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Sample GSM989719 Query DataSets for GSM989719
Status Public on Aug 23, 2012
Title PC 538T
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 538T2
Organism Homo sapiens
Characteristics ethnicity: Caucasian
age: 63
pre-operation treatment: None
individual: PC 563T
disease free survival: 5.57
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/2008-08/81161.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 GPL15973
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 20806 13142 80 81 20725 13060 22043 14899 104 93 21962 14817 0 0 4333 4578 88 50 100 100 100 100 33785 36779 1.587 .63 .675 .553 .675 2.48 52 350 .645 .95 90 1830 7030 22 31 30 39 0 12847 79 12767 .616 14564 14484 1.623 .66 -.699 -.601
2 17336 12734 81 83 17254 12650 22498 15493 109 95 22416 15410 0 0 9527 5962 93 59 90 98 90 96 29904 37826 1.364 .733 .687 .917 .696 2.553 52 292 .668 .96 90 1970 7030 22 31 44 53 0 12448 81 12366 .717 15145 15064 1.395 .672 -.481 -.573
3 36412 42708 94 90 36317 42618 40133 49778 110 109 40038 49688 0 0 12095 16099 62 120 100 100 100 98 78935 89726 .852 1.174 1.241 1.032 1.224 2.028 52 239 1.198 .97 80 2130 7050 25 33 61 69 0 41749 88 41661 1.147 48660 48572 .872 1.213 .198 .279
4 20667 13664 88 95 20579 13568 22648 15085 101 109 22560 14990 0 0 6242 3970 42 61 100 100 100 100 34147 37550 1.517 .659 .664 .686 .675 1.65 52 333 .648 .96 90 2280 7020 21 30 75 84 0 13357 93 13263 .645 14746 14653 1.552 .65 -.634 -.623
5 1866 359 91 85 1775 273 1881 372 98 95 1790 286 0 0 232 110 30 40 100 93 100 90 2048 2076 6.502 .154 .16 .132 .163 2.423 32 211 .16 .89 70 2430 7010 21 28 91 98 0 351 83 267 .15 364 280 6.651 .156 -2.734 -2.679
6 13398 16473 134 123 13264 16350 15702 15309 168 148 15568 15185 0 0 10822 13873 153 96 99 100 99 99 29614 30753 .811 1.233 .975 1.15 1.275 2.187 120 471 1.26 .97 120 2580 7030 21 33 104 116 0 16103 120 15983 1.205 14965 14844 .83 .953 .269 -.069
7 343 159 106 101 237 58 373 153 132 115 266 52 0 0 136 50 170 73 71 36 25 1 295 318 4.086 .245 .195 .291 .286 3.196 52 263 .274 .7 90 2720 7020 21 30 119 128 -50 155 99 57 .239 150 51 4.18 .191 -2.064 -2.388
8 30232 35845 94 93 30138 35751 44841 55438 373 426 44747 55345 0 0 22428 27969 2456 2718 73 67 73 67 65889 100092 .843 1.186 1.237 .973 1.231 2.431 52 304 1.218 .99 90 2870 7020 21 30 134 143 0 35040 91 34948 1.16 54193 54102 .862 1.209 .214 .274
9 143 182 85 90 58 92 143 179 381 410 58 89 0 0 35 94 2555 2813 0 0 0 0 150 147 .63 1.586 1.534 1.552 2.029 3.448 52 281 .64 .66 90 3020 7020 21 30 149 158 -50 178 88 90 1.551 175 87 .645 1.5 .633 .585
10 153 393 77 83 76 309 157 409 82 94 80 326 0 0 32 93 29 52 92 100 78 98 385 406 .246 4.066 4.075 4.153 4.082 1.98 52 246 4.345 .69 80 3170 7030 23 31 165 173 0 384 81 302 3.974 400 319 .252 3.983 1.991 1.994
11 1549 1983 72 73 1477 1909 1579 2015 78 80 1507 1941 0 0 396 506 24 37 100 100 100 100 3386 3448 .774 1.292 1.288 1.292 1.359 1.646 52 243 1.296 .95 80 3330 7030 23 31 181 189 0 1938 71 1866 1.263 1970 1897 .791 1.259 .337 .332
12 543 3148 70 81 472 3066 579 3240 78 95 508 3159 0 0 162 794 30 69 100 100 96 100 3538 3667 .154 6.496 6.219 6.988 6.447 1.737 52 313 6.461 .94 90 3470 7020 21 30 194 203 0 3077 79 2997 6.35 3167 3088 .157 6.079 2.667 2.604
13 521 459 70 82 451 376 541 488 79 96 471 406 0 0 126 142 40 70 98 92 98 88 827 877 1.199 .834 .862 .794 .814 1.945 52 292 .903 .91 90 3630 7030 22 31 210 219 0 449 80 368 .815 477 397 1.227 .843 -.295 -.247
14 327 342 71 81 255 261 349 374 80 102 277 293 0 0 88 108 38 99 96 84 94 75 516 570 .977 1.024 1.058 .995 1.09 2.104 52 269 1.087 .88 80 3780 7010 21 29 226 234 0 334 79 255 1.001 366 286 .999 1.034 .001 .048
15 73 57 67 82 6 -25 69 48 73 91 1 -34 0 0 26 31 24 42 5 5 1 3 -19 -33 null null null 4.403 4.964 3.024 52 314 3.77 .46 90 3930 7010 20 29 240 249 -50 56 80 -24 null 47 -33 null null null null
16 6338 3409 72 82 6265 3327 6424 3477 80 93 6351 3395 0 0 910 897 32 48 100 100 100 100 9592 9746 1.883 .531 .535 .497 .557 2.002 52 286 .537 .95 90 4080 7020 21 30 255 264 0 3332 80 3252 .519 3399 3319 1.926 .523 -.946 -.936
17 104 227 69 79 35 148 107 229 75 91 38 150 0 0 21 64 30 43 59 94 13 86 183 188 .236 4.229 3.947 4.413 4.739 2.448 52 268 4.409 .47 80 4230 7010 21 29 271 279 0 222 77 145 4.134 224 147 .242 3.859 2.047 1.948
18 60 49 68 82 -8 -32 61 42 73 94 -6 -39 0 0 10 17 25 46 0 0 0 0 -40 -45 null null null 4.015 2.65 3.59 52 314 3.586 .34 90 4380 7010 20 29 285 294 -50 48 80 -31 null 41 -38 null null null null
19 1042 758 70 87 971 670 1143 830 80 101 1072 742 0 0 493 361 50 73 95 88 91 86 1641 1814 1.449 .69 .692 .689 .692 2.27 80 354 .695 .89 100 4540 7010 20 30 301 311 0 741 85 655 .675 811 725 1.483 .677 -.568 -.564
20 5187 9785 73 92 5113 9692 5473 10082 80 106 5399 9990 0 0 1145 1807 39 62 100 100 100 100 14805 15389 .528 1.896 1.85 1.923 1.892 1.508 52 214 1.896 .96 80 4680 7020 22 30 316 324 0 9565 90 9474 1.853 9856 9766 .54 1.809 .89 .855

Total number of rows: 44544

Table truncated, full table size 9518 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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