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Sample GSM989728 Query DataSets for GSM989728
Status Public on Aug 23, 2012
Title PC 363N
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 363N2
Organism Homo sapiens
Characteristics individual: PC 363N
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/2008-08/81169.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 GPL9497
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 2750 3712 57 92 2692 3619 3154 3913 63 108 3096 3820 0 0 987 972 29 70 100 100 100 100 6311 6916 .744 1.344 1.234 1.505 1.24 3.077 52 291 1.292 .91 80 1680 7300 6 14 24 32 0 2893 72 2821 1.048 3050 2978 .954 .962 .067 -.056
2 3563 5234 57 94 3505 5139 3679 5498 61 107 3621 5403 0 0 538 1184 19 64 100 100 100 100 8644 9024 .682 1.466 1.492 1.424 1.493 1.774 32 212 1.567 .9 70 1820 7300 6 13 38 45 0 4080 73 4006 1.143 4286 4211 .875 1.163 .193 .218
3 2663 3687 58 84 2604 3603 3239 4190 61 92 3180 4105 0 0 1312 1466 13 43 100 100 98 100 6207 7285 .723 1.384 1.291 1.725 1.291 4.508 52 251 1.309 .92 80 1970 7300 6 14 53 61 0 2874 65 2808 1.079 3266 3200 .927 1.006 .109 .009
4 3783 5655 59 83 3723 5572 4565 6519 62 91 4506 6436 0 0 1635 1980 12 40 100 100 100 100 9295 10942 .668 1.497 1.428 1.727 1.426 3.668 52 229 1.451 .92 80 2130 7300 6 14 69 77 0 4408 65 4343 1.167 5081 5017 .857 1.113 .222 .155
5 245 127 57 84 187 42 251 119 58 92 193 34 0 0 38 53 12 40 100 46 100 28 229 227 4.452 .225 .176 .232 .28 3.474 32 181 .187 .31 70 2280 7300 6 13 84 91 0 99 65 33 .175 93 27 5.712 .137 -2.514 -2.864
6 2378 3618 64 86 2314 3531 2671 3940 66 93 2606 3853 0 0 835 961 13 45 100 100 100 100 5845 6459 .655 1.526 1.479 1.749 1.416 2.917 52 212 1.483 .94 80 2420 7300 6 14 98 106 0 2820 67 2752 1.189 3071 3003 .841 1.152 .25 .205
7 147 137 63 84 84 53 139 119 66 100 76 34 0 0 58 87 19 56 100 40 90 9 137 110 1.585 .631 .447 .71 .909 3.627 32 158 1.415 .5 60 2580 7300 7 13 115 121 0 107 65 41 .492 93 27 2.033 .349 -1.024 -1.52
8 4202 4925 62 117 4140 4807 5021 5552 64 134 4959 5434 0 0 1827 1535 18 116 98 100 98 100 8947 10393 .861 1.161 1.096 1.469 1.109 4.271 52 182 1.08 .92 80 2730 7300 6 14 129 137 0 3839 91 3747 .905 4328 4236 1.105 .854 -.144 -.227
9 82 124 63 108 19 16 75 83 65 121 12 -25 0 0 34 277 12 116 48 3 23 1 35 -13 1.188 .842 null 4.111 3.747 4.814 80 173 18.487 .35 100 2870 7290 4 14 142 152 -50 97 84 12 .656 65 -19 1.523 null -.607 null
10 77 112 63 114 14 -2 73 107 64 120 10 -6 0 0 20 45 14 56 41 11 22 1 12 4 null null null 1.807 2.007 7.573 80 203 20.186 .13 100 3020 7290 4 14 157 167 -50 87 89 -2 null 83 -5 null null null null
11 142 264 60 112 82 152 143 271 63 121 82 159 0 0 31 72 13 62 100 87 96 65 234 241 .539 1.854 1.939 1.706 1.785 3.128 32 205 2.598 .57 70 3170 7300 6 13 173 180 0 206 87 118 1.445 211 124 .692 1.511 .531 .596
12 159 2174 62 102 96 2071 172 2374 64 109 110 2271 0 0 58 718 14 56 84 100 82 100 2167 2381 .046 21.573 20.645 25.301 19.398 2.777 52 235 21.695 .86 80 3330 7300 6 14 189 197 0 1695 80 1614 16.815 1850 1770 .059 16.092 4.072 4.008
13 145 164 58 98 86 65 141 155 61 107 82 56 0 0 19 54 14 52 100 59 100 25 151 138 1.323 .756 .683 .616 .739 3.544 32 183 1.955 .36 70 3480 7290 5 12 204 211 0 128 76 51 .589 121 44 1.697 .532 -.763 -.91
14 77 107 59 100 18 6 75 101 61 112 15 1 0 0 20 47 15 63 48 11 28 1 24 16 3 .333 .067 1.783 1.943 5.081 80 193 23.602 .12 100 3620 7290 4 14 217 227 -50 83 78 5 .26 79 1 3.849 .052 -1.944 -4.266
15 62 67 63 109 0 -42 60 50 66 120 -2 -58 0 0 10 45 19 67 6 2 0 1 -42 -60 null null null 9.028 9.246 5.613 80 210 21.384 .18 100 3770 7290 4 14 232 242 -50 52 85 -33 null 39 -45 null null null null
16 278 341 61 121 216 219 288 343 64 131 227 222 0 0 46 76 19 61 100 100 100 87 435 449 .986 1.014 .978 .974 1.042 1.968 32 163 1.052 .8 60 3920 7290 6 12 249 255 0 266 94 171 .79 267 173 1.265 .762 -.34 -.392
17 71 102 61 105 10 -2 65 74 63 117 4 -31 0 0 25 136 15 62 22 10 11 2 8 -27 null null null 6.8 6.691 4.033 80 201 29.396 .14 100 4080 7290 4 14 263 273 -50 80 82 -2 null 58 -24 null null null null
18 60 83 62 105 -1 -21 60 63 63 128 -1 -41 0 0 12 63 12 83 12 6 2 1 -22 -42 null null null 6.885 6.118 3.872 80 145 27.606 .21 100 4230 7290 4 14 278 288 -50 65 82 -16 null 49 -32 null null null null
19 105 124 62 130 43 -5 107 117 65 145 44 -12 0 0 37 45 13 79 71 2 61 0 38 32 null null null 1.524 1.028 8.978 80 195 -16.52 -.07 100 4380 7290 4 14 293 303 -50 97 101 -4 null 91 -9 null null null null
20 515 1717 64 124 450 1592 602 1988 65 137 537 1863 0 0 191 648 15 72 100 96 100 94 2042 2400 .283 3.538 3.469 3.464 3.38 2.575 52 173 3.689 .94 80 4530 7290 5 13 309 317 0 1338 97 1241 2.758 1550 1452 .363 2.704 1.463 1.435

Total number of rows: 44544

Table truncated, full table size 9314 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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