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Sample GSM989770 Query DataSets for GSM989770
Status Public on Aug 23, 2012
Title PC 645N
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 645N2
Organism Homo sapiens
Characteristics individual: PC 645N
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/2008-08/81081.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) [email protected]
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 9784 14541 86 84 9698 14456 3921 6887 109 105 3834 6802 0 0 10170 15713 71 76 100 98 96 94 24154 10636 .671 1.491 1.774 1.34 1.312 2.995 52 330 1.57 .94 80 1770 6800 44 52 33 41 0 12986 75 12910 1.331 6151 6075 .751 1.584 .413 .664
2 11315 17588 121 123 11193 17464 9416 11115 149 137 9294 10991 0 0 10204 15722 81 78 96 100 90 100 28657 20285 .641 1.56 1.183 2.154 1.692 2.914 32 229 1.633 .9 70 1920 6820 46 53 48 55 0 15707 110 15597 1.393 9926 9816 .718 1.056 .479 .079
3 4672 5845 137 107 4534 5738 4662 5053 145 116 4525 4946 0 0 3762 5058 58 60 87 100 84 100 10272 9471 .79 1.266 1.093 1.521 1.293 3.168 32 167 1.335 .94 60 2070 6810 46 52 64 70 0 5220 96 5124 1.13 4513 4417 .885 .976 .177 -.035
4 10396 14978 98 85 10297 14892 3769 2727 119 106 3671 2642 0 0 11865 17558 64 73 98 98 98 96 25189 6313 .691 1.446 .72 1.224 1.225 2.519 52 293 1.503 .95 90 2230 6800 43 52 78 87 0 13376 76 13300 1.292 2435 2359 .774 .643 .369 -.638
5 360 160 89 74 271 85 169 133 102 91 79 59 0 0 309 99 49 62 59 50 48 32 356 138 3.188 .314 .747 .547 .381 4.141 52 284 .292 .57 90 2380 6800 43 52 93 102 0 143 66 76 .28 119 53 3.57 .667 -1.836 -.584
6 4033 7616 91 75 3942 7541 4468 8643 99 89 4376 8568 0 0 1479 3237 35 55 100 100 100 100 11483 12944 .523 1.913 1.958 1.858 2.028 1.813 32 174 2.06 .93 60 2530 6800 45 51 110 116 0 6802 67 6735 1.708 7719 7652 .585 1.749 .773 .806
7 246 147 69 67 177 80 255 132 75 94 185 65 0 0 103 71 27 123 84 28 84 0 257 250 2.213 .452 .351 .55 .593 2.916 32 176 .546 .45 60 2680 6810 46 52 125 131 0 131 60 71 .404 118 58 2.477 .314 -1.309 -1.672
8 6095 7193 76 64 6018 7128 6500 7642 85 93 6424 7577 0 0 3842 4957 47 134 100 100 93 100 13146 14001 .844 1.184 1.179 1.309 1.253 3.148 32 176 1.243 .94 60 2830 6810 46 52 140 146 0 6424 57 6366 1.058 6825 6767 .945 1.053 .081 .075
9 160 190 72 59 88 130 159 176 77 73 87 117 0 0 33 75 28 55 91 91 91 58 218 204 .677 1.477 1.345 1.422 1.337 1.947 12 104 2.193 .5 50 2980 6800 45 50 155 160 0 170 53 116 1.319 157 104 .758 1.201 .4 .264
10 120 191 67 50 53 140 119 193 70 61 52 142 0 0 27 83 23 33 84 90 62 81 193 194 .379 2.642 2.731 2.672 2.782 1.754 32 169 3.17 .73 60 3140 6800 45 51 171 177 0 171 45 125 2.359 172 127 .424 2.439 1.238 1.286
11 273 438 63 56 210 381 288 414 69 62 225 358 0 0 55 98 17 33 100 100 100 100 591 583 .551 1.814 1.591 1.84 2.027 1.386 12 104 2.145 .8 50 3280 6810 46 51 185 190 0 391 50 340 1.62 370 320 .617 1.421 .696 .507
12 262 565 65 51 196 513 287 587 70 62 222 535 0 0 112 225 25 43 90 100 81 96 709 757 .382 2.617 2.41 2.896 2.733 1.609 32 176 2.579 .92 60 3440 6800 45 51 201 207 0 505 46 458 2.337 524 478 .428 2.152 1.225 1.106
13 209 164 65 57 143 107 199 164 69 70 134 107 0 0 47 67 23 52 100 78 96 50 250 241 1.336 .748 .799 .563 .714 3.09 32 171 1.012 .63 60 3590 6810 46 52 216 222 0 146 51 96 .668 146 96 1.496 .713 -.582 -.488
14 124 88 64 57 60 31 113 77 67 72 49 19 0 0 108 56 18 66 63 23 55 3 91 68 1.935 .517 .388 .945 1.014 3.316 52 306 1.406 .34 90 3730 6800 43 52 228 237 -50 79 51 28 .461 69 17 2.167 .346 -1.116 -1.53
15 91 56 65 60 25 -3 95 50 72 77 29 -9 0 0 25 27 27 77 51 0 9 0 22 20 null null null .774 .889 3.664 52 321 20.605 .37 90 3880 6800 43 52 243 252 -50 50 54 -3 null 45 -8 null null null null
16 565 500 68 63 496 437 654 571 72 80 586 508 0 0 263 234 23 83 96 93 90 78 933 1094 1.135 .881 .867 .967 .924 2.447 32 174 .893 .9 60 4040 6800 45 51 261 267 0 447 56 390 .787 510 454 1.271 .774 -.346 -.369
17 126 115 65 56 60 58 122 112 69 60 57 55 0 0 23 41 23 39 100 66 75 41 118 112 1.034 .967 .965 1.07 1.474 2.021 12 68 5.875 .24 40 4190 6800 46 50 277 281 0 103 50 52 .863 100 49 1.158 .862 -.212 -.215
18 76 60 67 62 9 -1 75 45 195 184 8 -16 0 0 20 38 1321 1029 0 0 0 0 8 -8 null null null 1.862 1.707 2.492 52 345 3.946 .4 90 4340 6800 43 52 289 298 -50 54 55 -1 null 40 -14 null null null null
19 210 191 63 63 146 127 198 204 71 77 135 141 0 0 58 71 26 74 100 75 96 43 273 276 1.15 .87 1.044 .857 1.007 1.902 32 176 1.112 .66 60 4500 6800 45 51 307 313 0 171 56 113 .777 182 126 1.287 .933 -.364 -.1
20 1540 4833 65 55 1475 4777 1673 5693 69 65 1607 5637 0 0 963 3169 20 38 100 87 100 87 6252 7244 .309 3.239 3.508 2.253 3.142 4.052 32 174 3.412 .95 60 4650 6800 45 51 322 328 0 4316 49 4266 2.892 5084 5034 .346 3.133 1.532 1.647

Total number of rows: 44544

Table truncated, full table size 9130 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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