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Sample GSM989790 Query DataSets for GSM989790
Status Public on Aug 23, 2012
Title PC 455T
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 455T2
Organism Homo sapiens
Characteristics ethnicity: Caucasian
age: 55
pre-operation treatment: None
individual: PC 430T
disease free survival: 9.57
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/2008-08/81181.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 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 7999 10523 47 80 7951 10443 8708 11874 50 94 8661 11794 0 0 2478 3485 13 77 100 100 100 100 18394 20455 .761 1.313 1.362 1.296 1.352 3.126 52 313 1.309 .96 80 1690 7860 14 22 37 45 0 8734 66 8667 1.09 9855 9788 .917 1.13 .124 .177
2 8225 11093 50 84 8175 11008 9238 12663 53 101 9188 12578 0 0 2690 4141 15 84 100 100 100 100 19183 21766 .743 1.347 1.369 1.27 1.367 3.25 52 269 1.354 .96 80 1840 7860 14 22 52 60 0 9207 70 9136 1.118 10510 10439 .895 1.136 .16 .184
3 5034 7118 50 83 4984 7035 5304 7707 53 97 5254 7624 0 0 997 1914 19 63 100 100 100 100 12019 12878 .708 1.412 1.451 1.369 1.445 2.186 52 261 1.438 .97 80 2000 7860 14 22 68 76 0 5908 69 5839 1.171 6396 6328 .854 1.204 .228 .268
4 10919 13894 48 83 10871 13811 11132 14561 54 98 11083 14478 0 0 1488 2721 21 65 100 100 100 100 24682 25561 .787 1.27 1.306 1.249 1.324 2.23 52 232 1.275 .96 80 2150 7860 14 22 83 91 0 11531 69 11462 1.054 12085 12016 .948 1.084 .076 .117
5 345 191 49 77 296 113 348 180 50 92 298 102 0 0 62 72 13 56 100 78 100 48 409 400 2.619 .382 .342 .31 .377 4.338 52 233 .305 .49 90 2300 7860 13 22 97 106 0 159 64 94 .317 149 85 3.156 .284 -1.658 -1.816
6 1981 4108 56 93 1925 4014 2340 4806 62 112 2284 4713 0 0 992 2051 26 71 100 100 100 100 5939 6997 .48 2.085 2.063 2.101 2.14 2.516 80 313 2.091 .98 100 2450 7860 13 23 112 122 0 3409 77 3331 1.731 3989 3912 .578 1.713 .791 .776
7 120 141 50 90 69 50 130 138 57 106 79 47 0 0 47 55 25 67 75 36 63 8 119 126 1.38 .725 .595 .866 .752 6.496 80 364 1.196 .29 110 2610 7860 12 23 127 138 0 117 75 41 .601 115 39 1.663 .494 -.734 -1.018
8 5590 8453 47 85 5543 8367 5893 8719 50 97 5845 8634 0 0 1234 1427 12 51 100 100 100 100 13910 14479 .662 1.509 1.477 1.542 1.521 2.143 52 244 1.485 .98 80 2750 7860 14 22 143 151 0 7016 71 6944 1.253 7236 7166 .798 1.226 .325 .294
9 91 119 46 75 45 44 94 117 49 88 47 42 0 0 27 46 13 54 84 34 71 6 89 89 1.023 .978 .894 1.291 1.26 7.095 32 219 2.277 .32 70 2910 7850 13 20 159 166 0 99 62 37 .812 97 35 1.232 .742 -.301 -.431
10 84 150 45 76 38 73 84 141 49 97 39 64 0 0 19 42 12 79 93 37 68 6 111 103 .521 1.921 1.641 1.848 1.749 4.322 32 189 9.175 .35 70 3050 7860 14 21 173 180 0 124 63 61 1.594 117 53 .627 1.362 .673 .446
11 142 311 45 75 97 235 144 303 48 85 99 228 0 0 43 98 12 63 94 96 94 90 332 327 .413 2.423 2.303 2.673 2.346 3.653 52 280 3.026 .73 90 3200 7860 13 22 187 196 0 258 62 195 2.011 251 189 .497 1.911 1.008 .935
12 154 324 46 72 108 251 164 348 48 81 118 275 0 0 37 110 13 46 96 96 96 86 359 393 .43 2.324 2.331 2.212 2.436 3.206 52 240 2.619 .86 80 3360 7860 14 22 204 212 0 269 60 208 1.929 289 228 .518 1.934 .948 .952
13 109 126 47 84 61 42 110 126 53 101 62 42 0 0 26 50 26 77 92 21 57 1 103 104 1.452 .689 .677 .745 .941 5.096 52 246 2.335 .27 80 3500 7850 13 21 218 226 0 105 70 35 .571 105 35 1.75 .562 -.807 -.831
14 82 116 47 80 34 35 78 110 50 90 31 30 0 0 15 44 13 48 96 34 62 9 69 61 .971 1.029 .968 1.231 1.337 5.062 32 157 4.857 .33 60 3660 7850 14 20 235 241 0 96 66 29 .854 91 25 1.17 .803 -.227 -.316
15 52 72 47 79 4 -6 48 51 50 88 0 -27 0 0 15 101 13 50 16 6 7 5 -2 -27 null null null 3.945 5.215 7.041 80 299 9.656 .42 100 3810 7850 12 22 248 258 -50 60 66 -5 null 42 -22 null null null null
16 270 330 45 81 224 249 276 319 47 92 230 237 0 0 60 92 12 47 100 100 100 96 473 467 .9 1.112 1.03 1.076 1.039 2.534 52 180 1.11 .87 80 3960 7850 13 21 264 272 0 274 67 207 .923 265 197 1.084 .855 -.116 -.226
17 57 84 46 72 11 11 55 75 48 83 9 2 0 0 15 46 16 47 30 11 8 2 22 11 1 1 .222 2.803 2.354 7.627 80 254 4.981 .28 100 4100 7850 12 22 277 287 -50 70 60 9 .83 62 2 1.205 .184 -.269 -2.439
18 49 63 47 80 2 -17 46 56 52 94 0 -23 0 0 18 34 21 64 2 3 1 0 -15 -23 null null null 5.643 5.408 6.143 80 309 8.462 .29 100 4250 7840 11 21 292 302 -50 52 66 -14 null 46 -19 null null null null
19 131 168 47 87 84 81 128 163 50 104 81 76 0 0 38 56 17 69 90 50 90 15 165 157 1.037 .964 .938 .88 .975 5.755 52 232 1.689 .39 80 4410 7850 13 21 309 317 0 139 72 67 .8 135 63 1.25 .779 -.321 -.361
20 591 2561 47 81 543 2479 634 2680 53 96 586 2598 0 0 147 673 20 59 100 100 100 100 3022 3184 .219 4.565 4.433 4.662 4.652 2.303 52 280 4.64 .97 90 4560 7850 12 21 323 332 0 2125 67 2057 3.789 2224 2156 .264 3.68 1.922 1.88

Total number of rows: 44544

Table truncated, full table size 9394 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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