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Sample GSM989688 Query DataSets for GSM989688
Status Public on Aug 23, 2012
Title PC 375N
Sample type RNA
 
Channel 1
Source name Human 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 375N RNA
Organism Homo sapiens
Characteristics individual: PC 375N
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/2008-08/80873.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 6989 7730 82 76 6907 7654 9137 9898 124 94 9055 9822 0 0 3610 4219 335 112 92 92 90 88 14561 18877 .902 1.108 1.085 .942 1.077 3.243 52 377 1.168 .88 90 1780 7290 40 49 21 30 0 9506 93 9413 1.363 12173 12079 .734 1.334 .447 .416
2 8996 10484 94 80 8902 10404 10232 11661 154 101 10138 11581 0 0 2900 3805 402 130 100 98 100 98 19306 21719 .856 1.169 1.142 1.023 1.186 2.7 52 259 1.219 .9 90 1940 7290 40 49 37 46 0 12893 98 12795 1.437 14341 14242 .696 1.405 .523 .49
3 8306 7961 92 88 8214 7873 11324 11200 157 209 11232 11112 0 0 4922 5923 335 823 84 71 80 67 16087 22344 1.043 .958 .989 .626 1.037 2.619 52 241 1.169 .9 90 2080 7280 39 48 51 60 0 9790 108 9682 1.179 13774 13666 .848 1.217 .237 .283
4 9668 9655 89 85 9579 9570 9779 10078 134 189 9690 9993 0 0 1932 2699 272 715 100 100 100 97 19149 19683 1.001 .999 1.031 .957 1.035 1.556 80 373 1.065 .92 110 2230 7270 37 48 65 76 0 11874 105 11769 1.229 12394 12289 .814 1.268 .297 .343
5 378 128 99 86 279 42 484 108 105 124 385 22 0 0 221 68 39 325 71 0 65 0 321 407 6.643 .151 .057 .259 .267 5.112 52 267 .187 .47 90 2380 7270 38 47 81 90 0 157 106 52 .185 133 27 5.402 .07 -2.433 -3.831
6 3907 3861 120 95 3787 3766 4015 4111 133 123 3895 4016 0 0 857 1309 73 215 100 95 100 93 7553 7911 1.006 .994 1.031 .846 1.061 2.186 80 384 1.073 .93 110 2530 7270 37 48 95 106 0 4748 117 4631 1.223 5056 4939 .818 1.268 .29 .343
7 171 94 115 98 56 -4 175 83 135 130 60 -15 0 0 47 48 81 250 32 0 0 0 52 45 null null null .579 .58 4.146 52 279 .948 .19 90 2680 7270 38 47 111 120 -50 116 121 -5 null 102 -18 null null null null
8 8243 7397 108 89 8135 7308 11636 10296 190 284 11528 10207 0 0 5580 6088 511 1226 76 67 71 59 15443 21735 1.113 .898 .885 .716 1.028 5.442 52 291 1.077 .92 90 2830 7270 38 47 126 135 0 9097 109 8987 1.105 12662 12553 .905 1.089 .144 .123
9 106 99 92 85 14 14 103 90 173 266 11 5 0 0 23 47 512 1223 0 0 0 0 28 16 1 1 .455 1.984 2.33 3.144 52 291 .816 .88 90 2980 7270 38 47 141 150 -50 122 105 17 1.23 111 6 .813 .559 .298 -.839
10 119 129 86 79 33 50 121 131 87 89 35 52 0 0 29 41 20 49 65 53 36 11 83 87 .66 1.515 1.486 1.688 1.436 2.404 52 317 6.615 .22 90 3130 7270 38 47 156 165 -50 159 97 61 1.863 161 64 .537 1.827 .898 .87
11 285 432 83 71 202 361 291 440 86 84 208 369 0 0 37 145 21 48 100 100 100 96 563 577 .56 1.787 1.774 1.633 1.64 1.735 32 194 2.441 .77 70 3290 7280 40 47 173 180 0 531 87 444 2.198 541 454 .455 2.182 1.136 1.125
12 206 596 79 76 127 520 219 659 81 86 140 583 0 0 69 279 20 51 90 85 85 85 647 723 .244 4.094 4.164 3.387 3.952 2.415 80 339 4.828 .82 100 3440 7270 38 48 187 197 0 733 93 639 5.035 810 717 .199 5.121 2.332 2.357
13 154 122 79 73 75 49 149 112 80 90 70 39 0 0 35 51 20 70 100 32 84 7 124 109 1.531 .653 .557 .663 .72 2.696 52 289 4.553 .17 90 3590 7260 37 46 202 211 -50 150 90 60 .803 138 48 1.245 .685 -.316 -.545
14 124 129 75 73 49 56 127 126 80 88 52 53 0 0 34 66 22 66 73 40 55 11 105 105 .875 1.143 1.019 1.157 .974 2.904 52 291 6.032 .29 90 3740 7260 37 46 217 226 -50 159 90 69 1.405 155 65 .711 1.253 .491 .326
15 78 57 77 70 1 -13 78 53 79 80 1 -17 0 0 16 29 19 45 13 3 0 0 -12 -16 null null null 1.755 2 3.281 52 279 21.363 .08 90 3890 7260 37 46 232 241 -50 70 86 -16 null 65 -21 null null null null
16 624 626 79 71 545 555 619 642 81 82 540 571 0 0 96 126 24 50 100 100 100 100 1100 1111 .982 1.018 1.057 1.005 1.062 1.33 80 384 1.085 .87 110 4040 7260 36 47 246 257 0 770 87 683 1.252 790 702 .798 1.3 .325 .379
17 95 97 79 75 16 22 89 94 80 91 10 19 0 0 23 39 22 77 26 9 13 0 38 29 .727 1.375 1.9 2.216 2.429 3.247 52 279 6.858 .22 90 4190 7260 37 46 262 271 -50 119 92 27 1.691 116 23 .591 2.337 .758 1.224
18 76 56 78 82 -2 -26 76 51 80 91 -2 -31 0 0 18 27 21 47 9 0 0 0 -28 -33 null null null 2.573 2.502 3.51 52 291 15.661 .12 90 4340 7260 37 46 277 286 -50 69 101 -32 null 63 -38 null null null null
19 158 131 78 73 80 58 160 133 85 86 82 60 0 0 34 53 37 58 84 50 59 11 138 142 1.379 .725 .732 .847 .863 2.6 52 285 1.768 .42 90 4490 7260 37 46 292 301 -50 161 90 71 .892 164 74 1.122 .9 -.166 -.152
20 556 1632 85 73 471 1559 624 1802 108 128 539 1729 0 0 206 489 100 247 86 98 86 92 2030 2268 .302 3.31 3.208 4.054 3.221 2.085 52 209 3.468 .88 90 4640 7300 41 50 307 316 0 2007 90 1917 4.071 2216 2126 .246 3.945 2.025 1.98

Total number of rows: 44544

Table truncated, full table size 9472 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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