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Sample GSM798952 Query DataSets for GSM798952
Status Public on Sep 19, 2012
Title Patient 7, 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 05PB2061
Organism Homo sapiens
Characteristics cell type: acute myeloid leukemia peripheral blood
time: 0 h
individual: Patient 7
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/2005-11/65510.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 1468 1887 432 490 1036 1397 1556 1893 434 488 1124 1403 0 0 456 737 53 105 100 100 100 96 2433 2527 .742 1.348 1.248 1.268 1.408 1.665 32 176 1.457 .93 60 1950 6240 41 47 28 34 0 2043 530 1512 1.46 2049 1519 .685 1.351 .546 .434
2 15759 803 436 502 15323 301 17994 818 442 506 17558 316 0 0 8369 202 67 101 100 81 100 68 15624 17874 50.907 .02 .018 .02 .022 2.074 32 232 .019 .77 70 2090 6240 40 47 41 48 0 869 543 326 .021 885 342 47.03 .019 -5.555 -5.682
3 13267 7911 413 510 12854 7401 12988 8021 416 508 12575 7511 0 0 6498 4535 53 105 100 100 100 96 20255 20086 1.737 .576 .597 .464 .602 1.98 32 176 .596 .96 60 2250 6240 41 47 58 64 0 8563 552 8011 .623 8682 8130 1.605 .647 -.682 -.629
4 4804 580 399 459 4405 121 4618 573 400 465 4219 114 0 0 2092 138 54 91 100 56 100 21 4526 4333 36.405 .027 .027 .027 .03 2.48 32 176 .029 .52 60 2390 6240 41 47 72 78 0 628 497 131 .03 620 123 33.632 .029 -5.072 -5.095
5 3255 407 399 460 2856 -53 3191 410 404 467 2792 -50 0 0 1602 95 52 94 100 3 100 3 2803 2742 null null null .016 .025 5.352 32 176 -.018 -.25 60 2530 6250 42 48 86 92 0 441 498 -57 null 444 -54 null null null null
6 1964 404 428 445 1536 -41 1935 413 431 461 1507 -32 0 0 195 107 61 99 100 8 100 0 1495 1475 null null null .028 .025 2.449 12 68 -.032 -.19 40 2680 6250 43 47 102 106 0 437 482 -44 null 447 -35 null null null null
7 6214 581 419 466 5795 115 6791 584 427 468 6372 118 0 0 1336 120 64 93 100 58 100 33 5910 6490 50.391 .02 .019 .021 .026 2.367 12 104 .022 .42 50 2820 6250 42 47 115 120 0 629 504 124 .021 632 128 46.553 .02 -5.541 -5.641
8 3326 394 422 486 2904 -92 3449 402 423 486 3027 -84 0 0 477 65 66 104 100 0 100 0 2812 2943 null null null .007 .007 1 12 104 -.04 -.48 50 2970 6240 41 46 130 135 0 426 526 -100 null 435 -91 null null null null
9 2844 1717 405 449 2439 1268 3266 1751 406 442 2861 1302 0 0 1188 660 50 92 100 96 100 93 3707 4163 1.924 .52 .455 .504 .479 1.854 32 176 .502 .9 60 3120 6250 42 48 145 151 0 1859 486 1373 .563 1895 1409 1.777 .493 -.829 -1.021
10 5608 3478 408 458 5200 3020 6459 3928 411 460 6051 3470 0 0 1809 1391 58 96 100 100 100 96 8220 9521 1.722 .581 .573 .515 .576 1.568 32 176 .6 .96 60 3260 6250 42 48 159 165 0 3765 496 3269 .629 4252 3756 1.591 .621 -.67 -.688
11 8001 688 409 447 7592 241 8942 668 411 453 8533 221 0 0 3779 166 59 93 100 87 100 56 7833 8754 31.502 .032 .026 .031 .034 1.877 32 224 .032 .76 70 3410 6250 41 48 173 180 0 745 484 261 .034 723 239 29.103 .028 -4.863 -5.157
12 14710 9423 391 446 14319 8977 13019 8306 396 449 12628 7860 0 0 12623 7750 56 94 100 94 96 90 23296 20488 1.595 .627 .622 .623 .6 2.724 52 304 .607 .95 80 3550 6250 41 49 187 195 0 10200 483 9717 .679 8991 8508 1.474 .674 -.559 -.57
13 2601 2488 384 423 2217 2065 2536 2649 389 441 2152 2226 0 0 1130 1055 51 89 100 100 100 93 4282 4378 1.074 .931 1.034 .88 1.003 2.021 32 176 .928 .92 60 3700 6250 42 48 203 209 0 2693 458 2235 1.008 2867 2410 .992 1.12 .012 .163
14 1690 1789 384 439 1306 1350 1829 1852 383 433 1445 1413 0 0 474 641 51 92 100 100 100 96 2656 2858 .967 1.034 .978 .96 1.012 1.44 32 232 1.137 .94 70 3840 6250 41 48 216 223 0 1936 475 1461 1.119 2005 1529 .894 1.058 .162 .082
15 999 4151 367 433 632 3718 1062 4759 371 426 695 4326 0 0 198 1609 53 92 100 100 100 100 4350 5021 .17 5.883 6.224 5.398 6.199 1.558 32 231 6.452 .94 70 3990 6250 41 48 231 238 0 4493 469 4025 6.368 5151 4683 .157 6.738 2.671 2.752
16 13710 16410 377 417 13333 15993 15348 17809 379 426 14971 17392 0 0 8410 9210 59 95 100 100 100 100 29326 32363 .834 1.2 1.162 1.457 1.23 2.321 52 303 1.172 .97 80 4140 6240 40 48 246 254 0 17763 451 17312 1.298 19277 18826 .77 1.257 .377 .331
17 5863 11710 370 419 5493 11291 5375 10211 377 434 5005 9792 0 0 4490 8687 61 107 98 98 94 98 16784 14797 .486 2.056 1.956 2.323 2.031 2.347 52 286 2.047 .96 80 4290 6250 41 49 261 269 0 12675 454 12222 2.225 11053 10599 .449 2.118 1.154 1.083
18 2271 869 368 423 1903 446 2280 932 371 425 1912 509 0 0 784 246 57 97 100 87 100 78 2349 2421 4.267 .234 .266 .207 .236 1.964 32 170 .231 .86 60 4430 6250 42 48 276 282 0 941 458 483 .254 1009 551 3.942 .288 -1.979 -1.795
19 9354 7248 391 427 8963 6821 11012 7373 388 432 10621 6946 0 0 4213 3057 59 104 100 100 100 100 15784 17567 1.314 .761 .654 .806 .756 1.602 32 176 .742 .95 60 4580 6250 42 48 291 297 0 7846 462 7383 .824 7981 7519 1.214 .708 -.28 -.498
20 9755 7499 400 428 9355 7071 10416 8050 409 444 10016 7622 0 0 3713 2147 95 94 100 100 100 100 16426 17638 1.323 .756 .761 .793 .706 1.327 12 104 .661 .93 50 4720 6240 41 46 305 310 0 8117 463 7654 .818 8714 8250 1.222 .824 -.29 -.28

Total number of rows: 41472

Table truncated, full table size 9532 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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