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Sample GSM798938 Query DataSets for GSM798938
Status Public on Sep 19, 2012
Title Patient 5, 0 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 05PB2260
Organism Homo sapiens
Characteristics cell type: acute myeloid leukemia peripheral blood
time: 0 h
individual: Patient 5
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/2005-11/65503.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
1 651 4772 230 360 421 4412 647 4815 229 370 417 4455 0 0 75 964 44 84 100 100 100 100 4833 4872 .095 10.48 10.683 10.405 10.488 1.243 12 104 11.721 .89 50 2060 6030 40 45 71 76 0 5060 382 4678 11.113 5106 4724 .09 11.329 3.474 3.502
2 6427 1037 229 340 6198 697 6601 1159 236 342 6372 819 0 0 3174 509 50 69 100 81 100 75 6895 7191 8.892 .112 .129 .089 .115 2.15 32 176 .116 .91 60 2200 6040 41 47 85 91 0 1100 361 739 .119 1229 868 8.386 .136 -3.068 -2.875
3 7571 4076 219 329 7352 3747 7880 4566 228 336 7661 4237 0 0 3601 2277 49 68 100 90 100 84 11099 11898 1.962 .51 .553 .338 .495 3.072 32 176 .53 .94 60 2350 6030 40 46 100 106 0 4322 349 3973 .54 4842 4493 1.85 .586 -.888 -.77
4 2887 628 213 328 2674 300 2919 687 217 335 2706 359 0 0 507 166 36 65 100 91 100 83 2974 3065 8.913 .112 .133 .107 .128 1.604 12 104 .118 .8 50 2490 6030 40 45 114 119 0 666 348 318 .119 728 381 8.406 .141 -3.071 -2.83
5 1221 328 210 323 1011 5 1383 315 209 330 1173 -8 0 0 449 77 34 66 100 21 100 6 1016 1165 202.2 .005 null .047 .048 2.635 32 176 .022 .15 60 2640 6040 41 47 129 135 0 348 343 5 .005 334 -8 190.685 null -7.575 null
6 693 302 214 342 479 -40 702 319 215 340 488 -23 0 0 60 72 34 60 100 8 100 0 439 465 null null null .04 .093 7.601 12 68 -.07 -.19 40 2780 6030 41 45 144 148 0 320 363 -42 null 338 -24 null null null null
7 2617 1665 205 310 2412 1355 2970 1764 224 321 2765 1454 0 0 915 274 167 74 100 100 100 100 3767 4219 1.78 .562 .526 .616 .526 1.585 12 104 .466 .9 50 2930 6020 39 44 158 163 0 1766 329 1437 .596 1871 1542 1.679 .558 -.747 -.843
8 1143 263 199 307 944 -44 1232 264 210 315 1033 -43 0 0 234 69 48 67 100 0 100 0 900 990 null null null .038 .036 1.648 12 104 -.07 -.44 50 3070 6030 40 45 172 177 0 279 326 -47 null 280 -46 null null null null
9 1366 741 205 321 1161 420 1451 772 227 321 1246 451 0 0 358 133 136 75 100 100 100 91 1581 1697 2.764 .362 .362 .357 .409 1.793 12 104 .365 .84 50 3220 6020 39 44 187 192 0 786 340 445 .384 819 478 2.607 .384 -1.382 -1.382
10 2416 1349 196 311 2220 1038 2580 1434 198 318 2384 1123 0 0 602 318 35 72 100 100 100 100 3258 3507 2.139 .468 .471 .462 .484 1.565 32 176 .449 .92 60 3370 6040 41 47 202 208 0 1430 330 1101 .496 1521 1191 2.017 .5 -1.012 -1.001
11 4090 592 204 300 3886 292 4429 595 212 303 4225 295 0 0 1748 153 39 62 100 93 100 84 4178 4520 13.308 .075 .07 .077 .08 1.792 32 176 .066 .82 60 3510 6030 40 46 216 222 0 628 318 310 .08 631 313 12.55 .074 -3.65 -3.756
12 13841 19920 212 340 13629 19580 13290 17695 216 341 13078 17355 0 0 9617 12529 38 69 100 100 100 100 33209 30433 .696 1.437 1.327 1.655 1.391 2.202 32 168 1.415 .92 60 3690 6060 43 49 234 240 0 21123 361 20762 1.523 18764 18403 .656 1.407 .607 .493
13 1624 4212 201 331 1423 3881 1734 4506 203 336 1533 4175 0 0 712 1842 32 66 100 100 96 100 5304 5708 .367 2.727 2.723 2.99 2.851 2.265 32 168 2.928 .89 60 3810 6030 40 46 246 252 0 4466 351 4115 2.892 4778 4427 .346 2.888 1.532 1.53
14 545 632 209 341 336 291 552 654 220 355 343 313 0 0 74 88 66 87 100 100 100 91 627 656 1.155 .866 .913 .844 .908 1.568 12 104 1.137 .8 50 3950 6020 39 44 260 265 0 670 362 309 .918 693 332 1.089 .968 -.123 -.047
15 575 33442 209 377 366 33065 610 38941 212 392 401 38564 0 0 152 11456 42 93 93 100 90 100 33431 38965 .011 90.342 96.17 99.468 97.628 1.64 32 232 94.915 .92 70 4100 6040 40 47 274 281 0 35461 400 35062 95.797 41293 40893 .01 101.977 6.582 6.672
16 10667 15299 214 356 10453 14943 11544 18542 221 370 11330 18186 0 0 3095 6265 45 99 100 100 100 100 25396 29516 .7 1.43 1.605 1.224 1.477 1.685 32 232 1.621 .93 70 4240 6040 40 47 288 295 0 16223 377 15845 1.516 19662 19284 .66 1.702 .6 .767
17 4352 7307 213 330 4139 6977 4890 8288 217 347 4677 7958 0 0 1652 2641 42 78 100 100 100 100 11116 12635 .593 1.686 1.702 1.667 1.648 1.739 32 176 1.717 .92 60 4390 6030 40 46 304 310 0 7748 350 7398 1.787 8788 8439 .559 1.804 .838 .851
18 1425 296 201 315 1224 -19 1430 270 207 320 1229 -45 0 0 123 69 34 63 100 16 100 8 1205 1184 null null null .035 .041 3.078 12 104 -.014 -.1 50 4530 6030 40 45 318 323 0 314 334 -20 null 286 -48 null null null null
19 5812 2987 216 332 5596 2655 6221 3345 219 339 6005 3013 0 0 1935 1068 45 66 100 100 100 100 8251 9018 2.108 .474 .502 .43 .478 1.702 32 176 .453 .92 60 4680 6040 41 47 333 339 0 3167 352 2815 .503 3547 3195 1.988 .532 -.991 -.91
20 4410 4400 205 334 4205 4066 4970 5076 208 336 4765 4742 0 0 2464 2498 36 72 100 100 100 100 8271 9507 1.034 .967 .995 .931 .949 2.177 32 176 .976 .94 60 4830 6040 41 47 348 354 0 4666 354 4312 1.025 5383 5028 .975 1.055 .036 .078

Total number of rows: 41472

Table truncated, full table size 9295 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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