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Sample GSM989710 Query DataSets for GSM989710
Status Public on Aug 23, 2012
Title PC 86N
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 86N2
Organism Homo sapiens
Characteristics individual: PC 86N
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/2008-08/81121.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 3407 8737 56 191 3350 8545 4032 9830 68 214 3976 9638 0 0 1456 3339 122 140 96 100 90 98 11895 13614 .392 2.551 2.424 3.038 2.453 6.349 52 311 2.573 .9 80 1790 6980 18 26 15 23 0 6371 139 6231 1.86 7168 7028 .538 1.768 .895 .822
2 2720 7422 62 251 2657 7171 3236 8963 64 276 3173 8711 0 0 1417 4050 13 136 100 100 100 100 9828 11884 .371 2.699 2.745 2.779 2.706 6.103 52 256 2.804 .94 80 1950 6980 18 26 31 39 0 5412 183 5229 1.968 6536 6352 .508 2.002 .977 1.001
3 5127 9835 68 268 5058 9567 5624 11376 70 305 5555 11108 0 0 1249 3803 17 199 100 98 100 96 14625 16663 .529 1.891 2 1.569 1.951 4.682 52 233 2.029 .92 80 2100 6990 19 27 46 54 0 7172 195 6976 1.379 8296 8100 .725 1.458 .464 .544
4 2850 8030 64 218 2785 7811 3024 9063 68 261 2960 8844 0 0 726 3201 25 216 100 92 100 92 10596 11804 .357 2.805 2.988 1.983 2.895 5.784 52 273 3.062 .95 90 2250 6990 18 27 60 69 0 5856 159 5696 2.045 6609 6449 .489 2.179 1.032 1.124
5 239 142 59 154 179 -12 233 102 62 184 173 -51 0 0 37 94 13 128 100 12 100 3 167 122 null null null .192 .145 8.985 32 169 -9.686 -.1 60 2400 6970 18 24 77 83 0 104 112 -9 null 74 -37 null null null null
6 2831 4584 70 157 2760 4426 2847 4772 76 186 2777 4615 0 0 442 1480 26 120 100 98 100 98 7186 7392 .624 1.604 1.662 1.402 1.667 3.628 52 284 1.738 .93 90 2550 6970 16 25 90 99 0 3343 114 3228 1.169 3480 3365 .855 1.212 .226 .277
7 104 165 64 173 40 -8 111 158 68 201 46 -15 0 0 30 80 22 128 71 5 51 0 32 31 null null null 1.507 1.364 9.59 52 272 118.808 .15 90 2700 6970 16 25 105 114 -50 120 126 -6 null 115 -11 null null null null
8 6192 8502 65 175 6127 8327 7461 9831 71 194 7396 9656 0 0 2661 3751 23 108 100 98 100 96 14454 17052 .736 1.359 1.306 1.323 1.372 5.674 52 236 1.346 .94 80 2850 6970 17 25 121 129 0 6200 128 6072 .991 7169 7041 1.009 .952 -.013 -.071
9 74 161 62 183 11 -21 69 132 70 207 6 -50 0 0 19 102 28 124 19 9 1 1 -10 -44 null null null 4.533 5.887 7.713 52 272 17.114 .17 90 3000 6970 16 25 135 144 -50 117 133 -15 null 96 -36 null null null null
10 76 184 60 180 16 4 75 157 62 203 14 -23 0 0 13 109 13 113 50 9 15 5 20 -9 4 .25 null 4.353 5.347 7.127 52 274 84.036 .08 90 3150 6970 16 25 150 159 -50 134 131 3 .182 114 -17 5.485 null -2.456 null
11 154 320 60 179 94 140 159 335 62 195 98 155 0 0 32 125 16 106 96 59 90 25 234 253 .671 1.489 1.582 1.299 1.544 5.531 32 191 13.458 .29 70 3300 6970 17 24 166 173 0 233 131 102 1.086 244 113 .921 1.153 .119 .206
12 146 357 57 172 88 184 148 292 60 207 90 120 0 0 33 328 16 243 100 21 96 3 272 210 .478 2.091 1.333 1.422 1.909 6.97 32 182 16.534 .23 70 3440 6980 18 25 180 187 0 260 125 134 1.525 213 88 .656 .972 .609 -.041
13 109 157 57 177 51 -20 111 151 60 212 53 -25 0 0 27 73 18 221 86 0 67 0 31 28 null null null 2.177 1.984 9.965 52 294 -122.384 -.06 90 3600 6960 15 24 195 204 -50 114 129 -15 null 110 -18 null null null null
14 96 164 59 188 37 -24 100 142 63 225 41 -46 0 0 27 86 20 235 69 0 50 0 13 -5 null null null 2.716 2.461 6.835 52 278 -1 -1 90 3750 6960 15 24 210 219 -50 120 137 -18 null 104 -34 null null null null
15 51 162 60 176 -9 -13 49 140 62 195 -10 -35 0 0 10 98 18 106 1 5 1 3 -22 -45 null null null 6.69 7.696 5.617 52 272 18.205 .32 90 3900 6960 15 24 225 234 -50 118 128 -9 null 102 -26 null null null null
16 455 548 62 173 393 374 453 521 65 198 391 347 0 0 65 162 17 128 100 98 100 76 767 738 1.051 .952 .887 .884 .903 3.063 52 253 1.057 .64 90 4050 6970 16 25 240 249 0 400 126 273 .694 380 253 1.441 .647 -.527 -.628
17 60 149 63 181 -2 -32 62 132 65 222 -1 -49 0 0 11 87 16 191 5 3 0 0 -34 -50 null null null 6.046 4.804 7.051 52 272 -182.305 -.04 90 4200 6960 15 24 255 264 -50 109 132 -23 null 96 -36 null null null null
18 44 145 59 188 -14 -43 43 112 61 224 -16 -76 0 0 6 116 14 176 0 3 0 3 -57 -92 null null null 5.244 6.363 5.39 52 272 34.473 .22 90 4350 6960 15 24 270 279 -50 106 137 -31 null 82 -55 null null null null
19 115 162 58 169 57 -6 116 161 60 190 57 -8 0 0 25 83 15 121 98 3 82 1 51 49 null null null 1.122 1.169 4.893 52 282 -25.272 -.09 90 4500 6960 15 24 285 294 -50 118 123 -4 null 117 -6 null null null null
20 432 1764 59 195 372 1569 503 1954 62 213 443 1759 0 0 171 746 16 121 94 92 92 92 1941 2202 .237 4.218 3.971 4.419 4.065 4.561 52 235 4.541 .92 80 4660 6960 16 24 302 310 0 1286 142 1144 3.076 1425 1283 .325 2.895 1.621 1.534

Total number of rows: 44544

Table truncated, full table size 9537 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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