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Sample GSM989778 Query DataSets for GSM989778
Status Public on Aug 23, 2012
Title PC 616T
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 616T2
Organism Homo sapiens
Characteristics ethnicity: Caucasian
age: 47
pre-operation treatment: None
individual: PC 159T
disease free survival: 79.40
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/2008-08/81167.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 11584 11583 106 77 11478 11506 12688 12463 111 90 12582 12386 0 0 4201 4563 38 53 100 100 100 100 22984 24968 .998 1.002 .984 1.022 .98 1.45 32 229 1.031 .95 70 2060 6670 23 30 66 73 0 9874 66 9808 .855 10624 10558 1.17 .839 -.227 -.253
2 13604 12565 110 89 13493 12476 13778 13391 113 99 13668 13302 0 0 3109 4537 41 55 100 100 100 100 25969 26970 1.082 .925 .973 .854 .943 1.325 32 232 1.004 .94 70 2200 6660 22 29 80 87 0 10711 76 10635 .788 11415 11339 1.269 .83 -.343 -.27
3 3693 6383 116 91 3576 6292 4018 7561 120 101 3901 7469 0 0 2313 3997 44 58 90 100 87 100 9868 11370 .568 1.76 1.915 2.276 1.731 2.345 32 173 1.812 .94 60 2360 6670 24 30 97 103 0 5441 78 5363 1.5 6445 6367 .667 1.632 .585 .707
4 11932 10683 112 92 11819 10591 13037 12051 126 107 12924 11959 0 0 4022 4541 79 63 100 100 100 100 22410 24883 1.116 .896 .925 .752 .917 1.635 32 227 .968 .94 70 2510 6660 22 29 111 118 0 9107 78 9028 .764 10273 10194 1.309 .789 -.389 -.342
5 663 250 107 98 556 151 676 219 112 113 568 120 0 0 131 94 41 86 100 84 100 37 707 688 3.682 .272 .211 .261 .234 1.57 32 202 .278 .64 70 2660 6660 22 29 126 133 0 213 84 129 .232 187 102 4.32 .18 -2.111 -2.473
6 4366 5548 127 121 4239 5426 2060 3142 141 155 1933 3020 0 0 4158 4861 82 151 100 100 98 98 9665 4953 .781 1.28 1.562 1.535 1.303 1.714 120 451 1.226 .96 120 2820 6660 20 32 140 152 0 4729 103 4625 1.091 2678 2574 .916 1.332 .126 .413
7 179 114 128 109 51 4 172 104 133 132 44 -4 0 0 54 62 55 99 42 5 13 1 55 40 12.75 .078 null .796 .668 4.144 52 229 1.929 .32 90 2960 6660 21 30 155 164 -50 97 93 3 .067 89 -3 14.957 null -3.903 null
8 5479 9928 118 98 5361 9829 6654 11754 125 122 6535 11655 0 0 2803 5056 56 127 100 100 100 98 15190 18190 .545 1.833 1.783 2.002 1.836 1.956 52 218 1.867 .96 80 3110 6670 23 31 171 179 0 8463 84 8379 1.563 10019 9935 .64 1.52 .644 .604
9 146 116 108 92 37 24 133 93 117 111 25 0 0 0 58 75 55 116 34 11 13 1 61 25 1.542 .649 null .887 .841 4.614 52 272 2.702 .33 90 3260 6660 21 30 185 194 -50 99 78 20 .553 79 0 1.809 null -.855 null
10 155 95 107 93 48 1 148 78 119 118 41 -14 0 0 55 54 60 130 36 1 9 0 49 27 48 .021 null 1.113 1.143 3.714 52 293 19.945 .07 90 3410 6660 21 30 200 209 -50 81 79 1 .018 66 -12 56.31 null -5.815 null
11 425 615 121 91 303 524 396 562 141 125 274 470 0 0 95 235 79 141 100 100 96 81 827 744 .578 1.729 1.715 1.639 1.539 1.563 32 189 2.32 .67 70 3570 6670 23 30 217 224 0 524 78 447 1.474 479 401 .678 1.462 .56 .548
12 377 416 168 106 209 310 408 463 178 132 240 356 0 0 169 249 77 127 71 71 57 57 519 596 .674 1.483 1.483 1.265 1.41 1.921 52 286 2.271 .62 90 3710 6660 21 30 230 239 0 355 90 264 1.264 395 303 .791 1.264 .338 .338
13 314 125 160 100 153 24 320 120 170 110 159 19 0 0 103 57 66 65 76 23 57 3 177 178 6.375 .157 .119 .213 .306 3.326 52 288 .524 .25 90 3870 6660 21 30 246 255 -50 107 85 20 .134 102 16 7.479 .102 -2.903 -3.295
14 287 131 147 97 139 33 273 108 262 115 126 10 0 0 112 77 1489 88 0 19 0 5 172 136 4.212 .237 .079 .276 .314 4.52 52 285 .419 .49 90 4020 6660 21 30 261 270 -50 112 83 28 .202 92 9 4.941 .068 -2.305 -3.886
15 261 88 162 93 98 -4 236 77 310 118 73 -15 0 0 105 58 1705 102 0 6 0 0 94 58 null null null .327 .327 4.292 32 217 .029 .58 70 4170 6650 21 28 277 284 0 75 79 -3 null 66 -13 null null null null
16 1105 713 142 104 962 608 1082 872 164 148 939 767 0 0 805 546 118 195 67 61 65 55 1570 1706 1.582 .632 .817 .694 .651 1.854 52 285 .706 .83 90 4320 6660 21 30 291 300 0 608 89 518 .539 743 654 1.856 .696 -.892 -.522
17 166 99 118 93 47 6 161 85 128 110 43 -7 0 0 62 58 59 80 34 11 13 1 53 36 7.833 .128 null .778 .684 2.263 52 291 1.924 .25 90 4470 6650 20 29 306 315 -50 84 79 5 .109 72 -6 9.189 null -3.2 null
18 112 76 111 96 1 -19 107 69 128 137 -4 -26 0 0 39 38 93 258 0 0 0 0 -18 -30 null null null 1.184 1.024 3.673 52 291 57.349 .04 90 4620 6650 20 29 321 330 -50 65 82 -16 null 59 -22 null null null null
19 263 311 111 101 152 209 172 263 132 140 60 161 0 0 177 226 87 240 48 40 36 15 361 221 .727 1.375 2.683 1.691 1.597 2.051 52 308 1.496 .72 90 4770 6650 20 29 336 345 0 265 86 178 1.172 224 137 .853 2.287 .229 1.194
20 815 1892 113 97 702 1794 985 2465 126 116 871 2367 0 0 533 1384 69 95 73 73 71 71 2496 3238 .391 2.556 2.718 2.213 2.385 2.78 52 327 2.769 .93 90 4920 6650 20 29 351 360 0 1613 83 1529 2.178 2101 2018 .459 2.317 1.123 1.212

Total number of rows: 44544

Table truncated, full table size 9382 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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