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Sample GSM989685 Query DataSets for GSM989685
Status Public on Aug 23, 2012
Title PC 574N
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 574N2
Organism Homo sapiens
Characteristics individual: PC 574N
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/2008-08/81146.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 49779 50033 152 149 49627 49884 51619 50259 165 170 51466 50110 0 0 7340 6828 61 95 100 100 100 100 99511 101576 .995 1.005 .974 1.008 .991 1.162 52 347 .987 .98 90 1950 7430 38 47 34 43 0 45311 135 45177 .91 45516 45381 1.099 .882 -.136 -.182
2 38626 38396 174 169 38451 38226 50863 50347 198 180 50688 50177 0 0 21105 21831 90 84 100 100 100 100 76677 100865 1.006 .994 .99 1.005 1.013 1.896 80 313 1.006 .98 100 2100 7440 39 49 49 59 0 34773 153 34619 .9 45596 45442 1.111 .897 -.151 -.158
3 63135 64688 264 200 62870 64488 64404 66685 313 227 64140 66484 88 86 4754 6631 166 125 100 100 100 100 127358 130624 .975 1.026 1.037 1.022 1.037 1.154 52 267 1.02 .98 90 2240 7450 40 49 63 72 -100 58584 181 58402 .929 60392 60210 1.076 .939 -.106 -.091
4 46083 43211 199 185 45883 43026 52530 50096 253 216 52330 49911 0 0 16480 18295 158 149 100 100 100 100 88909 102241 1.066 .938 .954 .793 .941 2.017 80 341 .965 .98 100 2400 7440 39 49 79 89 0 39133 168 38966 .849 45369 45201 1.178 .864 -.236 -.211
5 2527 756 410 238 2116 517 2851 758 926 416 2441 519 0 0 972 280 1308 427 82 71 30 11 2633 2960 4.093 .244 .213 .25 .232 1.517 52 236 .287 .9 90 2540 7440 39 48 93 102 -50 685 216 468 .221 686 470 4.519 .193 -2.176 -2.377
6 26227 31661 546 298 25681 31362 28306 35306 925 414 27759 35008 0 0 8821 12774 1090 368 100 100 100 100 57043 62767 .819 1.221 1.261 1.13 1.259 1.472 80 314 1.285 .96 100 2690 7440 39 49 108 118 0 28673 270 28402 1.106 31974 31704 .904 1.142 .145 .192
7 789 411 248 204 540 206 767 381 314 233 518 177 0 0 135 149 190 138 100 65 96 21 746 695 2.621 .381 .342 .301 .298 2.165 32 188 .472 .45 70 2830 7430 39 46 123 130 0 372 185 187 .345 345 160 2.895 .309 -1.533 -1.692
8 36402 39646 227 206 36175 39440 53496 66228 2206 1863 53269 66021 48 50 29906 30714 9916 8892 61 65 57 61 75615 119290 .917 1.09 1.239 1.242 1.036 2.242 52 326 1.02 .98 90 2980 7420 37 46 137 146 -100 35905 187 35718 .987 59978 59791 1.013 1.122 -.018 .167
9 442 403 235 191 206 212 424 404 1916 1756 188 213 0 0 104 135 8929 8473 0 0 0 0 418 401 .972 1.029 1.133 1.011 .908 2.911 52 277 1.719 .33 80 3140 7420 38 46 154 162 0 365 173 192 .932 366 193 1.073 1.026 -.102 .037
10 489 640 160 163 329 476 470 623 192 254 310 459 0 0 115 176 170 679 94 11 42 0 805 769 .691 1.447 1.481 1.451 1.467 1.756 52 301 1.905 .77 90 3290 7420 37 46 168 177 0 580 148 431 1.31 564 416 .763 1.341 .39 .423
11 2399 3951 142 178 2257 3773 2443 3946 153 197 2300 3767 0 0 536 912 83 108 100 100 100 100 6030 6067 .598 1.672 1.638 1.679 1.728 1.364 52 281 1.799 .9 90 3450 7430 38 47 184 193 0 3578 161 3417 1.514 3574 3412 .661 1.483 .598 .569
12 1398 6148 141 189 1256 5958 1472 6305 148 220 1330 6116 0 0 459 2285 56 156 100 100 100 100 7214 7446 .211 4.744 4.598 4.678 4.555 1.454 80 362 4.959 .96 100 3600 7420 37 47 199 209 0 5568 171 5396 4.296 5710 5539 .233 4.165 2.103 2.058
13 1398 1261 133 175 1264 1086 1354 1008 149 245 1220 833 0 0 341 962 97 501 100 96 100 34 2350 2053 1.164 .859 .683 .746 .722 1.512 52 277 1.694 .69 90 3750 7420 37 46 214 223 0 1142 158 984 .778 913 754 1.285 .618 -.362 -.693
14 457 551 134 174 323 377 499 539 148 238 364 365 0 0 174 228 95 468 85 37 75 1 700 729 .857 1.167 1.003 1.185 1.208 2.501 80 372 3.558 .69 100 3900 7410 36 46 229 239 0 499 158 341 1.057 488 331 .946 .908 .08 -.139
15 89 104 137 182 -48 -77 85 81 147 219 -52 -100 0 0 24 69 69 227 0 0 0 0 -125 -152 null null null 1.585 2.062 3.282 52 320 3.221 .84 90 4040 7410 36 45 243 252 -50 94 165 -70 null 73 -91 null null null null
16 6945 5190 145 184 6799 5006 6826 5086 152 204 6680 4902 0 0 1167 1239 47 123 100 100 100 100 11805 11582 1.358 .736 .734 .716 .766 1.428 52 315 .737 .95 90 4190 7420 37 46 258 267 0 4700 167 4534 .667 4606 4439 1.5 .665 -.585 -.589
17 214 441 145 194 68 247 208 417 156 236 62 222 0 0 59 121 58 181 51 69 19 15 315 284 .275 3.632 3.581 3.693 3.191 2.832 52 277 4.346 .55 80 4350 7410 37 45 275 283 0 399 176 224 3.29 378 201 .304 3.243 1.718 1.697
18 102 108 148 188 -46 -79 81 82 159 215 -66 -105 0 0 85 97 52 119 3 3 3 3 -125 -171 null null null 1.555 1.655 2.341 52 285 2.159 .47 90 4500 7420 37 46 289 298 -50 98 170 -72 null 74 -95 null null null null
19 1610 1343 149 186 1461 1156 1785 1321 160 212 1636 1135 0 0 639 586 54 160 98 91 97 86 2617 2771 1.264 .791 .694 .786 .769 1.87 80 345 .829 .92 100 4650 7430 38 48 304 314 0 1216 168 1047 .717 1196 1028 1.396 .628 -.481 -.67
20 7267 20403 152 185 7115 20218 7745 20506 165 212 7592 20321 0 0 1813 4219 67 129 100 100 100 100 27333 27913 .352 2.842 2.677 2.961 2.804 1.441 52 306 2.796 .97 90 4800 7420 37 46 319 328 0 18478 168 18310 2.573 18571 18403 .389 2.424 1.364 1.277

Total number of rows: 44544

Table truncated, full table size 9987 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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