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Sample GSM989694 Query DataSets for GSM989694
Status Public on Aug 23, 2012
Title PC 366N
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 366N2
Organism Homo sapiens
Characteristics individual: PC 366N
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/2008-08/81068.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 2934 4308 50 77 2883 4230 757 338 52 90 706 261 0 0 3397 5540 10 62 82 63 67 57 7113 967 .682 1.467 .37 1.182 1.404 3.055 52 381 1.692 .9 90 1720 7550 34 43 19 28 0 3487 62 3424 1.188 274 211 .842 .299 .248 -1.741
2 2502 4581 52 75 2449 4505 737 2742 54 88 684 2666 0 0 3031 4968 11 66 88 90 82 86 6954 3350 .544 1.84 3.898 3.27 1.901 4.684 52 291 1.741 .96 80 1880 7550 35 43 36 44 0 3708 61 3646 1.489 2219 2158 .672 3.155 .574 1.658
3 1393 1978 50 67 1342 1910 182 532 52 74 131 464 0 0 1885 2361 10 36 84 78 71 76 3252 595 .703 1.423 3.542 2.315 1.651 3.427 52 280 1.323 .92 80 2040 7550 35 43 52 60 0 1601 54 1546 1.152 431 376 .868 2.867 .204 1.52
4 3839 7563 49 78 3789 7485 4716 8864 51 84 4666 8785 0 0 2778 3999 10 39 100 100 96 100 11274 13451 .506 1.975 1.883 3.535 1.937 3.64 32 170 1.844 .92 60 2180 7550 36 42 67 73 0 6122 63 6059 1.599 7175 7111 .625 1.524 .677 .608
5 310 147 49 69 260 77 317 129 51 76 267 59 0 0 217 81 9 39 90 59 87 37 337 326 3.377 .296 .221 .367 .312 4.916 32 169 .245 .53 60 2330 7550 36 42 82 88 0 119 56 62 .24 104 48 4.172 .179 -2.061 -2.483
6 1924 3649 50 78 1873 3570 2276 4076 52 93 2225 3998 0 0 1008 1345 11 64 98 100 98 100 5443 6223 .525 1.906 1.797 2.496 1.734 2.798 52 288 1.841 .91 80 2490 7540 34 42 97 105 0 2954 63 2890 1.543 3299 3236 .648 1.454 .626 .54
7 157 105 49 66 107 38 163 104 50 74 113 37 0 0 16 31 6 47 100 33 100 8 145 150 2.816 .355 .327 .447 .408 1.609 12 68 .61 .43 40 2630 7550 37 41 113 117 0 85 53 31 .287 84 30 3.479 .265 -1.799 -1.916
8 3744 5191 49 64 3695 5126 4143 5609 52 87 4093 5545 0 0 2325 1934 10 83 100 100 100 100 8821 9638 .721 1.387 1.355 2.077 1.318 3.003 32 169 1.236 .92 60 2790 7540 35 41 128 134 0 4202 52 4149 1.123 4540 4488 .891 1.097 .167 .133
9 117 199 48 77 68 121 113 195 51 87 64 117 0 0 48 83 10 56 81 78 78 50 189 181 .562 1.779 1.828 2.374 1.994 3.169 32 147 2.387 .76 60 2940 7550 36 42 143 149 0 161 62 98 1.44 158 95 .694 1.48 .526 .565
10 123 213 47 70 75 142 124 213 49 83 77 142 0 0 47 78 16 52 84 90 71 71 217 219 .528 1.893 1.844 2.18 1.913 3.192 32 169 2.532 .65 60 3090 7540 35 41 158 164 0 172 57 115 1.533 172 115 .653 1.493 .616 .578
11 287 586 47 63 239 523 327 592 49 78 279 529 0 0 119 164 9 58 96 100 96 100 762 808 .457 2.188 1.896 2.39 2.003 1.934 32 227 2.244 .86 70 3240 7540 34 41 172 179 0 474 51 423 1.771 479 428 .565 1.535 .825 .618
12 315 780 48 70 266 709 355 881 51 118 306 811 0 0 182 302 12 245 87 87 87 78 975 1117 .375 2.665 2.65 3.218 2.707 2.308 32 223 3.756 .71 70 3390 7530 33 40 187 194 0 631 57 574 2.157 713 656 .464 2.145 1.109 1.101
13 208 226 48 67 160 158 210 225 51 99 162 157 0 0 78 79 14 120 96 68 96 18 318 319 1.013 .988 .969 1.032 1.074 2.561 32 158 1.158 .72 60 3540 7540 35 41 203 209 0 183 54 128 .799 182 127 1.251 .784 -.323 -.35
14 125 166 49 77 76 89 124 166 50 100 75 89 0 0 28 30 8 80 100 66 100 0 165 164 .854 1.171 1.187 1.161 1.115 2 12 68 2.211 .47 40 3700 7540 36 40 220 224 0 134 62 72 .948 134 72 1.055 .961 -.077 -.058
15 58 53 47 79 10 -26 58 44 50 107 10 -35 0 0 10 29 9 104 50 0 21 0 -16 -25 null null null 2.347 2.839 3.392 52 299 28.556 .3 90 3840 7530 32 41 231 240 -50 43 64 -21 null 36 -28 null null null null
16 392 869 49 83 342 785 361 397 52 102 311 313 0 0 452 2138 13 70 90 90 90 87 1127 624 .436 2.295 1.006 1.725 1.021 3.727 32 206 14.227 .27 70 3990 7530 33 40 247 254 0 703 67 635 1.858 321 253 .538 .815 .894 -.296
17 78 149 51 86 26 63 71 103 54 114 19 17 0 0 26 243 15 131 55 9 36 1 89 36 .413 2.423 .895 2.376 2.127 4.388 52 284 171.422 .05 90 4140 7530 32 41 261 270 -50 121 70 51 1.961 83 14 .51 .724 .972 -.465
18 53 88 49 72 3 15 53 57 53 102 3 -15 0 0 9 114 13 98 13 7 1 3 18 -12 .2 5 null 4.696 3.446 4.057 52 292 25.696 .29 90 4290 7530 32 41 276 285 -50 71 58 12 4.047 46 -12 .247 null 2.017 null
19 207 329 51 75 155 253 215 319 52 98 164 243 0 0 98 105 9 89 96 90 90 75 408 407 .613 1.632 1.482 2.003 1.627 2.784 32 174 1.729 .71 60 4450 7530 34 40 294 300 0 266 61 205 1.321 258 197 .757 1.199 .402 .262
20 1093 5519 52 78 1040 5440 1265 6105 55 106 1212 6026 0 0 805 2294 13 103 90 100 87 100 6480 7238 .191 5.231 4.972 10.585 5.063 4.449 32 174 4.821 .88 60 4600 7530 34 40 309 315 0 4467 63 4403 4.234 4942 4878 .236 4.024 2.082 2.009

Total number of rows: 44544

Table truncated, full table size 9112 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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