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Sample GSM989744 Query DataSets for GSM989744
Status Public on Aug 23, 2012
Title PC 485T
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 485T2
Organism Homo sapiens
Characteristics ethnicity: Caucasian
age: 50
pre-operation treatment: None
individual: PC 498T
disease free survival: 50.66666667
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/2008-08/81183.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 8072 8401 39 75 8032 8326 8691 8794 44 86 8652 8718 0 0 2017 2229 21 47 100 100 100 100 16358 17370 .965 1.037 1.008 1.028 1.042 2.388 52 313 1.031 .98 80 1660 7350 19 27 38 46 0 6109 55 6055 .754 6395 6340 1.327 .733 -.408 -.449
2 6603 7355 40 76 6563 7278 7707 8200 45 89 7667 8123 0 0 2772 2461 21 58 100 100 100 100 13841 15790 .902 1.109 1.059 1.336 1.091 3.523 52 293 1.051 .99 90 1810 7360 19 28 52 61 0 5349 55 5293 .806 5963 5907 1.24 .77 -.31 -.376
3 4666 7450 40 78 4626 7372 4856 8072 43 92 4816 7993 0 0 944 1909 18 86 100 100 100 100 11998 12809 .628 1.594 1.66 1.554 1.615 2.342 52 289 1.622 .98 90 1970 7350 18 27 68 77 0 5418 57 5361 1.159 5870 5813 .863 1.207 .213 .271
4 7560 7671 40 81 7520 7590 8007 8114 43 90 7967 8033 0 0 1997 2312 12 48 100 100 100 100 15110 16000 .991 1.009 1.008 .981 1.021 2.502 52 260 1.013 .98 90 2110 7350 18 27 82 91 0 5578 59 5519 .734 5901 5842 1.362 .733 -.446 -.448
5 325 176 40 83 284 92 322 170 44 93 281 86 0 0 120 55 14 54 100 78 100 32 376 367 3.087 .324 .306 .272 .288 5.419 52 245 .257 .47 80 2270 7350 19 27 99 107 0 128 60 67 .236 124 63 4.245 .223 -2.086 -2.168
6 1805 2449 50 100 1755 2348 2166 2917 60 124 2115 2816 0 0 1028 1360 32 82 98 95 97 95 4103 4931 .747 1.338 1.331 1.352 1.345 2.674 80 432 1.328 .98 110 2420 7340 16 27 112 123 0 1781 73 1707 .973 2121 2048 1.028 .968 -.04 -.047
7 136 135 45 89 91 46 136 127 50 111 91 37 0 0 34 55 21 81 96 26 94 3 137 128 1.978 .505 .407 .61 .657 4.543 52 240 .961 .31 80 2560 7350 19 27 128 136 0 98 65 33 .368 92 27 2.72 .296 -1.444 -1.758
8 6204 9410 40 81 6164 9329 6489 10025 44 100 6449 9944 0 0 930 1791 15 85 100 100 100 100 15493 16393 .661 1.513 1.542 1.496 1.529 2.179 52 243 1.521 .99 80 2720 7350 19 27 144 152 0 6843 59 6784 1.101 7290 7231 .909 1.121 .138 .165
9 90 110 39 74 51 36 91 85 42 86 52 11 0 0 26 67 13 50 92 30 78 13 87 63 1.417 .706 .212 1.079 .914 8.174 52 223 1.977 .17 80 2880 7350 19 27 160 168 0 80 54 26 .513 62 8 1.948 .154 -.962 -2.701
10 88 100 38 74 49 26 90 100 43 89 51 26 0 0 19 36 14 54 100 21 81 0 75 77 1.885 .531 .51 .68 .744 4.788 32 181 1.278 .3 70 3020 7350 19 26 174 181 0 73 54 19 .386 73 19 2.592 .371 -1.374 -1.432
11 216 512 41 76 174 435 215 502 46 97 173 426 0 0 47 134 22 65 100 100 98 100 609 599 .4 2.5 2.462 2.494 2.512 2.938 52 286 2.606 .89 90 3170 7350 18 27 188 197 0 372 55 316 1.818 365 310 .55 1.791 .862 .841
12 175 445 43 76 131 368 170 428 47 90 126 352 0 0 46 136 15 54 100 100 96 98 499 478 .356 2.809 2.794 2.802 2.67 3.08 52 291 2.96 .9 90 3320 7350 18 27 203 212 0 324 55 268 2.043 311 256 .49 2.032 1.031 1.023
13 133 122 46 82 86 40 133 118 49 90 86 36 0 0 31 50 15 44 100 40 92 15 126 122 2.15 .465 .419 .449 .522 5.457 52 251 .66 .37 80 3470 7340 18 26 219 227 0 89 60 29 .338 86 26 2.957 .304 -1.564 -1.716
14 99 113 45 81 54 32 96 110 47 92 51 29 0 0 24 37 16 57 92 17 82 3 86 80 1.688 .593 .569 .655 .687 5.131 52 254 1.695 .28 90 3620 7340 17 26 233 242 0 82 59 23 .431 80 21 2.321 .414 -1.214 -1.274
15 55 71 40 81 15 -9 54 62 44 94 13 -18 0 0 16 39 15 60 42 3 8 1 6 -5 null null null 2.357 2.771 7.815 80 341 8.236 .3 100 3770 7340 17 27 248 258 -50 52 59 -7 null 45 -13 null null null null
16 259 452 40 86 219 366 270 451 43 101 230 364 0 0 81 104 12 107 98 100 94 88 585 594 .598 1.671 1.583 1.871 1.711 3.814 52 235 1.827 .78 80 3930 7350 19 27 265 273 0 329 63 266 1.215 328 265 .823 1.151 .281 .203
17 72 117 42 83 29 33 71 118 47 92 28 34 0 0 12 34 15 43 91 41 41 8 62 62 .879 1.138 1.214 1.615 1.752 6.128 12 104 5.712 .17 50 4060 7330 18 23 279 284 0 85 60 24 .828 86 25 1.208 .883 -.273 -.179
18 46 68 39 81 7 -12 45 62 42 90 5 -18 0 0 12 33 12 46 23 3 5 1 -5 -13 null null null 3.867 4.905 9.188 80 395 50.605 .06 100 4220 7330 16 26 293 303 -50 49 59 -9 null 45 -13 null null null null
19 151 212 39 79 112 132 150 194 43 101 110 114 0 0 36 74 17 103 100 59 100 11 244 224 .848 1.179 1.036 1.074 1.181 3.856 52 252 1.365 .66 80 4380 7340 18 26 310 318 0 154 57 96 .857 141 83 1.167 .754 -.223 -.408
20 850 5536 40 83 809 5452 879 5518 60 134 838 5434 0 0 130 804 131 251 100 100 100 100 6261 6272 .148 6.739 6.484 6.753 6.854 2.272 52 261 6.734 .94 90 4530 7340 17 26 324 333 0 4026 60 3965 4.901 4013 3952 .204 4.716 2.293 2.237

Total number of rows: 44544

Table truncated, full table size 9077 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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