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Sample GSM989730 Query DataSets for GSM989730
Status Public on Aug 23, 2012
Title PC 582N
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 582N2
Organism Homo sapiens
Characteristics individual: PC 582N
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/2008-08/81112.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 3790 5707 54 164 3735 5542 4350 6426 64 234 4295 6261 0 0 2811 3872 41 297 96 88 90 80 9277 10556 .674 1.484 1.458 1.799 1.408 6.79 52 315 1.408 .92 80 1820 6950 27 35 22 30 0 4425 127 4297 1.15 4982 4854 .869 1.13 .202 .177
2 5269 7091 54 175 5214 6915 6189 8344 61 228 6134 8168 0 0 1994 3390 38 301 100 93 100 93 12129 14302 .754 1.326 1.332 1.047 1.26 4.019 32 228 1.357 .93 70 1970 6950 27 34 37 44 0 5498 136 5361 1.028 6469 6333 .973 1.032 .04 .046
3 5160 7685 57 170 5103 7515 5775 8150 64 205 5718 7979 0 0 1553 2370 25 164 100 100 100 100 12618 13697 .679 1.473 1.395 1.469 1.404 2.95 32 176 1.438 .9 60 2120 6950 28 34 53 59 0 5958 132 5827 1.142 6319 6186 .876 1.082 .191 .114
4 4258 6178 55 171 4203 6006 5474 7581 60 203 5419 7409 0 0 2701 3401 21 142 96 98 92 94 10209 12828 .7 1.429 1.367 2.066 1.323 6.805 52 264 1.34 .92 80 2270 6960 28 36 67 75 0 4790 133 4657 1.108 5878 5744 .903 1.06 .148 .084
5 311 166 55 177 255 -10 333 163 62 225 278 -13 0 0 108 85 33 230 96 0 90 0 245 265 null null null .11 .178 12.719 32 226 -.19 -.06 70 2420 6940 26 33 82 89 0 129 137 -8 null 126 -10 null null null null
6 3679 4447 71 198 3608 4249 3814 4658 82 232 3743 4459 0 0 600 828 42 162 100 100 100 100 7857 8202 .849 1.178 1.191 1.169 1.19 2.133 32 224 1.193 .93 70 2570 6940 26 33 97 104 0 3448 154 3294 .913 3611 3457 1.095 .924 -.131 -.115
7 93 162 61 193 32 -30 89 130 70 254 28 -63 0 0 32 112 43 293 34 1 5 0 2 -35 null null null 10.653 8.109 8.383 52 345 19.707 .33 90 2720 6940 25 34 111 120 -50 126 150 -23 null 101 -49 null null null null
8 6051 7608 59 185 5991 7423 6747 8930 64 233 6688 8745 0 0 1928 3270 26 170 100 100 100 100 13414 15433 .807 1.239 1.308 1.146 1.278 2.637 32 202 1.303 .94 70 2880 6950 27 34 128 135 0 5899 143 5755 .961 6924 6780 1.041 1.014 -.058 .02
9 69 155 57 182 11 -26 67 132 63 230 9 -49 0 0 17 85 26 171 15 5 1 0 -15 -40 null null null 4.396 6.342 7.267 52 295 26.277 .24 90 3020 6940 25 34 141 150 -50 120 141 -20 null 102 -38 null null null null
10 74 252 58 187 16 64 63 185 61 224 5 -2 0 0 52 472 22 163 25 7 7 1 80 3 .25 4 null 5.1 4.451 6.722 52 312 11.759 .7 90 3170 6940 25 34 156 165 -50 195 145 50 3.101 143 -2 .322 null 1.633 null
11 232 548 58 213 174 335 230 507 64 261 172 293 0 0 66 142 31 321 96 46 93 0 509 465 .519 1.925 1.703 1.926 1.868 4.005 32 209 8.499 .49 70 3330 6950 27 34 173 180 0 425 165 260 1.493 393 227 .67 1.321 .578 .401
12 137 438 55 187 81 250 136 466 61 225 80 279 0 0 67 218 20 146 76 65 63 46 331 359 .324 3.086 3.488 3.583 3.78 4.077 52 304 5.801 .58 90 3480 6940 25 34 187 196 -50 340 145 194 2.393 361 216 .418 2.704 1.259 1.435
13 117 189 56 203 60 -14 116 171 60 230 59 -32 0 0 44 91 20 131 76 7 65 1 46 27 null null null 1.997 2.41 6.514 52 291 38.025 .06 90 3630 6940 25 34 202 211 -50 147 157 -11 null 133 -25 null null null null
14 105 323 55 189 49 134 96 174 60 218 40 -14 0 0 64 521 20 124 69 17 50 15 183 26 .366 2.735 null 4.005 3.543 12.497 52 296 15.857 .42 90 3780 6940 25 34 217 226 -50 250 147 104 2.12 135 -11 .472 null 1.084 null
15 62 126 53 181 8 -54 61 111 61 234 7 -69 0 0 17 83 29 169 9 3 1 0 -46 -62 null null null 8.994 11.065 5.12 52 303 27.279 .26 90 3930 6940 25 34 232 241 -50 98 140 -42 null 86 -53 null null null null
16 970 657 57 206 913 450 1084 634 63 250 1027 427 0 0 305 201 29 175 100 93 100 68 1363 1454 2.029 .493 .416 .456 .475 3.634 32 215 .45 .74 70 4080 6940 26 33 248 255 0 509 160 349 .382 492 331 2.617 .322 -1.388 -1.633
17 67 152 58 194 9 -41 61 127 64 225 3 -67 0 0 20 104 27 144 15 9 3 0 -32 -64 null null null 8.429 9.062 6.343 52 303 24.524 .22 90 4230 6940 25 34 262 271 -50 118 150 -32 null 98 -52 null null null null
18 59 201 57 197 2 4 55 119 64 229 -1 -77 0 0 17 197 35 170 5 15 0 7 6 -78 .5 2 null 10.579 11.966 5.052 52 311 12.429 .45 90 4380 6940 25 34 277 286 -50 156 153 3 1.551 92 -60 .645 null .633 null
19 231 178 55 203 175 -25 240 159 59 236 184 -44 0 0 46 80 19 181 100 0 100 0 150 140 null null null .224 .371 13.28 32 176 -1 -1 60 4540 6940 27 33 295 301 0 138 157 -19 null 123 -34 null null null null
20 911 2433 56 190 854 2242 1008 2630 70 270 952 2439 0 0 228 802 83 466 100 96 100 90 3096 3391 .381 2.625 2.562 2.363 2.582 3.134 32 224 2.818 .93 70 4690 6940 26 33 309 316 0 1886 147 1738 2.035 2039 1891 .491 1.986 1.025 .99

Total number of rows: 44544

Table truncated, full table size 9461 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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