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Sample GSM798947 Query DataSets for GSM798947
Status Public on Sep 19, 2012
Title Patient 15, 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 05PB4360
Organism Homo sapiens
Characteristics cell type: acute myeloid leukemia peripheral blood
time: 48 h
individual: Patient 15
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/2005-11/65544.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
1 876 357 141 297 735 60 896 350 145 300 755 53 0 0 129 66 29 65 100 41 100 25 795 808 12.25 .082 .07 .063 .111 4.101 12 104 .017 .07 50 2140 6490 38 43 27 32 0 424 353 71 .097 416 63 10.307 .083 -3.366 -3.583
2 6307 680 146 304 6161 376 6556 657 150 301 6410 353 0 0 3661 237 31 61 100 93 100 87 6537 6763 16.386 .061 .055 .066 .062 3.365 32 176 .057 .87 60 2290 6500 39 45 42 48 0 808 361 447 .073 781 420 13.787 .065 -3.785 -3.933
3 7843 4631 143 306 7700 4325 8154 4924 144 309 8011 4618 0 0 4316 2703 25 63 100 100 100 96 12025 12629 1.78 .562 .576 .459 .481 2.381 32 176 .552 .9 60 2440 6490 38 44 57 63 0 5504 364 5140 .668 5852 5488 1.498 .685 -.583 -.546
4 2124 445 136 297 1988 148 2548 440 136 298 2412 143 0 0 1233 111 22 62 100 78 100 56 2136 2555 13.432 .074 .059 .095 .086 2.096 32 176 .068 .72 60 2580 6490 38 44 71 77 0 529 353 176 .088 523 170 11.302 .07 -3.499 -3.827
5 2634 317 145 283 2489 34 2693 304 150 285 2548 21 0 0 429 63 28 57 100 33 100 8 2523 2569 73.206 .014 .008 .019 .022 2.303 12 104 .015 .25 50 2720 6490 38 43 85 90 0 377 336 40 .016 361 25 61.595 .01 -5.945 -6.674
6 892 350 151 294 741 56 885 355 153 292 734 61 0 0 135 60 29 66 100 41 100 8 797 795 13.232 .076 .083 .087 .09 1.869 12 68 .039 .19 40 2870 6490 39 43 101 105 0 416 349 67 .09 422 72 11.133 .099 -3.477 -3.34
7 2241 487 137 286 2104 201 2426 485 142 294 2289 199 0 0 1357 160 31 61 100 84 100 68 2305 2488 10.468 .096 .087 .11 .107 2.162 32 176 .091 .79 60 3010 6490 38 44 114 120 0 579 340 239 .114 576 237 8.807 .103 -3.139 -3.275
8 1188 267 139 287 1049 -20 1268 260 140 292 1129 -27 0 0 524 70 24 67 100 15 100 0 1029 1102 null null null .075 .161 5.593 32 176 -.036 -.28 60 3160 6490 38 44 129 135 0 317 341 -24 null 309 -32 null null null null
9 1622 622 144 307 1478 315 1622 677 144 309 1478 370 0 0 329 139 29 67 100 91 100 91 1793 1848 4.692 .213 .25 .23 .23 1.441 12 104 .198 .77 50 3300 6490 38 43 143 148 0 739 365 374 .253 805 440 3.948 .298 -1.981 -1.749
10 2162 1107 138 291 2024 816 2221 1187 141 299 2083 896 0 0 766 427 24 63 100 93 100 90 2840 2979 2.48 .403 .43 .361 .429 1.698 32 176 .413 .92 60 3450 6500 39 45 158 164 0 1316 346 970 .479 1411 1065 2.087 .511 -1.061 -.968
11 4280 484 149 299 4131 185 3979 461 372 316 3830 162 0 0 2062 151 802 85 100 66 91 50 4316 3992 22.33 .045 .042 .044 .041 1.548 12 104 .053 .84 50 3590 6480 37 42 172 177 0 575 355 220 .053 548 193 18.788 .05 -4.232 -4.314
12 8108 8383 144 319 7964 8064 9075 9131 151 323 8931 8812 0 0 4251 5090 35 70 100 100 100 96 16028 17743 .988 1.013 .987 .785 1.06 2.385 32 236 1.094 .92 70 3740 6490 37 44 186 193 0 9963 379 9584 1.203 10852 10473 .831 1.173 .267 .23
13 1336 1942 142 322 1194 1620 1142 2118 179 376 1000 1796 0 0 429 811 178 295 100 83 100 83 2814 2796 .737 1.357 1.796 1.121 1.669 2.356 12 104 1.591 .85 50 3880 6490 38 43 201 206 0 2308 383 1925 1.613 2517 2135 .62 2.135 .689 1.094
14 756 975 146 296 610 679 878 1004 149 305 732 708 0 0 266 306 27 63 100 100 100 90 1289 1440 .898 1.113 .967 1.111 1.081 1.58 32 176 1.168 .91 60 4040 6500 39 45 217 223 0 1159 352 807 1.323 1193 841 .756 1.15 .404 .201
15 344 18477 138 321 206 18156 361 21433 141 341 223 21112 0 0 87 7035 23 94 100 100 93 100 18362 21335 .011 88.136 94.673 91.212 86.579 1.974 32 226 95.128 .91 70 4180 6500 38 45 230 237 0 21960 382 21578 104.75 25473 25092 .01 112.519 6.711 6.814
16 5437 14001 141 315 5296 13686 6204 15303 144 330 6063 14988 0 0 3353 8272 29 90 100 100 100 100 18982 21051 .387 2.584 2.472 2.634 2.771 2.376 52 296 2.683 .93 80 4330 6500 38 46 245 253 0 16640 374 16266 3.071 18188 17813 .326 2.938 1.619 1.555
17 2556 9647 138 310 2418 9337 2880 9479 141 321 2742 9169 0 0 1958 7133 25 86 96 100 92 100 11755 11911 .259 3.861 3.344 4.713 4.102 2.533 52 289 4.074 .91 80 4480 6500 38 46 260 268 0 11465 368 11097 4.589 11266 10897 .218 3.974 2.198 1.991
18 1410 466 139 303 1271 163 1316 433 140 307 1177 130 0 0 237 96 31 56 100 83 100 75 1434 1307 7.798 .128 .11 .103 .117 2.178 12 104 .134 .71 50 4610 6490 38 43 274 279 0 554 360 194 .152 515 155 6.561 .131 -2.714 -2.929
19 4061 3546 141 304 3920 3242 4616 3804 143 304 4475 3500 0 0 2040 1330 24 61 100 100 100 100 7162 7975 1.209 .827 .782 1.027 .844 2.087 32 176 .773 .93 60 4770 6500 39 45 290 296 0 4214 361 3853 .983 4521 4160 1.017 .93 -.025 -.105
20 3048 2690 134 287 2914 2403 2566 2267 139 296 2432 1980 0 0 2441 1997 26 62 100 100 100 90 5317 4412 1.213 .825 .814 .784 .871 2.436 32 176 .809 .92 60 4910 6500 39 45 304 310 0 3197 341 2856 .98 2694 2353 1.02 .968 -.029 -.047

Total number of rows: 41472

Table truncated, full table size 9336 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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