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Sample GSM798931 Query DataSets for GSM798931
Status Public on Sep 19, 2012
Title Patient 7, 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 05PB2081
Organism Homo sapiens
Characteristics cell type: acute myeloid leukemia peripheral blood
time: 48 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/2005-11/65512.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 1301 724 497 690 804 34 1255 739 503 703 758 49 0 0 372 127 88 129 100 25 100 3 838 807 23.647 .042 .065 .146 .183 2.337 32 176 -1 -1 60 2040 6010 42 48 37 43 0 780 743 37 .046 796 53 21.963 .07 -4.457 -3.845
2 9984 850 607 814 9377 36 11961 834 602 830 11354 20 0 0 5288 113 112 165 96 12 96 0 9413 11374 260.472 .004 .002 .007 .01 5.166 32 176 .006 .21 60 2180 6010 42 48 51 57 0 915 876 39 .004 898 22 241.92 .002 -7.918 -9.042
3 9505 7211 614 851 8891 6360 11181 7992 622 851 10567 7141 0 0 5319 3714 102 129 100 100 93 96 15251 17708 1.398 .715 .676 .756 .704 2.41 32 176 .694 .94 60 2340 6000 41 47 67 73 0 7764 916 6848 .77 8605 7689 1.298 .728 -.377 -.459
4 4447 765 593 782 3854 -17 4582 727 595 786 3989 -55 0 0 756 118 93 125 100 16 100 0 3837 3934 null null null .022 .025 1.509 12 104 -.011 -.14 50 2470 6000 41 46 80 85 0 824 842 -18 null 783 -59 null null null null
5 2120 528 538 754 1582 -226 2242 546 536 760 1704 -208 0 0 910 208 89 116 96 3 93 0 1356 1496 null null null .067 .05 7.553 32 176 -.152 -.65 60 2620 6010 42 48 95 101 0 568 812 -243 null 588 -224 null null null null
6 1100 341 561 737 539 -396 1107 295 563 742 546 -442 0 0 294 134 89 147 100 0 91 0 143 104 null null null 0 0 1 12 104 -.766 -.7 50 2760 5980 39 44 109 114 0 367 794 -426 null 318 -476 null null null null
7 4893 771 573 834 4320 -63 4938 783 583 826 4365 -51 0 0 614 108 89 130 100 0 100 0 4257 4314 null null null .009 .006 1.844 12 104 -1 -1 50 2910 5990 40 45 124 129 0 830 898 -68 null 843 -55 null null null null
8 2417 344 577 820 1840 -476 2412 321 592 824 1835 -499 0 0 197 61 113 150 100 0 100 0 1364 1336 null null null 0 0 1 12 104 -.285 -.76 50 3060 6020 43 48 139 144 0 370 883 -513 null 346 -537 null null null null
9 1847 4926 566 827 1281 4099 1931 4960 574 846 1365 4133 0 0 696 1968 103 164 90 100 87 100 5380 5498 .313 3.2 3.028 3.233 3.16 1.907 32 176 3.365 .89 60 3210 6010 42 48 154 160 0 5304 890 4413 3.445 5340 4450 .29 3.26 1.785 1.705
10 4687 2675 519 765 4168 1910 5286 3053 525 777 4767 2288 0 0 1781 914 86 119 100 100 100 93 6078 7055 2.182 .458 .48 .434 .458 1.761 32 176 .443 .93 60 3350 6010 42 48 168 174 0 2880 824 2056 .493 3287 2463 2.027 .517 -1.019 -.952
11 5787 896 463 637 5324 259 6337 921 498 648 5874 284 0 0 1586 129 154 120 100 83 100 58 5583 6158 20.556 .049 .048 .044 .044 1.671 12 104 .046 .69 50 3490 6000 41 46 182 187 0 965 686 279 .052 992 306 19.092 .052 -4.255 -4.264
12 16073 13057 378 510 15695 12547 17952 14843 390 521 17574 14333 0 0 8452 7510 93 159 100 100 100 100 28242 31907 1.251 .799 .816 .647 .79 2.367 32 176 .8 .87 60 3650 6020 43 49 198 204 0 14058 549 13509 .861 15981 15432 1.162 .878 -.216 -.188
13 1747 1359 324 419 1423 940 1704 1406 336 428 1380 987 0 0 945 573 66 92 93 96 93 90 2363 2367 1.514 .661 .715 .732 .606 2.315 32 176 .619 .9 60 3790 6010 42 48 212 218 0 1463 451 1012 .711 1514 1063 1.406 .77 -.492 -.377
14 1463 1596 347 434 1116 1162 1597 1634 395 448 1250 1200 0 0 370 371 200 101 100 100 91 100 2278 2450 .96 1.041 .96 1.073 .987 1.353 12 104 .914 .87 50 3930 5990 40 45 226 231 0 1718 467 1251 1.121 1759 1292 .892 1.034 .165 .048
15 783 3161 323 414 460 2747 854 3697 326 420 531 3283 0 0 206 1100 61 80 96 100 90 100 3207 3814 .167 5.972 6.183 6.1 5.785 1.944 32 176 6.383 .89 60 4080 6010 42 48 241 247 0 3403 446 2958 6.43 3981 3535 .156 6.657 2.685 2.735
16 12729 17435 335 450 12394 16985 14613 20932 341 471 14278 20482 0 0 5123 8388 69 123 100 100 100 96 29379 34760 .73 1.37 1.435 1.178 1.399 1.525 32 232 1.503 .94 70 4220 6010 41 48 254 261 0 18772 485 18288 1.476 22537 22053 .678 1.545 .561 .627
17 5131 7066 325 464 4806 6602 5980 8463 329 472 5655 7999 0 0 1879 3022 56 109 100 100 100 100 11408 13654 .728 1.374 1.415 1.26 1.423 1.668 32 236 1.447 .96 70 4370 6010 41 48 269 276 0 7608 500 7108 1.479 9112 8612 .676 1.523 .565 .607
18 1755 711 308 433 1447 278 1765 717 317 425 1457 284 0 0 253 117 53 77 100 100 100 83 1725 1741 5.205 .192 .195 .176 .172 1.599 12 104 .187 .73 50 4510 6000 41 46 284 289 0 766 466 299 .207 772 306 4.834 .21 -2.273 -2.252
19 6291 4758 328 431 5963 4327 7035 5583 336 433 6707 5152 0 0 3151 2530 62 81 100 100 100 100 10290 11859 1.378 .726 .768 .64 .684 1.973 32 176 .728 .91 60 4660 6010 42 48 299 305 0 5123 464 4659 .781 6011 5547 1.28 .827 -.356 -.274
20 4416 4538 318 407 4098 4131 3857 3813 325 404 3539 3406 0 0 3380 3083 62 71 96 100 93 96 8229 6945 .992 1.008 .962 1.054 1.026 2.912 32 176 .96 .9 60 4810 6000 41 47 314 320 0 4886 438 4448 1.085 4105 3667 .921 1.036 .118 .051

Total number of rows: 41472

Table truncated, full table size 9490 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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