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Sample GSM989784 Query DataSets for GSM989784
Status Public on Aug 23, 2012
Title PC 205T
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 PT 205
Organism Homo sapiens
Characteristics ethnicity: Caucasian
age: 62
pre-operation treatment: None
individual: PC 452T
disease free survival: 19.17
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/2008-11/81786.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 GPL15972
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 2318 1287 46 94 2271 1192 2408 1309 51 121 2361 1214 0 0 575 401 35 284 100 96 100 90 3463 3575 1.905 .525 .514 .501 .53 1.976 52 388 .525 .95 90 1590 7380 33 42 38 47 0 1103 81 1022 .45 1122 1041 2.222 .441 -1.152 -1.182
2 1912 1123 47 107 1864 1015 2003 1096 55 146 1955 988 0 0 447 339 42 324 100 96 100 84 2879 2943 1.836 .545 .505 .536 .557 1.944 52 321 .534 .91 90 1740 7390 34 43 53 62 0 963 92 870 .467 940 847 2.142 .433 -1.099 -1.207
3 1386 2700 46 96 1339 2604 1391 2756 48 112 1344 2660 0 0 238 439 17 108 100 100 100 100 3943 4004 .514 1.945 1.979 1.947 1.971 1.638 52 299 1.959 .97 90 1890 7380 33 42 68 77 0 2315 82 2233 1.667 2363 2281 .6 1.697 .738 .763
4 2396 1304 46 94 2350 1210 2443 1297 49 117 2397 1203 0 0 364 336 15 93 100 100 100 100 3560 3600 1.942 .515 .502 .498 .527 1.855 52 253 .512 .95 90 2040 7380 33 42 83 92 0 1118 81 1037 .441 1112 1031 2.265 .43 -1.18 -1.217
5 78 89 45 106 33 -17 75 84 49 115 30 -22 0 0 24 48 15 66 76 7 50 1 16 8 null null null 1.153 1.172 10.85 80 266 -62.686 -.03 100 2190 7380 33 43 98 108 -50 76 91 -15 null 72 -19 null null null null
6 557 728 49 93 507 634 563 711 52 105 513 617 0 0 93 173 15 60 100 100 100 100 1141 1130 .8 1.25 1.203 1.227 1.203 1.795 52 266 1.251 .92 90 2340 7380 33 42 113 122 0 624 80 544 1.072 610 529 .933 1.031 .101 .044
7 88 144 47 83 40 60 87 139 53 92 39 56 0 0 24 80 18 49 83 50 58 16 100 95 .667 1.5 1.436 1.909 2.348 3.257 12 104 20.286 .39 50 2480 7360 33 38 129 134 0 123 71 51 1.286 119 48 .778 1.231 .363 .3
8 1271 2827 44 94 1226 2732 1285 2798 47 107 1241 2703 0 0 270 454 13 62 100 100 100 100 3958 3944 .449 2.228 2.178 2.259 2.251 1.633 52 370 2.219 .97 90 2650 7380 33 42 144 153 0 2424 81 2342 1.911 2399 2318 .523 1.867 .934 .901
9 59 201 46 73 13 127 64 132 49 93 17 58 0 0 17 196 14 59 58 50 16 33 140 75 .102 9.769 3.412 4.022 6.992 9.184 12 68 77.769 .09 40 2830 7330 31 35 165 169 0 172 63 109 8.376 113 50 .119 2.925 3.066 1.549
10 59 236 47 98 11 138 55 115 50 118 7 17 0 0 26 474 12 78 31 21 12 18 149 24 .08 12.545 2.429 4.372 6.611 10.971 32 170 27.551 .46 60 2980 7330 30 36 179 185 0 202 84 118 10.756 99 15 .093 2.082 3.427 1.058
11 102 174 46 108 56 65 96 162 47 121 50 53 0 0 20 57 11 64 100 40 96 15 121 103 .862 1.161 1.06 1.033 1.009 3.19 32 191 5.043 .31 70 3100 7370 33 40 190 197 0 149 93 56 .995 139 45 1.005 .909 -.007 -.138
12 62 110 44 98 17 11 58 94 49 119 13 -3 0 0 20 63 18 118 45 7 20 1 28 10 1.545 .647 null 2.403 3.035 5.618 80 454 12.512 .36 100 3240 7340 29 39 203 213 -50 94 84 9 .555 81 -3 1.803 null -.85 null
13 1843 6986 45 87 1797 6898 1395 6445 58 104 1350 6357 0 0 1857 4309 46 65 100 100 100 100 8695 7707 .261 3.839 4.709 4.589 4.607 2.023 12 104 3.738 .85 50 3380 7320 29 34 219 224 0 5990 75 5914 3.291 5526 5450 .304 4.037 1.719 2.013
14 55 91 45 91 10 0 56 84 50 110 11 -7 0 0 12 45 29 73 8 6 0 1 10 4 null null null 2.511 2.578 7.276 80 338 31.187 .11 100 3550 7360 31 41 234 244 -50 78 78 0 null 72 -6 null null null null
15 52 76 44 104 7 -28 50 67 46 128 5 -36 0 0 12 45 11 130 36 1 12 0 -21 -31 null null null 3.716 5.746 8.314 80 289 43.418 .19 100 3700 7360 31 41 249 259 -50 65 89 -24 null 57 -31 null null null null
16 105 258 45 104 59 154 106 256 48 147 61 152 0 0 27 87 16 173 90 44 84 1 213 213 .383 2.61 2.492 2.414 2.611 3.146 52 223 7.735 .54 90 3850 7370 32 41 264 273 0 221 89 132 2.238 219 130 .447 2.136 1.162 1.095
17 54 86 44 103 10 -16 53 69 46 121 9 -33 0 0 13 49 11 79 40 5 16 0 -6 -24 null null null 4.351 5.342 5.629 80 303 22.093 .2 100 4000 7360 31 41 279 289 -50 74 88 -14 null 59 -28 null null null null
18 51 73 44 100 6 -26 50 63 46 114 5 -37 0 0 10 43 12 71 26 2 2 1 -20 -32 null null null 4.153 5.863 5.435 80 300 23.106 .29 100 4160 7360 31 41 295 305 -50 63 86 -22 null 54 -32 null null null null
19 64 97 46 100 18 -3 64 96 48 117 17 -4 0 0 14 38 11 69 62 2 36 0 15 13 null null null 1.469 1.568 4.455 80 346 16.571 .23 100 4310 7360 31 41 310 320 -50 83 86 -3 null 82 -3 null null null null
20 211 851 45 98 166 753 209 829 46 114 163 730 0 0 42 190 9 77 100 100 100 100 919 893 .22 4.536 4.479 4.525 4.516 1.946 52 191 4.904 .91 80 4460 7380 34 42 326 334 0 730 84 646 3.889 711 626 .257 3.84 1.959 1.941

Total number of rows: 44544

Table truncated, full table size 9038 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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