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Sample GSM989679 Query DataSets for GSM989679
Status Public on Aug 23, 2012
Title PC 92T
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 92
Organism Homo sapiens
Characteristics ethnicity: Caucasian
age: 69
pre-operation treatment: None
individual: PC 233T
disease free survival: 15.40
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/2008-11/81784.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 11406 5370 53 101 11353 5269 11764 5451 54 115 11711 5349 0 0 2470 1145 15 69 100 100 100 100 16622 17060 2.155 .464 .457 .465 .446 1.734 52 358 .447 .94 90 1590 7490 24 33 22 31 0 5458 103 5355 .472 5540 5436 2.12 .464 -1.084 -1.107
2 11548 5249 53 104 11494 5145 11933 5280 57 120 11879 5176 0 0 2249 1021 16 83 100 100 100 100 16639 17055 2.234 .448 .436 .447 .425 1.688 52 253 .431 .95 80 1740 7490 25 33 38 46 0 5335 106 5229 .455 5366 5261 2.198 .443 -1.136 -1.175
3 4601 12356 50 97 4551 12258 5068 13112 53 105 5017 13014 0 0 1537 2557 12 50 100 100 100 100 16809 18031 .371 2.693 2.594 3.031 2.577 2.363 52 318 2.807 .95 90 1890 7480 23 32 52 61 0 12558 99 12458 2.737 13326 13227 .365 2.636 1.453 1.399
4 12334 5746 53 96 12281 5650 12570 5630 54 103 12517 5534 0 0 2559 967 13 43 100 100 100 100 17931 18051 2.174 .46 .442 .467 .427 1.815 52 270 .436 .94 90 2040 7490 24 33 67 76 0 5840 98 5742 .468 5722 5624 2.139 .449 -1.097 -1.154
5 259 139 59 110 199 28 259 133 62 120 200 23 0 0 53 51 19 57 100 34 100 3 227 223 7.107 .141 .115 .235 .261 2.983 52 202 .104 .11 80 2190 7490 25 33 83 91 0 141 112 28 .143 135 23 6.993 .117 -2.806 -3.097
6 1368 2102 61 116 1306 1986 1566 2290 69 132 1504 2174 0 0 751 919 26 70 100 97 98 97 3292 3678 .658 1.521 1.445 1.708 1.429 2.728 80 351 1.436 .93 100 2340 7490 24 34 97 107 0 2136 118 2018 1.546 2327 2210 .647 1.469 .628 .555
7 116 179 53 102 63 77 113 140 65 109 59 37 0 0 35 96 31 46 83 41 41 33 140 96 .818 1.222 .627 .936 1.267 7.315 12 100 3.29 .17 50 2520 7460 23 28 117 122 0 182 104 78 1.242 142 38 .805 .637 .313 -.65
8 4850 12692 51 105 4798 12586 5276 12899 53 117 5224 12793 0 0 1522 2125 13 60 100 100 100 100 17384 18017 .381 2.623 2.449 2.928 2.425 2.413 52 285 2.64 .94 90 2640 7480 23 32 127 136 0 12899 107 12792 2.666 13110 13002 .375 2.489 1.415 1.316
9 66 64 51 97 14 -33 59 52 52 109 8 -44 0 0 17 37 11 54 43 5 35 0 -19 -36 null null null 5.046 5.293 6.185 80 300 4.285 .13 100 2790 7480 23 33 142 152 -50 65 99 -34 null 53 -45 null null null null
10 67 81 53 97 14 -16 66 74 53 108 13 -23 0 0 19 37 13 56 48 3 35 1 -2 -10 null null null 2.019 2.343 6.044 80 301 -15.18 -.18 100 2940 7480 23 33 157 167 -50 82 99 -16 null 75 -23 null null null null
11 286 584 52 95 233 488 286 545 54 104 234 449 0 0 63 172 13 52 100 100 100 100 721 683 .477 2.094 1.919 2.068 1.948 1.955 52 284 2.415 .87 90 3100 7480 23 32 173 182 0 594 97 496 2.129 554 456 .47 1.95 1.09 .964
12 174 288 49 98 125 189 178 278 51 104 128 179 0 0 35 83 12 44 100 98 100 88 314 307 .661 1.512 1.398 1.42 1.469 2.382 52 227 1.95 .74 80 3250 7480 24 32 189 197 0 293 100 192 1.537 283 182 .651 1.421 .62 .507
13 113 97 52 95 60 2 119 98 56 105 66 3 0 0 33 37 19 56 84 9 81 0 62 69 30 .033 .045 .534 .599 4.606 32 145 -.084 -.03 60 3380 7480 25 31 203 209 0 99 97 2 .034 100 3 29.518 .046 -4.884 -4.436
14 74 125 50 92 24 33 74 118 53 98 24 26 0 0 21 43 13 46 62 31 46 15 57 50 .727 1.375 1.083 1.743 1.529 4.932 32 157 14.265 .09 60 3530 7480 25 31 218 224 0 127 94 34 1.397 120 26 .716 1.101 .483 .139
15 47 56 50 94 -2 -37 45 46 52 105 -5 -48 0 0 10 43 13 57 6 5 1 1 -39 -53 null null null 6.195 5.977 3.175 80 336 33.99 .15 100 3690 7480 23 33 232 242 -50 57 96 -38 null 47 -49 null null null null
16 246 624 48 105 197 518 255 639 50 116 206 533 0 0 64 164 12 54 100 100 100 98 715 739 .38 2.629 2.587 2.658 2.452 2.264 52 231 3.035 .84 90 3860 7480 23 32 249 258 0 634 107 526 2.672 649 542 .374 2.63 1.418 1.395
17 59 69 55 102 4 -33 56 63 57 111 0 -39 0 0 13 34 15 51 17 3 3 0 -29 -39 null null null 4.806 4.379 4.691 80 277 -1 -1 100 4000 7470 22 32 263 273 -50 70 104 -34 null 64 -40 null null null null
18 51 51 55 98 -4 -47 50 41 57 108 -5 -57 0 0 10 35 14 55 5 2 1 0 -51 -62 null null null 6.601 5.734 2.727 80 277 22.959 .15 100 4150 7470 22 32 278 288 -50 52 100 -48 null 42 -58 null null null null
19 121 132 57 105 64 26 119 127 59 113 61 21 0 0 43 49 13 48 86 28 75 11 90 82 2.462 .406 .344 .829 .954 4.749 52 231 .955 .26 80 4290 7480 24 32 293 301 0 134 107 26 .413 129 21 2.422 .35 -1.276 -1.515
20 908 4086 53 106 854 3979 969 4060 55 111 915 3953 0 0 257 611 13 46 100 100 100 100 4833 4868 .215 4.659 4.32 4.99 4.481 2.048 52 316 4.948 .93 90 4460 7470 22 31 309 318 0 4153 108 4044 4.735 4126 4018 .211 4.391 2.243 2.134

Total number of rows: 44544

Table truncated, full table size 9265 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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