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Sample GSM989802 Query DataSets for GSM989802
Status Public on Aug 23, 2012
Title PC 540N
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 540N2
Organism Homo sapiens
Characteristics individual: PC 540N
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/2008-08/81073.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 7884 11170 57 62 7826 11107 8345 11935 60 75 8288 11872 0 0 6163 7974 15 47 93 100 90 100 18933 20160 .705 1.419 1.432 2.287 1.388 4.816 32 165 1.394 .92 60 1780 6780 31 37 51 57 0 9486 53 9433 1.205 10136 10082 .83 1.217 .269 .283
2 6431 9051 58 65 6373 8985 6507 7065 60 79 6448 7000 0 0 5724 8036 15 46 100 87 100 87 15358 13448 .709 1.41 1.086 1.253 1.466 3.391 32 210 1.439 .94 70 1940 6770 29 36 66 73 0 7687 55 7631 1.197 6000 5945 .835 .922 .26 -.117
3 6632 8059 58 64 6573 7994 4510 5893 62 74 4452 5829 0 0 5630 7150 18 40 100 90 96 87 14567 10281 .822 1.216 1.309 1.077 1.206 3.311 32 169 1.263 .93 60 2080 6770 30 36 81 87 0 6844 54 6789 1.033 5005 4950 .968 1.112 .047 .153
4 5635 8111 58 77 5577 8034 1130 1019 63 102 1072 941 0 0 6925 9813 21 171 92 61 76 59 13611 2013 .694 1.441 .878 1.198 1.355 4.79 52 324 1.455 .94 90 2230 6760 27 36 94 103 0 6888 65 6823 1.223 865 799 .817 .745 .291 -.424
5 261 139 58 75 203 63 299 154 66 116 241 79 0 0 171 79 30 235 71 0 62 0 266 320 3.222 .31 .328 .595 .386 3.811 32 176 .761 .31 60 2390 6760 29 35 112 118 0 118 64 54 .264 131 67 3.794 .278 -1.924 -1.845
6 4159 6668 73 87 4086 6580 5078 7821 79 99 5005 7734 0 0 2125 2752 26 59 100 100 100 100 10666 12739 .621 1.61 1.545 2.007 1.55 1.933 32 236 1.534 .96 70 2540 6770 29 36 126 133 0 5663 74 5588 1.368 6642 6568 .731 1.312 .452 .392
7 219 226 66 77 153 149 232 234 68 85 166 156 0 0 43 93 18 41 100 75 100 75 302 322 1.027 .974 .94 .777 .83 2.577 12 104 1.931 .61 50 2680 6780 31 36 141 146 0 192 65 127 .827 199 132 1.209 .798 -.274 -.325
8 9057 12120 59 76 8997 12044 10383 13597 63 91 10324 13520 0 0 6460 8305 17 58 100 96 100 93 21041 23844 .747 1.339 1.31 1.113 1.268 4.767 32 171 1.351 .92 60 2840 6770 30 36 157 163 0 10293 65 10229 1.137 11547 11482 .88 1.112 .185 .153
9 98 126 57 69 41 56 100 100 60 77 43 30 0 0 41 74 17 41 62 46 56 34 97 73 .732 1.366 .698 1.682 1.704 3.298 32 175 3.663 .46 60 2980 6760 29 35 171 177 0 107 59 48 1.16 85 25 .862 .593 .214 -.755
10 144 182 55 63 89 119 137 165 58 76 82 102 0 0 28 59 15 49 100 91 100 58 208 184 .748 1.337 1.244 1.236 1.359 1.845 12 104 2.047 .6 50 3140 6770 30 35 187 192 0 155 54 101 1.136 140 87 .881 1.056 .183 .079
11 190 303 57 72 132 231 220 311 61 93 163 239 0 0 75 120 17 135 84 81 81 37 363 402 .571 1.75 1.466 2.069 1.564 3.385 32 215 6.448 .4 70 3290 6780 30 37 201 208 0 257 61 196 1.486 264 203 .673 1.245 .572 .316
12 240 614 58 68 182 546 257 742 63 84 199 673 0 0 115 324 21 67 87 87 84 81 728 872 .333 3 3.382 2.895 3.076 2.348 32 171 3.466 .82 60 3440 6770 30 36 217 223 0 521 58 464 2.548 630 572 .392 2.872 1.349 1.522
13 200 182 61 68 138 114 208 175 63 83 146 107 0 0 69 134 17 53 93 68 87 50 252 253 1.211 .826 .733 .714 .723 3.809 32 169 1.636 .56 60 3590 6770 30 36 232 238 0 155 58 97 .702 149 91 1.425 .622 -.511 -.684
14 129 215 56 68 73 147 134 223 59 81 78 154 0 0 55 77 16 47 75 90 68 62 220 232 .497 2.014 1.974 2.144 1.548 2.768 32 209 2.467 .67 70 3740 6770 29 36 246 253 0 183 58 125 1.71 189 131 .585 1.677 .774 .746
15 68 73 57 72 11 0 59 45 63 95 2 -26 0 0 46 70 24 107 13 9 3 1 11 -24 null null null 4.267 4.029 3.485 52 304 12.392 .21 90 3890 6760 27 36 260 269 -50 62 61 0 null 38 -22 null null null null
16 510 679 57 72 453 606 152 162 62 106 94 90 0 0 534 751 23 138 57 48 53 46 1059 184 .748 1.338 .957 2.037 1.619 3.352 52 291 1.527 .89 90 4040 6760 27 36 275 284 -50 577 61 515 1.136 138 76 .88 .813 .184 -.298
17 82 124 57 65 25 58 72 88 60 89 15 22 0 0 31 78 18 91 46 26 30 5 83 37 .431 2.32 1.467 1.871 1.674 4.082 52 291 6.586 .39 90 4190 6760 27 36 290 299 -50 105 55 49 1.97 75 19 .508 1.246 .978 .317
18 57 69 57 66 0 2 54 50 59 82 -3 -15 0 0 12 87 15 77 11 5 1 1 2 -18 null null null 2.594 2.89 4.481 52 315 51.324 .15 90 4340 6760 27 36 305 314 -50 59 56 2 null 42 -13 null null null null
19 245 276 55 65 190 210 243 294 58 80 188 228 0 0 48 89 15 89 100 91 100 66 400 416 .905 1.105 1.213 1.026 1.204 2.049 12 104 1.229 .74 50 4500 6760 29 34 323 328 0 234 55 178 .939 250 194 1.065 1.03 -.091 .043
20 962 3991 56 77 906 3913 902 4758 60 89 846 4680 0 0 616 2460 24 59 96 93 90 90 4819 5526 .232 4.319 5.532 3.635 3.85 3.276 32 158 4.445 .94 60 4650 6770 30 36 338 344 0 3389 65 3323 3.668 4041 3975 .273 4.698 1.875 2.232

Total number of rows: 44544

Table truncated, full table size 9241 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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