6880 26 30 301 305 0 184 106 78 1.816 187 81 .551 1.973 .861 .98
18 79 65 105 110 -25 -45 76 58 108 118 -28 -52 0 0 18 36 27 52 1 3 0 0 -70 -80 null null null 1.903 2.018 2.31 52 301 3.642 .33 90 4570 6880 23 32 312 321 -50 60 102 -42 null 54 -48 null null null null
19 865 659 110 114 754 544 863 678 114 128 752 563 0 0 197 249 29 86 100 90 100 84 1298 1315 1.386 .721 .749 .646 .797 2.52 52 295 .713 .7 90 4720 6890 24 33 327 336 0 613 106 506 .671 630 523 1.491 .696 -.576 -.523
20 3338 8091 108 117 3229 7974 3874 10186 112 130 3766 10069 0 0 1265 4227 31 70 100 90 98 90 11203 13835 .405 2.469 2.674 2.581 2.739 3.891 52 266 3.2 .77 90 4880 6900 25 34 343 352 0 7523 109 7414 2.296 9470 9362 .436 2.486 1.199 1.314

Total number of rows: 44544

Table truncated, full table size 9692 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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