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Sample GSM989773 Query DataSets for GSM989773
Status Public on Aug 23, 2012
Title TB 2682T
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 TB 2682T2
Organism Homo sapiens
Characteristics age: 72
individual: S 07 8980T
disease free survival: 4+3
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/2008-08/81141.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 8948 4782 84 141 8864 4641 9819 4497 91 159 9735 4356 0 0 4796 2349 38 93 100 100 100 100 13505 14091 1.91 .524 .447 .566 .541 2.99 52 315 .489 .95 80 1770 6860 78 86 57 65 0 4152 122 4029 .455 3904 3782 2.2 .388 -1.137 -1.364
2 14827 8695 97 177 14729 8518 15799 8887 110 201 15702 8710 0 0 3257 1243 80 123 100 100 100 100 23247 24412 1.729 .578 .555 .592 .555 1.996 32 220 .544 .98 70 1910 6860 78 85 71 78 0 7549 154 7395 .502 7716 7562 1.992 .482 -.994 -1.054
3 11809 6984 108 179 11701 6804 13333 8301 122 205 13224 8121 0 0 3767 2785 81 106 100 100 100 100 18505 21345 1.72 .581 .614 .537 .592 2.263 32 216 .607 .98 70 2080 6860 78 85 88 95 0 6064 155 5907 .505 7207 7051 1.981 .533 -.986 -.907
4 13145 7176 98 178 13047 6998 14796 8179 109 196 14698 8000 0 0 4240 2725 48 101 100 100 100 98 20045 22698 1.864 .536 .544 .465 .554 2.925 52 302 .54 .98 90 2220 6860 77 86 101 110 0 6230 155 6076 .466 7101 6946 2.147 .473 -1.103 -1.081
5 731 306 100 184 631 121 796 286 115 216 696 101 0 0 296 118 66 154 96 32 90 3 752 797 5.215 .192 .145 .146 .174 7.348 52 223 .281 .27 80 2380 6860 78 86 118 126 0 266 160 105 .166 248 88 6.006 .126 -2.587 -2.989
6 3557 5504 139 236 3418 5268 4043 6361 158 274 3903 6125 0 0 1814 2795 82 155 100 100 100 97 8686 10028 .649 1.541 1.569 1.556 1.577 2.318 80 333 1.535 .97 100 2520 6870 78 88 131 141 0 4779 205 4574 1.338 5523 5318 .747 1.362 .42 .446
7 292 222 100 170 192 51 304 198 116 195 204 28 0 0 63 73 55 93 100 41 83 0 243 232 3.765 .266 .137 .218 .501 8.932 12 68 -.347 -.21 40 2670 6840 78 82 149 153 0 193 148 44 .231 172 24 4.336 .119 -2.116 -3.069
8 13411 8163 97 180 13313 7982 14514 8830 107 193 14417 8649 0 0 3144 1915 58 91 100 100 100 100 21295 23066 1.668 .6 .6 .603 .604 1.941 32 230 .586 .98 70 2820 6850 77 84 162 169 0 7087 156 6930 .521 7666 7509 1.921 .521 -.942 -.941
9 148 168 92 183 55 -15 144 141 102 196 51 -42 0 0 49 97 52 97 48 7 17 3 40 9 null null null 1.068 1.875 7.389 52 337 9.864 .11 90 2970 6850 76 85 176 185 -50 146 159 -13 null 122 -36 null null null null
10 116 146 81 174 35 -28 112 133 88 189 31 -41 0 0 37 64 37 91 42 3 13 0 7 -10 null null null 1.63 1.267 11.211 52 320 7.944 .16 90 3120 6850 76 85 191 200 -50 127 151 -24 null 115 -36 null null null null
11 789 1369 78 165 710 1204 782 1396 92 178 704 1231 0 0 119 346 110 86 100 100 100 100 1914 1935 .59 1.696 1.749 1.634 1.726 2.329 32 221 1.81 .93 70 3290 6850 77 84 209 216 0 1189 143 1045 1.472 1212 1069 .679 1.518 .558 .602
12 378 920 84 170 294 749 374 962 93 183 290 792 0 0 96 223 49 105 96 100 96 98 1043 1082 .393 2.548 2.731 2.59 2.61 2.571 52 280 2.605 .86 80 3430 6850 77 85 223 231 0 799 148 650 2.212 835 688 .452 2.371 1.145 1.246
13 313 205 84 182 229 23 307 205 93 205 223 23 0 0 88 84 36 125 100 9 96 3 252 246 9.957 .1 .103 .331 .366 3.494 32 209 .119 .08 70 3590 6850 77 84 239 246 0 178 158 20 .087 178 20 11.468 .09 -3.52 -3.481
14 141 147 83 170 57 -23 135 138 87 186 52 -32 0 0 49 59 32 102 73 1 32 0 34 20 null null null .922 .618 8.186 52 295 13.62 .1 90 3730 6850 76 85 252 261 -50 128 148 -20 null 120 -28 null null null null
15 99 109 84 170 15 -61 98 100 89 184 14 -70 0 0 27 73 34 89 26 3 3 1 -46 -56 null null null 6.79 8.325 5.917 52 289 36.511 .07 90 3880 6850 76 85 267 276 -50 95 148 -53 null 87 -61 null null null null
16 1271 1369 85 189 1185 1179 1374 1490 93 195 1288 1300 0 0 421 410 34 78 100 100 98 98 2364 2588 1.005 .995 1.009 1.021 1.007 2.472 52 237 .962 .94 80 4030 6850 77 85 283 291 0 1189 164 1024 .864 1294 1129 1.158 .876 -.211 -.191
17 119 200 83 186 35 14 112 188 88 192 28 2 0 0 35 73 31 82 48 17 25 3 49 30 2.5 .4 .071 .993 1.39 11.983 52 274 11.019 .14 90 4180 6850 76 85 297 306 -50 174 161 12 .347 163 2 2.879 .062 -1.526 -4.011
18 90 106 82 174 7 -68 88 98 88 188 5 -75 0 0 19 59 36 84 11 1 0 0 -61 -70 null null null 4.349 3.923 4.831 52 302 4.741 .32 90 4330 6840 75 84 312 321 -50 92 151 -59 null 85 -65 null null null null
19 553 474 87 183 465 291 556 445 93 202 468 261 0 0 133 138 38 97 100 98 100 73 756 729 1.598 .626 .558 .602 .574 2.685 52 257 .599 .71 80 4490 6850 77 85 329 337 0 412 159 253 .543 386 227 1.841 .484 -.88 -1.046
20 3388 11854 90 174 3298 11679 3639 12936 95 197 3549 12761 0 0 930 2749 40 89 100 100 100 100 14977 16310 .282 3.541 3.596 3.699 3.473 2.129 52 255 3.521 .98 80 4640 6860 78 86 344 352 0 10292 151 10140 3.075 11231 11079 .325 3.122 1.62 1.642

Total number of rows: 44544

Table truncated, full table size 9645 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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