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Sample GSM989738 Query DataSets for GSM989738
Status Public on Aug 23, 2012
Title PC 625N
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 625N2
Organism Homo sapiens
Characteristics individual: PC 625N
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/2008-08/81154.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 16319 20099 110 87 16208 20011 17422 22301 132 112 17311 22213 0 0 3838 6071 103 115 100 100 100 100 36219 39524 .81 1.235 1.283 1.188 1.281 1.282 52 351 1.281 .98 90 1770 7260 37 46 32 41 0 19613 85 19527 1.205 21762 21676 .83 1.252 .269 .324
2 16695 21942 111 87 16583 21855 19113 24660 128 103 19001 24573 0 0 6348 6527 60 81 100 100 100 100 38438 43574 .759 1.318 1.293 1.468 1.291 1.44 52 307 1.257 .98 90 1910 7250 36 45 46 55 0 21412 85 21327 1.286 24064 23979 .778 1.262 .363 .336
3 37619 34726 117 88 37502 34637 38119 35285 135 102 38002 35196 0 0 3960 3833 69 75 100 100 100 100 72139 73198 1.083 .924 .926 .923 .938 1.099 52 264 .916 .98 90 2070 7270 38 47 62 71 0 33887 86 33800 .901 34432 34345 1.11 .904 -.15 -.146
4 17175 21684 107 84 17067 21599 20280 25587 122 96 20172 25502 0 0 6804 8384 61 67 100 100 100 100 38666 45674 .79 1.266 1.264 1.321 1.279 1.588 80 372 1.265 .98 100 2220 7260 37 47 77 87 0 21160 82 21077 1.235 24968 24886 .81 1.234 .304 .303
5 1000 281 109 82 890 198 1036 275 114 88 926 192 0 0 220 74 35 46 100 100 100 96 1088 1118 4.495 .222 .207 .215 .221 1.461 52 242 .213 .84 80 2370 7250 37 45 93 101 0 274 80 193 .217 268 187 4.606 .202 -2.204 -2.305
6 8884 9593 133 101 8750 9492 3437 3109 152 113 3304 3008 0 0 9001 9829 79 60 96 97 94 96 18242 6312 .922 1.085 .91 .99 1.058 1.63 156 608 1.094 .98 140 2530 7270 36 50 106 120 0 9361 99 9263 1.059 3034 2935 .945 .888 .082 -.171
7 394 151 147 104 246 47 393 152 166 119 245 48 0 0 84 40 79 63 100 34 81 3 293 293 5.234 .191 .196 .151 .248 3.138 32 141 .145 .31 60 2670 7250 38 44 124 130 0 147 101 46 .186 148 47 5.364 .191 -2.423 -2.387
8 37137 34249 130 101 37006 34148 39431 36114 146 120 39301 36013 0 0 7641 5692 70 78 100 100 100 100 71154 75314 1.084 .923 .916 .942 .926 1.259 52 308 .905 .98 90 2830 7250 36 45 138 147 0 33421 99 33322 .9 35241 35142 1.111 .894 -.151 -.161
9 253 307 112 96 140 211 249 308 147 137 136 212 0 0 56 67 157 192 40 57 0 0 351 348 .664 1.507 1.559 1.551 1.43 1.809 52 232 1.684 .68 80 2970 7260 38 46 153 161 0 300 94 206 1.471 301 207 .68 1.521 .557 .605
10 258 496 121 93 137 403 270 541 144 116 149 448 0 0 89 253 142 106 51 85 3 76 540 597 .34 2.942 3.007 3.1 3.186 1.73 80 308 2.112 .55 100 3120 7260 37 47 167 177 0 484 91 393 2.87 528 437 .348 2.934 1.521 1.553
11 1840 2999 122 106 1718 2893 1872 3080 148 117 1750 2974 0 0 364 670 137 75 100 100 100 100 4611 4724 .594 1.684 1.699 1.68 1.721 1.26 52 257 1.711 .93 90 3270 7260 37 46 182 191 0 2927 103 2823 1.643 3006 2902 .609 1.658 .717 .73
12 929 9872 123 111 806 9761 962 9929 141 122 839 9818 0 0 189 1584 84 62 100 100 100 100 10567 10657 .083 12.11 11.702 12.353 12.483 1.182 52 290 12.45 .93 90 3420 7250 36 45 197 206 0 9633 108 9525 11.818 9689 9581 .085 11.419 3.563 3.513
13 761 732 122 104 639 628 776 744 134 113 653 640 0 0 161 136 56 47 100 100 100 100 1267 1293 1.018 .983 .98 .997 .999 1.249 52 248 .952 .93 80 3570 7260 38 46 213 221 0 714 101 613 .959 726 625 1.043 .956 -.06 -.064
14 459 552 119 102 340 450 424 553 137 128 305 451 0 0 212 176 98 154 100 94 90 90 790 756 .756 1.324 1.479 1.314 1.448 1.638 52 261 1.22 .71 80 3720 7260 38 46 228 236 0 539 100 439 1.292 540 440 .774 1.443 .369 .529
15 138 45 122 101 16 -55 130 38 133 119 8 -62 0 0 31 22 76 101 3 0 0 0 -39 -54 null null null 3.135 2.761 1.718 52 276 .359 .35 90 3870 7250 36 45 242 251 -50 44 99 -54 null 37 -61 null null null null
16 5256 3757 127 104 5129 3653 6420 4666 137 118 6293 4562 0 0 2279 1730 66 54 100 97 97 96 8782 10855 1.404 .712 .725 .662 .721 1.444 80 326 .716 .98 100 4020 7250 36 46 257 267 0 3666 101 3565 .695 4553 4452 1.439 .707 -.525 -.499
17 190 238 118 103 72 135 188 246 132 118 70 143 0 0 48 52 65 85 55 80 11 19 207 213 .533 1.875 2.043 1.983 1.827 2.357 52 237 2.754 .44 80 4180 7260 38 46 274 282 0 232 101 132 1.83 240 140 .547 1.993 .872 .995
18 121 49 124 111 -3 -61 123 40 145 132 -1 -70 0 0 28 25 112 130 0 0 0 0 -64 -71 null null null 3.202 2.541 2.313 52 276 .415 .37 90 4330 7250 36 45 288 297 -50 48 108 -60 null 39 -68 null null null null
19 1214 961 128 109 1086 852 1264 1004 140 122 1136 895 0 0 391 325 75 61 98 97 96 96 1938 2031 1.275 .785 .788 .776 .767 1.629 80 337 .783 .95 100 4480 7240 35 45 303 313 0 938 106 831 .766 980 873 1.306 .769 -.385 -.379
20 5158 13102 130 115 5027 12987 5588 14007 143 130 5457 13892 0 0 1344 3115 59 62 100 100 98 100 18014 19349 .387 2.583 2.546 2.692 2.582 1.294 52 280 2.568 .97 90 4620 7240 35 44 317 326 0 12785 112 12673 2.521 13668 13556 .397 2.484 1.334 1.313

Total number of rows: 44544

Table truncated, full table size 9778 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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