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Sample GSM798945 Query DataSets for GSM798945
Status Public on Sep 19, 2012
Title Patient 12, 48 h, in vivo
Sample type RNA
 
Channel 1
Source name aCR (Stratagene)
Organism Homo sapiens
Characteristics reference: Stratagene Universal reference (derived from 11 different established human cell lines)
Extracted molecule total RNA
Extraction protocol not provided
Label Cy3
Label protocol not provided
 
Channel 2
Source name 05PB3789
Organism Homo sapiens
Characteristics cell type: acute myeloid leukemia peripheral blood
time: 48 h
individual: Patient 12
Extracted molecule total RNA
Extraction protocol Freshly frozen Ficoll-enriched mononuclear cells from peripheral blood samples (tumor cell content >85%), isolation of total RNA using Trizol reagent
Label Cy5
Label protocol For the cell line experiments and on patient sample experiment (ExpID 65407) 50 ug of total RNA from each untreated cell line and 50 ug of total RNA from each VPA treated cell line were differentially labeled with Cy5 and Cy3, respectively, using oligo-dT and random hexamer primers during a first strand reverse transcription reaction. For the other 14 matched patient samples 50 ug of total RNA from each sample (either collected at diagnosis or following treatment) and 50 ug of universal reference mRNA (derived from 11 different established human cell lines) were differentially labeled with Cy5 and Cy3, respectively, using oligo-dT and random hexamer primers during a first strand reverse transcription reaction
 
 
Hybridization protocol not provided
Scan protocol Arrays were then imaged using a GenePix 4000B scanner (Axon). Fluorescence ratios were extracted using SpotReader software, and the data uploaded into the Stanford Microarray Database (SMD) for storage, retrieval and analysis
Description Image: http://smd.stanford.edu/MicroArray/gifs/2005-11/65490.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 Sep 20, 2011
Last update date Sep 19, 2012
Contact name Jonathan Pollack
E-mail(s) [email protected]
Phone 650-736-1987
Organization name Stanford University
Department Pathology
Lab Pollack Lab
Street address 269 Campus Drive, CCSR3245A
City Stanford
State/province CA
ZIP/Postal code 94305-5176
Country USA
 
Platform ID GPL10108
Series (1)
GSE32240 In vitro and in vivo monitoring of valproic acid effects on gene expression signatures in adult acute myeloid leukemia

