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Sample GSM798958 Query DataSets for GSM798958
Status Public on Sep 19, 2012
Title Patient 14, 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 05PB4309
Organism Homo sapiens
Characteristics cell type: acute myeloid leukemia peripheral blood
time: 48 h
individual: Patient 14
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/2005-11/65554.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
1 953 7017 228 198 725 6819 1058 7215 234 203 830 7017 0 0 351 3323 39 55 100 100 100 100 7544 7847 .106 9.406 8.454 9.336 9.689 1.871 32 176 10.6 .92 60 2250 6160 29 35 22 28 0 6658 188 6470 8.924 6845 6658 .112 8.021 3.158 3.004
2 8056 899 241 192 7815 707 9678 855 255 188 9437 663 0 0 4370 325 72 48 100 100 100 96 8522 10100 11.054 .09 .07 .109 .087 2.217 32 176 .076 .88 60 2400 6160 29 35 37 43 0 853 182 671 .086 811 629 11.651 .067 -3.542 -3.907
3 6774 8977 235 185 6539 8792 7099 8894 239 189 6864 8709 0 0 4075 4795 44 55 100 100 100 100 15331 15573 .744 1.345 1.269 1.655 1.309 2.57 32 176 1.319 .93 60 2550 6160 29 35 52 58 0 8517 176 8342 1.276 8438 8263 .784 1.204 .351 .268
4 2541 592 237 179 2304 413 2864 644 238 182 2627 465 0 0 1103 265 44 53 100 90 100 81 2717 3092 5.579 .179 .177 .146 .183 1.919 32 176 .184 .9 60 2690 6170 30 36 66 72 0 562 170 392 .17 611 441 5.88 .168 -2.556 -2.574
5 2199 466 248 180 1951 286 2202 460 249 182 1954 280 0 0 199 68 44 55 100 100 100 100 2237 2234 6.822 .147 .143 .143 .143 1.28 12 104 .12 .75 50 2830 6170 30 35 80 85 0 442 171 271 .139 436 266 7.19 .136 -2.846 -2.879
6 1128 389 235 179 893 210 1172 381 243 182 937 202 0 0 237 93 51 46 100 91 100 91 1103 1139 4.252 .235 .216 .212 .247 1.724 12 104 .236 .75 50 2970 6170 30 35 94 99 0 369 170 199 .223 361 192 4.482 .205 -2.164 -2.29
7 3324 606 246 174 3078 432 3789 591 269 175 3543 417 0 0 787 113 115 52 100 100 100 100 3510 3960 7.125 .14 .118 .141 .142 1.215 12 104 .126 .83 50 3120 6170 30 35 109 114 0 575 165 410 .133 561 396 7.51 .112 -2.909 -3.163
8 1285 1018 225 170 1060 848 1363 1190 228 170 1138 1020 0 0 489 436 35 39 100 100 100 96 1908 2158 1.25 .8 .896 .722 .774 2.214 32 170 .819 .86 60 3270 6170 30 36 124 130 0 966 161 805 .759 1129 968 1.317 .85 -.398 -.234
9 1356 571 220 181 1136 390 1347 594 222 182 1127 413 0 0 314 136 38 47 100 100 100 100 1526 1540 2.913 .343 .366 .336 .353 1.484 12 104 .27 .78 50 3410 6160 29 34 138 143 0 542 172 370 .326 564 392 3.07 .348 -1.618 -1.524
10 3128 2543 213 169 2915 2374 3478 2987 217 169 3265 2818 0 0 1078 1121 42 45 100 100 100 100 5289 6083 1.228 .814 .863 .744 .874 2.236 32 176 .85 .9 60 3560 6170 30 36 153 159 0 2413 160 2252 .773 2834 2674 1.294 .819 -.372 -.288
11 4311 377 232 175 4079 202 4169 370 349 181 3937 195 0 0 1206 84 606 49 100 100 100 91 4281 4132 20.193 .05 .05 .047 .049 1.818 12 104 .047 .82 50 3700 6150 28 33 167 172 0 358 166 192 .047 351 185 21.283 .047 -4.412 -4.411
12 7766 13380 221 187 7545 13193 8071 14737 227 212 7850 14550 0 0 3807 6368 53 138 100 100 100 100 20738 22400 .572 1.749 1.854 1.666 1.823 1.926 32 232 1.799 .89 70 3850 6160 28 35 181 188 0 12695 177 12517 1.659 13982 13805 .603 1.759 .73 .814
13 987 2224 215 178 772 2046 1129 2599 218 194 914 2421 0 0 581 1303 48 109 84 93 68 81 2818 3335 .377 2.65 2.649 3.183 2.6 3.235 32 176 2.651 .83 60 3990 6160 29 35 196 202 0 2110 169 1941 2.515 2466 2297 .398 2.513 1.33 1.329
14 1020 949 219 171 801 778 1041 1034 219 174 822 863 0 0 224 325 43 53 100 96 100 96 1579 1685 1.03 .971 1.05 .852 .988 2.026 32 232 1.109 .9 70 4140 6170 29 36 210 217 0 900 162 738 .922 981 819 1.085 .996 -.118 -.006
15 512 18900 211 217 301 18683 577 21043 214 247 366 20826 0 0 171 8269 39 134 93 100 81 100 18984 21192 .016 62.07 56.902 65.887 58.841 1.942 32 176 64.164 .87 60 4280 6160 29 35 225 231 0 17932 206 17726 58.89 19965 19759 .017 53.987 5.88 5.755
16 8783 13273 225 206 8558 13067 8712 14309 235 229 8487 14103 0 0 2065 4539 52 108 100 100 100 100 21625 22590 .655 1.527 1.662 1.385 1.63 1.763 32 176 1.817 .87 60 4430 6170 30 36 240 246 0 12593 195 12398 1.449 13576 13381 .69 1.577 .535 .657
17 3421 6459 216 184 3205 6275 3701 6761 221 196 3485 6577 0 0 1261 1894 41 72 100 100 100 100 9480 10062 .511 1.958 1.887 2.155 1.907 2.048 32 236 1.954 .9 70 4580 6160 28 35 254 261 0 6128 175 5954 1.858 6415 6240 .538 1.791 .893 .84
18 1058 349 211 165 847 184 1170 338 218 169 959 173 0 0 360 69 41 51 100 100 100 90 1031 1132 4.603 .217 .18 .237 .214 1.98 32 176 .18 .77 60 4730 6170 30 36 270 276 0 331 157 175 .206 321 164 4.852 .171 -2.279 -2.547
19 4103 2911 221 167 3882 2744 4548 2977 224 168 4327 2810 0 0 1933 900 38 48 100 100 100 100 6626 7137 1.415 .707 .649 .925 .697 2.494 32 176 .6 .89 60 4870 6160 29 35 284 290 0 2762 158 2603 .671 2825 2666 1.491 .616 -.576 -.699
20 3454 2824 210 175 3244 2649 2692 2592 211 179 2482 2417 0 0 2541 2317 40 47 100 87 100 84 5893 4899 1.225 .817 .974 .525 .687 4.191 32 176 .836 .86 60 5020 6170 30 36 299 305 0 2679 166 2513 .775 2459 2293 1.291 .924 -.368 -.114

Total number of rows: 41472

Table truncated, full table size 9372 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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