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Sample GSM798928 Query DataSets for GSM798928
Status Public on Sep 19, 2012
Title Patient 9, 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 05PB3925
Organism Homo sapiens
Characteristics cell type: acute myeloid leukemia peripheral blood
time: 48 h
individual: Patient 9
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/2005-11/65500.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 1237 1000 291 520 946 480 1307 970 293 511 1016 450 0 0 140 253 60 109 100 91 100 83 1426 1466 1.971 .507 .443 .437 .461 1.734 12 104 .628 .82 50 1980 6430 52 57 47 52 0 1167 607 560 .592 1132 525 1.688 .517 -.756 -.952
2 11417 695 287 488 11130 207 13422 696 293 500 13135 208 0 0 6430 145 66 107 100 68 100 50 11337 13343 53.768 .019 .016 .022 .02 2.14 32 176 .018 .69 60 2130 6440 53 59 62 68 0 811 570 242 .022 812 243 46.061 .018 -5.525 -5.757
3 13087 3995 279 491 12808 3504 12997 4346 282 494 12718 3855 0 0 8190 1960 53 94 100 100 100 100 16312 16573 3.655 .274 .303 .332 .266 2.492 32 176 .25 .94 60 2290 6420 51 57 78 84 0 4663 573 4090 .319 5073 4500 3.131 .354 -1.647 -1.499
4 3447 493 265 482 3182 11 3922 486 270 489 3657 4 0 0 1506 103 53 97 100 18 100 3 3193 3661 289.273 .003 .001 .019 .018 6.43 32 176 -1 -1 60 2430 6440 53 59 92 98 0 575 563 13 .004 567 5 247.81 .001 -7.953 -9.613
5 3387 396 271 481 3116 -85 3445 353 279 479 3174 -128 0 0 422 123 60 95 100 8 100 8 3031 3046 null null null .05 .066 2.998 12 104 -.034 -.37 50 2560 6420 51 56 105 110 0 462 561 -99 null 412 -149 null null null null
6 1231 552 280 490 951 62 1249 592 283 495 969 102 0 0 237 98 47 103 100 50 100 0 1013 1071 15.339 .065 .105 .097 .128 2.821 12 104 .099 .33 50 2710 6440 53 58 120 125 0 644 572 72 .076 691 119 13.14 .123 -3.716 -3.025
7 4620 1112 273 496 4347 616 5341 1200 281 495 5068 704 0 0 1552 284 59 106 100 91 100 83 4963 5772 7.057 .142 .139 .123 .141 1.541 12 104 .152 .87 50 2860 6420 51 56 135 140 0 1298 579 719 .165 1401 822 6.045 .162 -2.596 -2.625
8 2113 467 282 459 1831 8 2152 472 291 456 1870 13 0 0 331 85 67 82 100 16 100 8 1839 1883 228.875 .004 .007 .032 .021 2.151 12 104 .015 .13 50 3000 6410 50 55 149 154 0 545 536 9 .005 551 15 196.069 .008 -7.615 -6.945
9 1725 9532 267 469 1458 9063 2031 11083 270 469 1764 10614 0 0 914 4825 47 95 90 100 87 100 10521 12378 .161 6.216 6.017 7.342 6.156 1.887 32 176 6.286 .94 60 3160 6420 51 57 165 171 0 11127 547 10579 7.256 12937 12390 .138 7.024 2.859 2.812
10 4190 2526 265 442 3925 2084 4927 2460 270 453 4662 2018 0 0 1983 1277 46 92 100 96 100 96 6009 6680 1.883 .531 .433 .506 .546 2.251 32 176 .537 .92 60 3300 6430 52 58 179 185 0 2949 516 2433 .62 2872 2356 1.613 .505 -.69 -.985
11 4270 1487 264 446 4006 1041 4209 1441 278 455 3945 995 0 0 2095 540 99 100 100 100 100 96 5047 4940 3.848 .26 .252 .269 .279 1.959 32 159 .234 .89 60 3470 6460 55 61 196 202 0 1736 521 1215 .303 1682 1161 3.297 .294 -1.721 -1.764
12 11091 7349 262 438 10829 6911 8880 6116 277 450 8618 5678 0 0 7961 5262 99 115 96 100 96 100 17740 14296 1.567 .638 .659 .641 .637 2.304 32 170 .635 .95 60 3590 6420 51 57 208 214 0 8579 511 8067 .745 7139 6628 1.342 .769 -.425 -.379
13 2441 3551 251 424 2190 3127 2379 3622 254 432 2128 3198 0 0 343 516 48 103 100 100 100 100 5317 5326 .7 1.428 1.503 1.424 1.36 1.206 12 104 1.547 .91 50 3740 6440 53 58 223 228 0 4145 495 3650 1.667 4228 3733 .6 1.754 .737 .811
14 1046 828 256 422 790 406 1085 748 257 428 829 326 0 0 365 383 46 90 100 75 96 59 1196 1155 1.946 .514 .393 .45 .528 2.427 32 176 .432 .66 60 3880 6440 53 59 237 243 0 967 493 474 .6 873 381 1.667 .459 -.737 -1.123
15 556 10683 247 453 309 10230 493 8014 250 450 246 7561 0 0 218 7135 47 105 96 100 84 100 10539 7807 .03 33.107 30.736 30.242 33.852 1.835 32 176 36.086 .9 60 4030 6440 53 59 252 258 0 12470 529 11942 38.646 9355 8826 .026 35.878 5.272 5.165
16 8740 15391 252 424 8488 14967 8232 11842 258 442 7980 11418 0 0 5921 10750 55 110 100 100 100 100 23455 19398 .567 1.763 1.431 1.777 1.78 1.835 32 232 1.826 .96 70 4180 6440 52 59 266 273 0 17966 495 17471 2.058 13823 13328 .486 1.67 1.041 .74
17 5609 11012 260 462 5349 10550 6269 12334 266 479 6009 11872 0 0 2405 4625 49 118 100 100 100 100 15899 17881 .507 1.972 1.976 1.799 1.814 1.817 32 176 2.02 .94 60 4320 6430 52 58 281 287 0 12854 539 12315 2.302 14398 13858 .434 2.306 1.203 1.206
18 1712 583 251 432 1461 151 1694 553 255 435 1443 121 0 0 294 134 51 89 100 58 100 33 1612 1564 9.675 .103 .084 .066 .084 2.861 12 104 .095 .51 50 4460 6420 51 56 295 300 0 681 504 176 .121 646 141 8.289 .098 -3.051 -3.353
19 3000 2517 264 430 2736 2087 1521 1647 266 441 1257 1217 0 0 2738 2135 56 107 96 84 96 81 4823 2474 1.311 .763 .968 .804 .789 2.55 32 176 .761 .95 60 4610 6430 52 58 310 316 0 2938 502 2436 .89 1923 1421 1.123 1.13 -.167 .177
20 8275 5388 270 411 8005 4977 8222 5752 275 428 7952 5341 0 0 2757 2291 56 103 100 100 100 100 12982 13293 1.608 .622 .672 .586 .64 1.515 12 68 .66 .91 40 4760 6430 53 57 326 330 0 6289 480 5810 .726 6714 6235 1.378 .784 -.462 -.351

Total number of rows: 41472

Table truncated, full table size 9523 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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