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
1 868 4540 184 314 684 4226 971 4998 188 324 787 4684 0 0 236 1899 39 79 100 100 100 100 4910 5471 .162 6.178 5.952 5.702 6.229 1.469 32 236 6.919 .94 70 2130 5980 50 57 29 36 0 5117 354 4763 6.964 5633 5279 .144 6.708 2.8 2.746
2 9119 958 191 313 8928 645 9817 969 200 319 9626 656 0 0 4029 313 53 70 100 96 100 90 9573 10282 13.842 .072 .068 .073 .073 1.607 32 176 .07 .92 60 2280 5980 51 57 45 51 0 1080 353 727 .081 1092 739 12.281 .077 -3.618 -3.703
3 12641 6773 186 325 12455 6448 13866 7105 189 327 13680 6780 0 0 5981 2780 38 72 100 100 100 100 18903 20460 1.932 .518 .496 .521 .523 1.305 32 176 .487 .96 60 2430 5980 51 57 60 66 0 7634 366 7267 .583 8008 7642 1.714 .559 -.777 -.84
4 2788 748 183 316 2605 432 3238 722 185 315 3055 406 0 0 1159 169 37 71 100 100 100 96 3037 3461 6.03 .166 .133 .185 .173 1.961 32 176 .157 .89 60 2570 5980 51 57 74 80 0 843 356 487 .187 814 458 5.35 .15 -2.42 -2.739
5 2646 578 175 317 2471 261 2950 559 179 321 2775 242 0 0 841 148 31 73 100 90 100 71 2732 3017 9.467 .106 .087 .093 .095 1.962 32 176 .103 .79 60 2710 5980 51 57 88 94 0 651 357 294 .119 630 273 8.4 .098 -3.07 -3.347
6 1062 439 185 315 877 124 1053 436 191 321 868 121 0 0 139 86 38 76 100 66 100 33 1001 989 7.073 .141 .139 .106 .135 2.731 12 104 .124 .49 50 2850 5970 50 55 102 107 0 495 355 140 .159 491 136 6.275 .157 -2.65 -2.67
7 4867 890 185 327 4682 563 4584 850 190 329 4399 523 0 0 748 206 38 72 100 100 100 100 5245 4922 8.316 .12 .119 .114 .113 1.358 12 104 .13 .86 50 3000 5970 50 55 117 122 0 1003 369 635 .136 958 589 7.378 .134 -2.883 -2.9
8 1678 375 178 315 1500 60 1825 370 179 317 1647 55 0 0 582 74 35 71 100 40 100 15 1560 1702 25 .04 .033 .04 .061 3.872 32 176 .043 .38 60 3150 5980 51 57 132 138 0 423 355 68 .045 417 62 22.181 .038 -4.471 -4.732
9 2083 415 175 316 1908 99 2221 401 179 317 2046 85 0 0 902 82 31 70 100 59 96 28 2007 2131 19.273 .052 .042 .061 .057 2.469 32 176 .048 .52 60 3300 5980 51 57 147 153 0 468 356 112 .058 452 96 17.1 .047 -4.096 -4.417
10 3426 2540 174 321 3252 2219 3600 2658 178 322 3426 2337 0 0 737 496 34 75 100 100 100 100 5471 5763 1.466 .682 .682 .688 .677 1.429 32 224 .66 .93 70 3440 5990 51 58 160 167 0 2863 362 2501 .769 2996 2634 1.3 .769 -.379 -.379
11 5919 558 193 307 5726 251 6277 514 200 311 6084 207 0 0 2307 158 51 70 100 93 100 68 5977 6291 22.813 .044 .034 .039 .043 1.951 32 176 .046 .85 60 3580 5980 51 57 175 181 0 629 346 283 .049 579 233 20.241 .038 -4.339 -4.705
12 8588 7248 179 299 8409 6949 10055 8777 186 310 9876 8478 0 0 6398 4940 43 74 100 100 100 100 15358 18354 1.21 .826 .858 .915 .873 2.171 52 312 .795 .96 80 3740 5980 50 58 190 198 0 8169 337 7832 .931 9892 9555 1.074 .968 -.103 -.048
13 1609 4188 176 308 1433 3880 1650 4145 177 314 1474 3837 0 0 566 1601 34 74 100 100 100 100 5313 5311 .369 2.708 2.603 2.752 2.755 1.696 32 170 2.947 .91 60 3880 5980 51 57 205 211 0 4720 347 4373 3.052 4672 4325 .328 2.934 1.61 1.553
14 819 1104 173 312 646 792 869 1155 177 325 696 843 0 0 167 316 38 95 100 96 100 96 1438 1539 .816 1.226 1.211 1.132 1.245 1.492 32 222 1.376 .92 70 4020 5990 51 58 218 225 0 1244 352 893 1.382 1302 950 .724 1.365 .467 .449
15 488 29335 172 320 316 29015 573 33300 179 329 401 32980 0 0 214 18065 73 89 76 100 67 100 29331 33381 .011 91.82 82.244 99.477 88.588 2.232 52 330 94.31 .93 90 4170 5990 50 59 232 241 0 33063 361 32702 103.488 37532 37171 .01 92.696 6.693 6.534
16 8515 12599 175 313 8340 12286 10781 14924 178 317 10606 14611 0 0 6468 9168 31 80 100 100 100 100 20626 25217 .679 1.473 1.378 1.567 1.49 1.734 80 400 1.469 .96 100 4320 5990 50 60 247 257 0 14200 353 13847 1.66 16821 16468 .602 1.553 .731 .635
17 3996 7434 179 326 3817 7108 4958 9073 181 326 4779 8747 0 0 2486 3692 34 81 100 100 100 100 10925 13526 .537 1.862 1.83 2.481 1.895 2.335 52 271 1.771 .95 80 4470 5990 51 59 263 271 0 8379 367 8011 2.099 10226 9859 .476 2.063 1.07 1.045
18 1505 362 181 322 1324 40 1518 347 185 322 1337 25 0 0 153 71 47 70 100 33 100 8 1364 1362 33.1 .03 .019 .051 .06 2.551 12 104 .031 .22 50 4600 5980 51 56 277 282 0 408 363 45 .034 391 28 29.368 .021 -4.876 -5.568
19 6055 4475 178 320 5877 4155 6158 4882 183 322 5980 4562 0 0 1912 1458 37 70 100 100 100 100 10032 10542 1.414 .707 .763 .683 .718 1.381 32 232 .684 .93 70 4750 5990 51 58 291 298 0 5044 361 4683 .797 5502 5142 1.255 .86 -.328 -.218
20 5650 4302 183 313 5467 3989 5692 3851 186 317 5509 3538 0 0 3260 2534 36 74 100 100 100 100 9456 9047 1.371 .73 .642 .716 .727 1.786 32 176 .728 .94 60 4900 5980 51 57 307 313 0 4849 353 4496 .822 4340 3988 1.216 .724 -.282 -.466

Total number of rows: 41472

Table truncated, full table size 9401 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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