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Sample GSM989677 Query DataSets for GSM989677
Status Public on Aug 23, 2012
Title PC 547T
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 547T2
Organism Homo sapiens
Characteristics ethnicity: Caucasian
age: 50
pre-operation treatment: None
individual: PC 593T
disease free survival: 8.83
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/2008-08/81204.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 28107 9518 49 46 28058 9472 28318 10865 76 57 28269 10818 0 0 2538 4188 206 85 100 90 100 90 37530 39087 2.962 .338 .383 .221 .395 9.737 52 238 .337 .86 90 1780 7160 15 24 1 10 0 9637 47 9590 .342 11001 10953 2.926 .387 -1.549 -1.368
2 22278 8268 49 45 22229 8223 27072 10856 70 53 27023 10811 0 0 9804 5117 184 78 100 90 100 90 30452 37834 2.703 .37 .4 .298 .413 8.98 80 292 .36 .87 100 1940 7170 16 26 17 27 0 8371 46 8326 .375 10992 10946 2.67 .405 -1.417 -1.304
3 25317 24459 46 42 25271 24417 29292 29754 49 46 29246 29712 0 0 9424 11324 15 19 100 100 100 100 49688 58958 1.035 .966 1.016 .751 1.051 8.637 80 261 .937 .89 100 2100 7160 15 25 33 43 0 24765 43 24722 .978 30126 30083 1.022 1.029 -.032 .041
4 25798 9780 45 39 25753 9740 27997 11576 51 45 27952 11536 0 0 9565 5372 31 22 100 92 100 91 35493 39488 2.644 .378 .413 .231 .385 11.97 80 243 .364 .86 100 2230 7150 14 24 46 56 0 9902 39 9862 .383 11721 11680 2.611 .418 -1.385 -1.259
5 1376 502 44 43 1332 458 1487 582 51 46 1443 539 0 0 409 237 32 22 100 90 98 85 1790 1982 2.908 .344 .374 .248 .356 6.873 80 246 .337 .87 100 2390 7150 14 24 62 72 0 508 44 464 .348 589 546 2.872 .378 -1.522 -1.403
6 13073 8581 49 42 13024 8538 12900 9353 58 47 12851 9311 0 0 1978 2814 41 33 100 98 100 98 21562 22162 1.525 .656 .725 .557 .69 5.242 80 228 .643 .88 110 2530 7160 14 25 75 86 0 8688 43 8645 .664 9470 9427 1.507 .734 -.591 -.447
7 284 185 45 42 239 143 347 143 52 46 301 101 0 0 202 143 36 29 65 64 61 57 382 402 1.671 .598 .336 .585 .654 6.855 120 327 .571 .83 120 2680 7150 13 25 90 102 0 187 43 145 .606 145 102 1.651 .34 -.723 -1.557
8 24663 22969 44 43 24618 22925 28141 28628 69 60 28096 28584 0 0 9351 11836 214 128 97 92 96 92 47543 56680 1.074 .931 1.017 .606 .984 14.676 80 217 .919 .86 100 2830 7150 14 24 106 116 0 23256 44 23212 .943 28986 28941 1.061 1.03 -.085 .043
9 266 289 41 39 224 250 321 322 58 53 279 282 0 0 157 205 172 104 62 62 25 58 474 561 .896 1.116 1.011 .921 1.161 6.56 120 338 .793 .84 120 2990 7150 13 25 121 133 0 293 39 253 1.13 326 286 .885 1.023 .176 .033
10 186 175 39 39 147 136 218 194 41 42 179 154 0 0 105 115 11 15 83 69 78 65 283 333 1.081 .925 .86 1.044 1.033 5.362 120 316 .9 .83 120 3140 7150 13 25 136 148 0 177 39 138 .937 196 156 1.068 .871 -.094 -.199
11 1678 1466 40 38 1638 1428 1801 1666 43 42 1761 1628 0 0 541 676 11 15 100 95 98 91 3066 3389 1.147 .872 .924 .776 .909 7.895 80 258 .836 .84 100 3290 7150 14 24 152 162 0 1484 38 1446 .883 1687 1648 1.133 .936 -.18 -.095
12 1126 1187 41 39 1084 1148 1208 1307 44 43 1167 1268 0 0 354 446 21 16 98 98 97 95 2232 2435 .944 1.059 1.087 1.014 1.078 6.717 80 279 1.017 .88 100 3450 7150 14 24 168 178 0 1202 39 1162 1.072 1323 1284 .933 1.1 .101 .138
13 735 433 41 38 693 395 754 467 43 45 712 429 0 0 209 185 11 21 100 91 98 91 1088 1141 1.754 .57 .603 .532 .579 5.671 80 307 .533 .85 110 3600 7150 13 24 182 193 0 438 38 400 .577 473 434 1.733 .61 -.793 -.713
14 321 529 43 39 277 489 321 557 44 47 278 517 0 0 51 170 12 26 100 94 100 92 766 795 .566 1.765 1.86 1.407 1.748 6.013 52 245 1.775 .81 90 3750 7140 13 22 198 207 0 536 39 495 1.787 564 523 .559 1.883 .838 .913
15 110 140 41 39 68 101 108 140 44 45 67 101 0 0 24 56 13 21 100 90 98 84 169 168 .673 1.485 1.507 1.374 1.531 4.782 52 208 1.427 .56 80 3900 7140 14 22 214 222 -100 142 39 102 1.504 142 102 .665 1.526 .589 .61
16 2436 2425 39 40 2397 2384 2697 2702 43 46 2658 2661 0 0 857 855 18 19 98 100 97 100 4781 5319 1.005 .995 1.001 1.001 1.02 6.553 80 225 .902 .85 100 4060 7150 14 24 229 239 0 2455 41 2414 1.007 2736 2694 .993 1.014 .01 .02
17 170 367 40 38 130 329 195 451 41 40 154 413 0 0 88 246 10 14 80 80 77 74 459 567 .395 2.531 2.682 2.309 2.738 6.294 120 410 2.787 .83 120 4200 7140 12 24 242 254 -100 372 38 333 2.562 457 418 .39 2.715 1.357 1.441
18 112 161 40 39 72 122 111 152 41 42 71 112 0 0 39 81 9 14 100 92 94 84 194 183 .59 1.694 1.577 1.379 1.971 6.779 52 238 1.725 .69 90 4350 7140 13 22 258 267 -100 163 39 124 1.716 154 113 .583 1.597 .779 .676
19 1259 1337 39 39 1219 1297 1310 1441 42 43 1270 1401 0 0 323 498 11 15 100 96 98 95 2516 2671 .94 1.064 1.103 .936 1.128 6.927 80 290 1.047 .88 110 4500 7150 13 24 272 283 0 1354 39 1313 1.077 1459 1419 .928 1.117 .107 .16
20 6414 10711 43 39 6371 10672 6509 11901 45 43 6465 11861 0 0 1313 3436 12 19 100 100 100 100 17043 18326 .597 1.675 1.835 1.493 1.807 4.687 80 314 1.736 .9 110 4650 7150 13 24 287 298 0 10845 39 10805 1.696 12050 12009 .59 1.858 .762 .893

Total number of rows: 44544

Table truncated, full table size 9465 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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