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Sample GSM798920 Query DataSets for GSM798920
Status Public on Sep 19, 2012
Title Patient 18, 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 05PB4023
Organism Homo sapiens
Characteristics cell type: acute myeloid leukemia peripheral blood
time: 0 h
individual: Patient 18
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/2005-11/65545.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 1062 795 193 367 869 428 1041 809 196 381 848 442 0 0 91 93 33 80 100 100 100 100 1297 1290 2.03 .493 .521 .484 .532 1.275 12 104 .536 .82 50 2110 6540 27 32 20 25 0 936 432 504 .58 952 520 1.725 .613 -.787 -.705
2 6492 2295 193 380 6299 1915 7777 2619 193 379 7584 2239 0 0 4363 1279 33 78 100 100 100 90 8214 9823 3.289 .304 .295 .37 .316 2.998 32 232 .28 .92 70 2260 6540 26 33 34 41 0 2701 447 2254 .358 3082 2635 2.795 .347 -1.483 -1.525
3 8345 7488 184 367 8161 7121 8699 8495 190 368 8515 8128 0 0 5663 5125 36 71 100 90 100 87 15282 16643 1.146 .873 .955 .667 .95 3.181 32 176 .877 .92 60 2400 6530 26 32 49 55 0 8813 432 8381 1.027 9998 9566 .974 1.123 .038 .168
4 3613 601 190 360 3423 241 3702 618 191 361 3512 258 0 0 489 121 36 82 100 83 100 66 3664 3770 14.203 .07 .073 .06 .074 1.84 12 104 .073 .73 50 2540 6530 26 31 63 68 0 707 424 284 .083 727 304 12.068 .086 -3.593 -3.532
5 2759 404 187 353 2572 51 2884 402 192 356 2697 49 0 0 346 77 34 70 100 33 100 8 2623 2746 50.431 .02 .018 .03 .035 1.854 12 104 .011 .16 50 2690 6540 27 32 78 83 0 475 415 60 .023 473 58 42.851 .021 -5.421 -5.547
6 981 487 189 350 792 137 1030 509 186 352 841 159 0 0 203 102 26 70 100 75 100 58 929 1000 5.781 .173 .189 .196 .193 1.854 12 68 .154 .5 40 2830 6530 27 31 93 97 0 573 412 161 .204 599 187 4.912 .223 -2.296 -2.168
7 3835 843 187 353 3648 490 3969 904 201 358 3782 551 0 0 712 229 111 68 100 100 100 83 4138 4333 7.445 .134 .146 .114 .144 1.84 12 104 .132 .85 50 2980 6530 26 31 107 112 0 992 415 577 .158 1064 648 6.326 .171 -2.661 -2.544
8 1840 381 186 359 1654 22 1869 394 188 370 1683 35 0 0 199 67 32 70 100 16 100 0 1676 1718 75.182 .013 .021 .031 .03 1.764 12 104 .015 .14 50 3130 6540 27 32 122 127 0 448 423 26 .016 464 41 63.881 .024 -5.997 -5.353
9 1257 3783 179 366 1078 3417 1429 3714 180 377 1250 3348 0 0 738 2109 28 78 96 100 93 100 4495 4598 .315 3.17 2.678 4.001 3.879 2.221 32 176 3.264 .91 60 3280 6540 27 33 137 143 0 4452 431 4021 3.73 4371 3940 .268 3.152 1.899 1.656
10 2265 2886 179 346 2086 2540 2522 3281 180 353 2343 2935 0 0 978 1481 28 81 100 87 100 87 4626 5278 .821 1.218 1.253 .897 1.234 2.395 32 176 1.319 .94 60 3420 6550 28 34 151 157 0 3397 407 2989 1.433 3861 3454 .698 1.474 .519 .56
11 4014 535 187 354 3827 181 4149 567 190 351 3962 213 0 0 2003 140 46 74 100 68 100 62 4008 4175 21.144 .047 .054 .038 .047 2.611 32 176 .046 .74 60 3570 6550 28 34 166 172 0 630 417 213 .056 667 251 17.965 .063 -4.167 -3.982
12 10544 7536 188 352 10356 7184 13161 8700 195 369 12973 8348 0 0 5635 3674 54 86 100 100 100 100 17540 21321 1.442 .694 .643 .77 .704 2.448 32 176 .664 .93 60 3720 6550 28 34 181 187 0 8869 414 8455 .816 10239 9825 1.225 .757 -.293 -.401
13 1521 3319 181 366 1340 2953 1562 3307 180 365 1381 2941 0 0 305 814 28 72 100 100 100 100 4293 4322 .454 2.204 2.13 2.183 2.129 1.329 12 104 2.408 .89 50 3860 6540 27 32 195 200 0 3906 431 3475 2.594 3892 3461 .386 2.506 1.375 1.326
14 940 1197 183 328 757 869 948 1256 192 350 765 928 0 0 163 262 55 109 100 100 100 100 1626 1693 .871 1.148 1.213 1.117 1.157 1.365 12 104 1.219 .89 50 4000 6530 26 31 209 214 0 1409 386 1023 1.351 1478 1092 .74 1.428 .434 .514
15 395 18295 174 367 221 17928 320 15213 177 369 146 14846 0 0 198 16806 29 80 78 100 63 100 18149 14992 .012 81.122 101.685 57.055 74.802 3.238 52 310 89.387 .92 80 4150 6550 27 35 223 231 0 21531 432 21100 95.473 17904 17472 .01 119.673 6.577 6.903
16 6496 13873 176 381 6320 13492 8417 17708 180 393 8241 17327 0 0 4356 9102 69 126 100 100 100 98 19812 25568 .468 2.135 2.103 2.175 2.157 2.196 52 302 2.194 .94 80 4300 6550 27 35 238 246 0 16327 448 15879 2.512 20841 20392 .398 2.474 1.329 1.307
17 3835 8140 182 389 3653 7751 4523 9372 183 399 4341 8983 0 0 1838 3418 35 83 100 100 100 100 11404 13324 .471 2.122 2.069 2.272 2.134 1.984 32 176 2.119 .94 60 4450 6550 28 34 254 260 0 9580 458 9122 2.497 11030 10572 .4 2.435 1.32 1.284
18 1003 511 172 361 831 150 1157 526 174 368 985 165 0 0 438 138 27 73 100 71 100 56 981 1150 5.54 .181 .168 .195 .221 2.336 32 176 .19 .7 60 4590 6550 28 34 268 274 0 601 425 177 .212 619 194 4.707 .197 -2.235 -2.343
19 4592 2816 181 357 4411 2459 5700 3657 184 362 5519 3300 0 0 2768 1474 32 68 100 100 100 100 6870 8819 1.794 .557 .598 .602 .555 2.314 32 176 .529 .93 60 4740 6550 28 34 283 289 0 3314 420 2894 .656 4304 3884 1.524 .704 -.608 -.507
20 6180 3694 188 353 5992 3341 7542 3658 188 357 7354 3305 0 0 3169 2469 32 68 100 100 100 100 9333 10659 1.793 .558 .449 .403 .447 1.927 12 104 .661 .92 50 4880 6550 28 33 297 302 0 4347 415 3932 .656 4305 3890 1.524 .529 -.608 -.919

Total number of rows: 41472

Table truncated, full table size 9367 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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