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Sample GSM989768 Query DataSets for GSM989768
Status Public on Aug 23, 2012
Title PC 233T
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 233
Organism Homo sapiens
Characteristics ethnicity: Caucasian
age: 62
pre-operation treatment: None
individual: PC 223T
disease free survival: 61.73
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/2008-11/81787.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
1 996 735 83 58 913 677 1136 769 102 66 1052 711 0 0 381 192 109 50 88 100 88 100 1590 1763 1.349 .742 .676 .882 .685 2.338 52 308 .677 .93 80 1660 7200 28 36 46 54 0 693 55 639 .7 726 671 1.429 .638 -.515 -.649
2 762 2584 79 63 682 2521 836 2850 82 65 757 2786 0 0 299 699 24 27 92 100 90 100 3203 3543 .271 3.696 3.68 5.066 3.649 3.109 52 308 3.6 .95 90 1810 7200 27 36 60 69 0 2438 59 2379 3.488 2689 2629 .287 3.472 1.802 1.796
3 1199 858 88 63 1110 795 1301 918 92 71 1212 855 0 0 346 299 33 40 100 98 100 96 1905 2067 1.396 .716 .705 .696 .759 1.692 52 233 .702 .92 80 1960 7190 27 35 76 84 0 810 59 750 .676 866 807 1.48 .666 -.565 -.587
4 110 57 90 70 20 -13 105 48 95 79 14 -21 0 0 44 27 31 40 33 6 17 0 7 -7 null null null .621 .87 4.153 80 281 .972 .1 100 2110 7190 26 36 90 100 -50 54 66 -12 null 45 -20 null null null null
5 486 1586 93 77 392 1509 476 1654 103 85 383 1577 0 0 110 400 61 45 100 100 98 100 1901 1960 .26 3.849 4.117 3.807 4.038 1.553 52 244 4.334 .88 90 2270 7190 26 35 106 115 0 1496 73 1424 3.632 1561 1488 .275 3.885 1.861 1.958
6 102 71 94 71 7 0 92 44 103 79 -1 -26 0 0 66 145 60 41 5 5 1 3 7 -27 null null null 2.402 1.925 3.741 80 298 6.591 .19 100 2420 7190 26 36 121 131 -50 67 67 0 null 42 -25 null null null null
7 1166 3454 99 82 1067 3372 1171 3765 104 84 1072 3682 0 0 282 946 32 37 100 100 100 100 4439 4754 .316 3.16 3.435 3.134 3.191 1.423 52 160 3.311 .95 80 2570 7190 27 35 137 145 0 3259 77 3181 2.982 3552 3474 .335 3.241 1.576 1.696
8 86 47 101 76 -14 -28 82 39 113 87 -18 -36 0 0 26 26 75 49 0 1 0 0 -42 -54 null null null 1.36 1.296 2.815 80 307 .378 .46 100 2710 7190 26 36 150 160 -50 44 72 -26 null 37 -34 null null null null
9 100 57 107 84 -6 -27 98 50 123 96 -8 -33 0 0 39 32 89 54 2 1 1 1 -33 -41 null null null 1.412 1.488 3.707 80 262 .615 .26 100 2870 7190 26 36 166 176 -50 54 79 -25 null 47 -31 null null null null
10 127 171 109 87 17 83 113 178 122 97 3 90 0 0 54 50 59 50 15 76 7 40 100 93 .205 4.882 30 2.51 2.988 4.537 52 233 1.248 .3 80 3020 7200 28 36 182 190 0 161 82 78 4.606 168 85 .217 28.305 2.204 4.823
11 184 280 132 113 52 166 145 195 146 124 12 82 0 0 213 372 65 58 15 65 9 34 218 94 .313 3.192 6.833 2.314 1.843 2.699 32 182 1.927 .81 70 3190 7190 27 34 199 206 0 264 107 157 3.012 184 77 .332 6.447 1.591 2.689
12 271 263 156 104 114 158 262 216 169 123 106 112 0 0 85 220 76 74 58 58 41 33 272 218 .722 1.386 1.057 .894 .967 2.718 12 58 2.319 .62 40 3360 7160 26 30 218 222 0 248 98 149 1.308 204 106 .765 .997 .387 -.004
13 116 98 128 98 -11 0 108 84 152 118 -20 -14 0 0 49 61 117 78 3 7 0 1 -11 -34 null null null .975 .926 2.553 80 358 1.031 .57 100 3470 7180 25 35 226 236 -50 92 92 0 null 79 -13 null null null null
14 90 51 101 79 -10 -27 86 44 109 86 -14 -34 0 0 32 30 46 51 3 2 1 1 -37 -48 null null null 1.512 1.481 3.087 80 363 1.362 .29 100 3620 7180 25 35 241 251 -50 48 75 -25 null 42 -32 null null null null
15 202 374 95 71 107 303 205 390 104 80 109 319 0 0 63 141 38 40 86 92 69 92 410 428 .353 2.832 2.927 2.926 2.646 2.51 52 191 3.336 .67 80 3780 7180 26 34 258 266 0 353 67 286 2.672 368 301 .374 2.761 1.418 1.465
16 102 63 100 74 1 -11 101 58 110 83 0 -16 0 0 30 24 78 38 0 3 0 1 -10 -16 null null null 1.023 .889 3.323 80 270 .103 .25 100 3920 7180 25 35 271 281 -50 59 70 -10 null 55 -15 null null null null
17 88 44 100 71 -11 -26 84 37 106 76 -15 -33 0 0 31 24 36 33 7 2 1 0 -37 -48 null null null 1.162 1.083 3.017 80 263 .695 .25 100 4080 7180 25 35 287 297 -50 42 67 -25 null 35 -31 null null null null
18 98 71 98 66 0 5 91 67 107 72 -6 1 0 0 30 25 47 30 8 20 0 0 5 -5 null null null .749 .818 4.014 80 311 .737 .1 100 4230 7180 25 35 302 312 -50 67 62 5 null 63 1 null null null null
19 238 1408 97 69 141 1338 222 1469 104 76 125 1400 0 0 83 330 49 34 86 100 69 100 1479 1525 .105 9.489 11.2 10.823 9.331 1.997 52 243 10.144 .76 80 4390 7180 26 34 319 327 0 1328 65 1262 8.953 1386 1321 .112 10.567 3.162 3.402
20 79 42 99 70 -19 -27 77 35 104 76 -21 -34 0 0 22 29 32 34 2 2 0 1 -46 -55 null null null 1.126 1.234 2.954 80 321 1.117 .25 100 4540 7180 25 35 333 343 -50 40 66 -25 null 33 -32 null null null null

Total number of rows: 44544

Table truncated, full table size 9348 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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