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Sample GSM989764 Query DataSets for GSM989764
Status Public on Aug 23, 2012
Title PC 450N
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 450N2
Organism Homo sapiens
Characteristics individual: PC 450N
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/2008-08/81241.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 8134 7485 59 43 8075 7441 9502 8467 62 52 9443 8423 0 0 3194 2912 20 29 100 100 100 100 15516 17866 1.085 .921 .892 .895 .918 3.188 80 429 .901 .97 100 1810 6750 50 60 20 30 0 8474 49 8424 1.043 9586 9536 .959 1.01 .061 .014
2 18506 15417 77 53 18429 15363 18891 16172 85 61 18813 16118 0 0 2955 2949 32 34 100 100 100 100 33792 34931 1.2 .834 .857 .827 .869 2.45 52 263 .822 .96 90 1950 6750 50 59 34 43 0 17455 60 17393 .944 18309 18248 1.06 .97 -.083 -.044
3 27208 13249 73 55 27134 13194 28656 13846 87 116 28583 13791 0 0 9755 5463 71 314 100 100 100 98 40328 42374 2.057 .486 .482 .459 .482 3.035 80 343 .493 .97 110 2110 6760 50 61 49 60 0 15000 62 14938 .551 15676 15614 1.816 .546 -.861 -.872
4 11281 10621 65 53 11215 10567 12336 11107 70 65 12270 11053 0 0 3914 2721 24 39 100 100 100 100 21782 23323 1.061 .942 .901 1.085 .907 4.292 80 316 .885 .96 100 2250 6760 51 61 64 74 0 12025 60 11964 1.067 12575 12514 .937 1.02 .093 .028
5 534 162 79 62 455 100 560 139 90 72 481 77 0 0 167 88 52 46 96 67 95 46 555 558 4.55 .22 .16 .208 .229 4.798 80 308 .211 .62 100 2400 6760 51 61 79 89 0 183 70 113 .249 157 87 4.019 .181 -2.007 -2.464
6 3600 3133 110 62 3490 3070 3439 2830 120 72 3328 2768 0 0 1132 1221 55 42 100 100 100 100 6560 6096 1.137 .88 .832 .859 .863 2.552 80 310 .925 .96 110 2550 6750 49 60 93 104 0 3547 70 3476 .996 3204 3134 1.004 .942 -.006 -.087
7 173 110 101 64 72 46 149 100 113 72 47 36 0 0 81 78 49 40 48 40 26 17 118 83 1.565 .639 .766 .925 1.086 7.865 52 184 .418 .34 80 2690 6750 51 59 109 117 0 125 72 52 .723 113 41 1.382 .867 -.467 -.206
8 10976 5520 84 55 10892 5464 14289 6742 92 69 14205 6686 0 0 8582 4179 37 43 91 90 84 85 16356 20891 1.993 .502 .471 .687 .514 4.943 120 423 .479 .98 120 2840 6750 49 61 122 134 0 6250 62 6186 .568 7633 7570 1.761 .533 -.816 -.908
9 236 292 66 50 169 241 226 270 81 66 160 219 0 0 60 110 44 97 100 94 98 63 410 379 .701 1.426 1.369 1.342 1.349 3.685 52 228 1.274 .8 90 3000 6760 51 60 139 148 0 331 57 273 1.615 306 248 .619 1.55 .691 .632
10 182 343 54 45 127 298 186 344 57 58 131 299 0 0 43 130 20 80 97 91 96 87 425 430 .426 2.346 2.282 2.122 2.262 4.152 80 341 2.482 .8 110 3160 6750 49 60 154 165 0 388 51 337 2.657 389 339 .376 2.584 1.41 1.37
11 1327 1483 54 45 1273 1438 1360 1463 56 56 1306 1418 0 0 409 471 16 36 100 100 100 98 2711 2724 .885 1.13 1.086 1.142 1.082 3.242 80 264 1.086 .94 100 3310 6760 51 61 170 180 0 1679 51 1628 1.279 1656 1605 .782 1.229 .355 .298
12 703 2366 52 46 650 2320 737 2384 55 58 684 2337 0 0 193 792 17 36 98 100 98 100 2970 3021 .28 3.569 3.417 3.599 3.601 3.517 80 305 3.78 .93 110 3470 6760 50 61 185 196 0 2679 52 2627 4.041 2699 2646 .247 3.868 2.015 1.952
13 539 356 50 46 489 309 549 360 52 56 499 314 0 0 172 162 15 36 97 95 96 92 798 813 1.583 .632 .629 .599 .599 3.366 80 282 .621 .86 100 3620 6750 50 60 201 211 0 403 52 350 .715 408 356 1.398 .712 -.483 -.489
14 182 320 52 39 129 280 178 289 54 55 125 250 0 0 45 129 15 48 100 100 100 97 409 375 .461 2.171 2 2.098 1.927 3.914 80 321 2.411 .72 110 3760 6750 49 60 214 225 0 362 44 317 2.457 327 283 .407 2.264 1.297 1.179
15 54 53 52 40 1 13 51 42 56 55 -1 1 0 0 15 32 19 36 13 16 1 5 14 0 .077 13 null 1.39 1.525 7.455 120 447 .62 .12 120 3910 6750 49 61 229 241 -50 60 45 15 14.718 48 1 .068 null 3.88 null
16 2230 788 49 40 2181 747 2366 818 52 52 2317 778 0 0 686 295 15 29 100 98 100 98 2928 3095 2.92 .343 .336 .331 .346 3.072 80 281 .335 .94 110 4070 6750 49 60 245 256 0 892 45 846 .388 926 881 2.579 .38 -1.367 -1.395
17 118 333 49 45 69 288 115 333 50 53 65 288 0 0 30 126 15 29 96 100 91 97 357 353 .24 4.174 4.431 4.189 4.278 3.638 80 301 4.849 .75 110 4220 6750 49 60 260 271 0 377 51 326 4.726 377 326 .212 5.016 2.24 2.327
18 59 59 52 46 6 13 60 49 53 59 7 2 0 0 15 32 14 45 31 9 9 3 19 9 .462 2.167 .286 1.75 2.469 8.392 32 140 29.106 .06 70 4370 6770 53 60 277 284 0 67 52 15 2.453 55 2 .408 .323 1.295 -1.628
19 1093 541 52 43 1040 497 1036 519 55 58 984 475 0 0 259 190 18 55 100 97 100 97 1537 1459 2.093 .478 .483 .441 .48 3.493 80 332 .469 .88 110 4520 6740 48 59 290 301 0 613 49 563 .541 588 538 1.848 .547 -.886 -.872
20 3045 5507 52 48 2993 5459 3858 6838 54 58 3806 6790 0 0 1836 3213 17 36 94 95 90 92 8452 10596 .548 1.824 1.784 1.87 1.774 5.577 120 365 1.781 .96 120 4670 6740 48 60 305 317 0 6235 54 6181 2.065 7742 7687 .484 2.02 1.046 1.014

Total number of rows: 44544

Table truncated, full table size 9470 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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