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Sample GSM989797 Query DataSets for GSM989797
Status Public on Aug 23, 2012
Title PC 22N
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 22N2
Organism Homo sapiens
Characteristics individual: PC 22N
disease state: Normal
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/2008-09/81305.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 GPL15971
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 20089 30784 50 71 20039 30712 22949 32909 59 87 22899 32837 0 0 6973 6970 67 71 100 100 98 100 50751 55736 .652 1.533 1.434 1.868 1.469 3.233 80 365 1.468 .95 100 1760 6850 24 34 19 29 0 26705 62 26643 1.33 28548 28486 .752 1.244 .411 .315
2 19252 29803 57 81 19194 29722 24138 34709 64 97 24080 34628 0 0 9061 11406 32 67 98 100 97 100 48916 58708 .646 1.549 1.438 1.949 1.492 3.575 80 212 1.483 .95 100 1900 6850 24 34 33 43 0 25854 70 25784 1.343 30110 30040 .744 1.247 .426 .319
3 38665 49906 57 81 38607 49824 39788 50738 89 161 39730 50657 0 0 5710 5104 350 699 100 100 100 100 88431 90387 .775 1.291 1.275 1.31 1.271 1.724 80 294 1.273 .97 110 2050 6830 21 32 47 58 0 43293 70 43222 1.12 44015 43945 .893 1.106 .163 .145
4 19347 29722 50 83 19296 29638 23321 33475 77 143 23270 33391 0 0 8180 11155 312 623 97 99 96 98 48934 56661 .651 1.536 1.435 1.657 1.461 2.749 120 372 1.502 .96 120 2200 6830 21 33 62 74 0 25784 72 25711 1.332 29039 28967 .75 1.245 .414 .316
5 1134 696 50 77 1084 618 1130 709 65 95 1080 631 0 0 159 237 44 74 100 100 100 100 1702 1711 1.754 .57 .584 .53 .553 2.123 80 279 .569 .85 110 2350 6830 21 32 77 88 0 604 67 536 .495 615 547 2.022 .507 -1.016 -.98
6 14524 22644 61 93 14462 22551 17061 25998 93 118 16999 25905 0 0 6405 8899 73 91 100 100 98 100 37013 42904 .641 1.559 1.524 1.706 1.509 2.569 120 354 1.528 .97 120 2500 6830 21 33 92 104 0 19644 81 19563 1.353 22553 22473 .739 1.322 .436 .403
7 329 447 56 91 273 355 331 435 83 115 275 343 0 0 60 142 72 85 98 98 97 87 628 618 .769 1.3 1.247 1.222 1.267 2.258 80 266 1.526 .78 110 2650 6830 21 32 107 118 0 388 79 308 1.128 377 298 .886 1.082 .174 .114
8 32581 43984 49 74 32532 43910 39811 51205 54 89 39762 51131 0 0 14655 16956 20 64 100 100 100 100 76442 90893 .741 1.35 1.286 1.495 1.294 2.74 120 361 1.301 .97 120 2800 6830 21 33 122 134 0 38156 64 38092 1.171 44420 44356 .854 1.116 .228 .158
9 288 395 46 71 241 323 284 392 51 84 237 320 0 0 55 153 18 58 100 96 100 91 564 557 .746 1.34 1.35 1.182 1.362 2.566 80 291 1.638 .76 110 2950 6820 20 31 137 148 0 343 62 280 1.163 340 278 .86 1.171 .217 .228
10 338 631 44 71 293 559 341 632 46 84 296 560 0 0 66 173 11 57 100 100 100 100 852 856 .524 1.908 1.892 1.884 1.907 2.169 80 279 2.069 .86 110 3100 6830 21 32 152 163 0 547 62 485 1.655 548 486 .604 1.641 .727 .715
11 1583 2909 44 67 1539 2842 1715 3078 45 82 1671 3010 0 0 636 1066 11 54 98 99 98 99 4381 4681 .542 1.847 1.801 1.997 1.809 2.767 120 345 1.834 .94 120 3250 6830 21 33 167 179 0 2524 58 2465 1.602 2670 2611 .624 1.563 .68 .644
12 861 2990 41 68 820 2922 994 3045 43 80 953 2976 0 0 384 1274 10 49 99 98 96 97 3742 3929 .281 3.563 3.123 4.06 3.366 3.565 120 301 3.682 .93 120 3410 6830 21 33 183 195 0 2594 59 2535 3.091 2642 2582 .323 2.709 1.628 1.438
13 699 846 44 68 655 778 709 835 49 87 665 766 0 0 163 270 29 88 98 100 98 100 1433 1431 .842 1.188 1.152 1.193 1.145 2.448 80 295 1.178 .87 110 3550 6830 21 32 197 208 0 734 59 675 1.03 724 665 .97 .999 .043 -.001
14 170 295 48 75 122 220 140 220 62 115 91 144 0 0 123 220 63 159 53 46 46 31 342 235 .555 1.803 1.582 2.048 1.81 4.935 32 162 1.871 .81 60 3710 6800 21 27 216 222 0 256 65 191 1.564 191 125 .639 1.373 .646 .457
15 63 78 44 67 18 11 61 65 51 94 16 -1 0 0 16 48 43 111 6 4 0 0 29 15 1.636 .611 null 2.158 2.355 6.489 120 384 25.7 .1 120 3860 6810 19 31 228 240 -100 68 58 10 .53 56 -1 1.886 null -.916 null
16 3031 5226 46 70 2984 5156 3494 5786 48 83 3448 5715 0 0 1378 2155 12 54 99 99 96 99 8140 9163 .579 1.728 1.657 2.113 1.696 3.993 120 296 1.694 .96 120 4010 6830 21 33 243 255 0 4534 61 4473 1.499 5019 4958 .667 1.438 .584 .524
17 227 260 44 73 182 187 220 247 47 84 175 174 0 0 41 108 13 56 100 91 100 73 369 349 .973 1.027 .994 .871 .966 2.641 80 240 1.32 .69 110 4160 6820 20 31 258 269 0 226 63 162 .891 214 151 1.122 .863 -.166 -.213
18 61 67 45 77 16 -10 60 55 48 98 14 -22 0 0 12 45 21 160 30 0 3 0 6 -8 null null null 3.26 3.259 7.437 120 331 -1 -1 120 4310 6820 20 32 273 285 -100 58 67 -9 null 48 -19 null null null null
19 1353 2055 50 85 1303 1969 1322 2099 54 103 1272 2013 0 0 271 534 19 83 100 100 100 100 3272 3285 .662 1.511 1.583 1.487 1.484 1.79 80 297 1.523 .91 110 4460 6820 20 31 288 299 0 1783 74 1708 1.311 1821 1746 .763 1.373 .391 .457
20 4828 21985 48 89 4780 21895 4731 21284 55 129 4683 21194 0 0 483 2575 28 183 100 100 100 100 26675 25877 .218 4.581 4.526 4.573 4.533 1.519 80 281 4.735 .97 110 4610 6820 20 31 303 314 0 19072 77 18994 3.974 18464 18386 .252 3.926 1.99 1.973

Total number of rows: 44544

Table truncated, full table size 9650 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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