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Sample GSM989774 Query DataSets for GSM989774
Status Public on Aug 23, 2012
Title PC 370N
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 370N2
Organism Homo sapiens
Characteristics individual: PC 370N
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/2008-08/81134.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 2287 3035 76 222 2210 2812 1932 2611 86 265 1855 2388 0 0 1517 2288 39 194 100 92 100 90 5022 4243 .786 1.272 1.287 1.105 1.216 3.756 52 276 1.353 .97 80 1760 7670 43 51 32 40 0 2364 173 2190 .991 2034 1860 1.009 1.003 -.013 .004
2 2066 2758 78 216 1987 2542 2507 2754 86 246 2428 2537 0 0 957 1410 60 173 100 98 100 92 4529 4965 .782 1.279 1.045 1.19 1.292 3.77 52 248 1.304 .9 80 1910 7670 43 51 47 55 0 2148 168 1980 .997 2145 1976 1.003 .814 -.005 -.297
3 3804 2974 75 200 3728 2773 3744 2945 87 241 3668 2745 0 0 708 715 70 201 100 100 100 100 6501 6413 1.344 .744 .748 .732 .713 2.845 32 199 .739 .95 70 2060 7670 43 50 62 69 0 2317 156 2160 .579 2294 2138 1.726 .583 -.787 -.779
4 1172 1487 71 182 1100 1305 1024 1124 76 225 953 942 0 0 581 944 30 200 100 98 100 88 2405 1895 .843 1.186 .988 1.039 1.016 3.449 52 228 1.266 .89 80 2210 7670 43 51 77 85 0 1158 142 1017 .924 876 734 1.082 .77 -.114 -.377
5 119 241 72 173 46 68 118 224 78 206 46 50 0 0 44 156 28 146 65 21 40 7 114 96 .676 1.478 1.087 2.928 3.115 7.9 52 282 42.327 .07 90 2360 7660 41 50 91 100 -50 188 135 53 1.151 174 39 .868 .847 .203 -.24
6 1535 2935 77 186 1458 2748 1583 3150 83 218 1506 2963 0 0 373 1038 36 165 100 98 100 98 4206 4469 .531 1.885 1.967 1.712 1.939 3.671 52 234 1.968 .95 80 2520 7660 42 50 108 116 0 2286 145 2141 1.468 2454 2308 .681 1.533 .554 .616
7 117 233 81 219 36 13 104 218 86 267 23 -1 0 0 46 129 38 195 38 9 21 0 49 22 2.769 .361 null 3.629 3.481 7.388 52 272 23.29 .14 90 2660 7660 41 50 121 130 -50 181 171 10 .281 170 -1 3.555 null -1.83 null
8 4780 4544 85 221 4695 4322 4727 4558 89 265 4642 4337 0 0 820 1000 34 197 100 100 100 100 9017 8979 1.086 .921 .934 .906 .939 2.64 32 202 .906 .97 70 2810 7660 42 49 137 144 0 3540 172 3367 .717 3550 3378 1.395 .728 -.48 -.458
9 106 215 77 200 28 14 105 170 89 250 28 -29 0 0 35 174 49 222 23 9 5 3 42 -1 2 .5 null 5.011 6.045 7.667 52 275 10.046 .32 90 2960 7660 41 50 151 160 -50 167 156 11 .389 132 -23 2.568 null -1.36 null
10 111 222 74 209 36 13 102 188 83 250 27 -20 0 0 39 153 46 173 30 9 9 1 49 7 2.769 .361 null 2.779 3.533 16.579 52 273 29.027 .1 90 3110 7660 41 50 166 175 -50 173 163 10 .281 146 -16 3.555 null -1.83 null
11 150 389 71 188 78 201 141 383 78 224 69 195 0 0 50 213 34 152 81 56 50 31 279 264 .388 2.577 2.826 3.129 2.936 7.111 32 152 8.224 .28 60 3270 7660 43 49 184 190 0 303 146 157 2.007 298 152 .498 2.201 1.005 1.138
12 135 298 74 198 60 100 123 268 83 261 49 70 0 0 50 206 36 198 55 23 38 9 160 119 .6 1.667 1.429 2.969 3.024 8.821 52 267 20.832 .18 90 3410 7660 41 50 196 205 -50 232 154 78 1.298 209 55 .77 1.113 .377 .154
13 130 234 73 216 56 17 125 195 82 255 51 -20 0 0 44 171 34 200 67 9 30 3 73 31 3.294 .304 null 2.981 2.026 8.703 52 263 59.189 .06 90 3570 7660 41 50 212 221 -50 182 168 13 .236 152 -16 4.229 null -2.08 null
14 123 259 74 194 48 65 111 198 79 250 37 4 0 0 51 215 31 262 55 15 30 3 113 41 .738 1.354 .108 3.258 2.709 7.844 52 253 38.477 .11 90 3720 7660 41 50 227 236 -50 202 151 51 1.055 154 3 .948 .084 .077 -3.57
15 95 280 76 192 18 88 81 256 80 227 4 64 0 0 33 153 27 144 36 32 15 9 106 68 .205 4.889 16 4.595 3.684 9.04 52 272 67.246 .05 90 3870 7660 41 50 242 251 -50 218 150 69 3.808 199 50 .263 12.463 1.929 3.64
16 324 361 75 182 248 179 317 349 81 213 242 167 0 0 82 194 30 143 100 56 100 25 427 409 1.385 .722 .69 .599 .69 6.034 32 190 .905 .43 70 4020 7660 42 49 258 265 0 281 142 139 .562 272 130 1.779 .538 -.831 -.896
17 105 244 75 182 29 62 101 206 81 216 26 23 0 0 44 167 30 162 48 28 19 7 91 49 .468 2.138 .885 3.822 4.641 14.451 52 285 8.308 .51 90 4170 7650 40 49 272 281 -50 190 142 48 1.665 160 18 .6 .689 .736 -.537
18 88 261 76 195 12 65 85 219 81 250 8 23 0 0 32 165 31 203 19 25 11 1 77 31 .185 5.417 2.875 7.283 7.921 6.276 52 272 26.318 .17 90 4320 7650 40 49 287 296 -50 203 152 51 4.219 171 18 .237 2.239 2.077 1.163
19 135 236 77 200 58 35 141 194 83 241 63 -5 0 0 54 155 34 197 57 17 44 1 93 58 1.657 .603 null 3.038 2.991 12.855 52 308 43.091 .04 90 4470 7650 40 49 302 311 -50 184 156 27 .47 151 -4 2.127 null -1.089 null
20 518 1082 76 192 441 890 516 1024 81 236 439 832 0 0 126 348 32 180 100 100 100 96 1331 1271 .496 2.018 1.895 1.942 2.028 3.417 32 198 2.22 .8 70 4630 7660 42 49 319 326 0 843 150 693 1.572 798 648 .636 1.476 .653 .562

Total number of rows: 44544

Table truncated, full table size 9480 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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