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Sample GSM798949 Query DataSets for GSM798949
Status Public on Sep 19, 2012
Title Patient 8, 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 05KM2121
Organism Homo sapiens
Characteristics cell type: acute myeloid leukemia peripheral blood
time: 0 h
individual: Patient 8
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/2005-11/65514.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 1381 643 361 573 1020 70 1448 631 366 566 1087 58 0 0 201 95 53 84 100 41 100 25 1090 1145 14.571 .069 .053 .082 .113 2.434 12 104 .084 .36 50 2030 6030 40 45 32 37 0 703 626 76 .075 690 63 13.334 .058 -3.737 -4.1
2 9781 6099 364 568 9417 5531 11137 6548 378 578 10773 5980 0 0 5327 3061 82 101 100 100 100 100 14948 16753 1.703 .587 .555 .6 .592 2.187 32 176 .566 .94 60 2180 6040 41 47 47 53 0 6665 621 6044 .642 7156 6535 1.558 .607 -.64 -.721
3 9350 10442 371 577 8979 9865 11086 11752 384 592 10715 11175 0 0 5788 5641 152 115 93 100 90 100 18844 21890 .91 1.099 1.043 1.368 1.174 2.736 32 176 1.061 .94 60 2340 6040 41 47 63 69 0 11411 631 10780 1.201 12843 12212 .833 1.14 .264 .189
4 4169 1940 376 559 3793 1381 4402 1933 388 568 4026 1374 0 0 1134 255 77 98 100 100 100 100 5174 5400 2.747 .364 .341 .379 .374 1.38 12 104 .337 .91 50 2470 6020 39 44 76 81 0 2120 611 1509 .398 2112 1502 2.513 .373 -1.33 -1.423
5 2994 642 365 554 2629 88 3212 674 370 561 2847 120 0 0 801 124 59 110 100 50 100 8 2717 2967 29.875 .033 .042 .053 .053 2.15 12 104 .008 .08 50 2610 6030 40 45 90 95 0 702 605 96 .037 737 131 27.338 .046 -4.773 -4.44
6 1307 966 362 544 945 422 1324 944 359 550 962 400 0 0 261 104 49 88 100 100 100 100 1367 1362 2.239 .447 .416 .454 .402 1.544 12 104 .401 .78 50 2760 6020 39 44 105 110 0 1056 594 461 .488 1032 437 2.049 .454 -1.035 -1.138
7 5233 1011 372 533 4861 478 5260 993 391 531 4888 460 0 0 441 172 160 97 100 100 100 91 5339 5348 10.169 .098 .094 .092 .095 1.494 12 68 .085 .81 40 2910 6030 41 45 121 125 0 1105 582 522 .107 1085 503 9.306 .103 -3.218 -3.282
8 1707 1410 341 535 1366 875 1769 1465 342 539 1428 930 0 0 690 432 51 83 100 96 96 96 2241 2358 1.561 .641 .651 .656 .659 2.361 32 176 .63 .91 60 3060 6030 40 46 135 141 0 1541 585 956 .7 1601 1016 1.429 .712 -.515 -.491
9 2013 2982 331 531 1682 2451 2324 3164 416 591 1993 2633 0 0 872 1075 400 360 83 100 83 100 4133 4626 .686 1.457 1.321 1.786 1.547 2.558 12 104 1.462 .87 50 3200 6020 39 44 149 154 0 3259 580 2678 1.592 3458 2877 .628 1.444 .671 .53
10 4520 2725 324 480 4196 2245 5418 3090 324 489 5094 2610 0 0 2119 1167 49 89 100 100 100 96 6441 7704 1.869 .535 .512 .513 .517 1.935 32 176 .518 .94 60 3350 6040 41 47 164 170 0 2978 525 2453 .585 3377 2852 1.71 .56 -.774 -.837
11 7510 945 344 475 7166 470 7271 948 355 480 6927 473 0 0 1483 246 74 81 100 100 100 100 7636 7400 15.247 .066 .068 .059 .065 1.646 12 104 .065 .79 50 3490 6030 40 45 178 183 0 1033 519 514 .072 1036 517 13.952 .075 -3.802 -3.744
12 12168 17574 333 481 11835 17093 15240 19297 333 484 14907 18816 0 0 7668 8691 55 88 100 100 100 100 28928 33723 .692 1.444 1.262 2.114 1.438 2.659 32 176 1.363 .92 60 3650 6040 41 47 194 200 0 19205 526 18679 1.578 21088 20562 .634 1.379 .658 .464
13 2287 4582 315 489 1972 4093 2444 4208 332 483 2129 3719 0 0 976 1379 143 105 100 100 100 100 6065 5848 .482 2.076 1.747 2.284 2.007 1.721 12 104 1.975 .85 50 3780 6020 39 44 207 212 0 5007 534 4473 2.268 4598 4064 .441 1.909 1.182 .933
14 1156 1547 306 468 850 1079 1257 1543 312 468 951 1075 0 0 342 601 51 89 100 90 100 87 1929 2026 .788 1.269 1.13 1.055 1.136 1.957 32 176 1.475 .91 60 3930 6040 41 47 222 228 0 1691 511 1179 1.387 1686 1175 .721 1.235 .472 .305
15 916 34382 306 494 610 33888 1062 39532 310 516 756 39038 0 0 333 14127 44 148 90 100 84 100 34498 39794 .018 55.554 51.638 77.064 54.359 2.526 32 176 54.898 .93 60 4080 6030 40 46 237 243 0 37573 540 37033 60.709 43200 42661 .016 56.429 5.924 5.818
16 9325 16197 312 465 9013 15732 11894 20807 317 473 11582 20342 0 0 5703 9913 53 101 100 100 100 100 24745 31924 .573 1.745 1.756 1.869 1.722 2.72 52 313 1.837 .9 80 4230 6040 40 48 251 259 0 17700 508 17192 1.907 22738 22230 .524 1.919 .932 .941
17 6051 11766 312 484 5739 11282 7481 12777 318 499 7169 12293 0 0 2939 3149 55 106 100 100 96 100 17021 19462 .509 1.966 1.715 2.621 1.785 2.468 32 226 1.838 .93 70 4380 6040 40 47 266 273 0 12858 529 12329 2.148 13963 13434 .465 1.874 1.103 .906
18 2166 809 315 455 1851 354 2202 826 317 460 1887 371 0 0 294 110 50 84 100 100 100 91 2205 2258 5.229 .191 .197 .182 .194 1.466 12 104 .188 .75 50 4510 6030 40 45 280 285 0 884 497 387 .209 903 405 4.785 .215 -2.258 -2.219
19 8639 6460 352 491 8287 5969 8026 6171 357 488 7674 5680 0 0 2081 1457 75 89 100 100 100 100 14256 13354 1.388 .72 .74 .72 .716 1.265 12 104 .675 .9 50 4660 6040 41 46 295 300 0 7059 537 6523 .787 6744 6207 1.27 .809 -.345 -.306
20 6773 6596 344 492 6429 6104 7114 6737 343 498 6770 6245 0 0 2639 2146 50 90 100 100 100 100 12533 13015 1.053 .949 .922 .989 .952 1.467 12 104 .829 .88 50 4810 6040 41 46 310 315 0 7208 538 6670 1.038 7362 6825 .964 1.008 .053 .012

Total number of rows: 41472

Table truncated, full table size 9455 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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