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Sample GSM798925 Query DataSets for GSM798925
Status Public on Sep 19, 2012
Title Patient 1, 0 h against 48 h
Sample type RNA
 
Channel 1
Source name 05PB2584
Organism Homo sapiens
Characteristics cell type: acute myeloid leukemia peripheral blood
time: 0 h
individual: Patient 1
Extracted molecule total RNA
Extraction protocol not provided
Label Cy3
Label protocol not provided
 
Channel 2
Source name 05PB2606
Organism Homo sapiens
Characteristics cell type: acute myeloid leukemia peripheral blood
time: 48 h
individual: Patient 1
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/2005-11/65407.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
1 360 201 142 190 218 11 335 197 142 193 193 7 0 0 172 63 22 53 92 23 80 5 229 200 19.818 .05 .036 .45 .312 6.226 52 304 -.021 -.04 80 2020 6110 31 39 30 38 0 210 199 12 .053 206 7 18.94 .038 -4.243 -4.72
2 403 217 142 197 261 20 283 220 143 194 141 23 0 0 252 70 24 49 86 28 65 13 281 164 13.05 .077 .163 .402 .405 5.345 52 293 .058 .15 80 2170 6110 31 39 45 53 0 227 206 21 .08 230 24 12.472 .171 -3.641 -2.551
3 2112 1860 139 198 1973 1662 2425 2043 144 197 2286 1845 0 0 1299 1299 33 54 96 84 93 81 3635 4131 1.187 .842 .807 .696 .896 1.843 32 219 .939 .95 70 2320 6100 30 37 60 67 0 1946 207 1739 .881 2138 1931 1.135 .844 -.182 -.244
4 299 384 137 186 162 198 248 305 139 188 111 119 0 0 151 235 30 53 75 55 65 51 360 230 .818 1.222 1.072 1.211 1.445 3.126 52 285 1.619 .78 80 2460 6110 31 39 74 82 0 402 195 207 1.279 319 125 .782 1.122 .355 .166
5 296 175 137 182 159 -7 233 170 139 186 96 -12 0 0 137 57 23 53 84 13 69 1 152 84 null null null .333 .514 6.053 52 272 -.088 -.11 80 2610 6110 31 39 89 97 0 183 190 -7 null 178 -13 null null null null
6 291 204 139 188 152 16 216 204 140 188 77 16 0 0 151 62 21 49 76 26 63 9 168 93 9.5 .105 .208 .631 .9 5.361 52 272 -1 -1 80 2750 6110 31 39 103 111 0 213 197 17 .11 213 17 9.079 .217 -3.183 -2.201
7 323 203 138 183 185 20 233 199 138 184 95 16 0 0 193 62 23 49 80 30 67 5 205 111 9.25 .108 .168 .299 .251 3.908 52 272 .117 .21 80 2900 6110 31 39 118 126 0 212 191 21 .113 208 17 8.84 .176 -3.144 -2.504
8 271 155 139 192 132 -37 216 145 140 191 77 -47 0 0 132 52 22 51 75 7 67 0 95 30 null null null .467 .419 4.208 52 272 -.334 -.4 80 3040 6110 31 39 132 140 0 162 201 -39 null 152 -49 null null null null
9 318 404 137 191 181 213 240 353 138 188 103 162 0 0 188 210 22 52 69 67 59 55 394 265 .85 1.177 1.573 1.436 1.166 2.98 52 272 1.235 .86 80 3190 6110 31 39 147 155 0 423 200 223 1.231 369 170 .812 1.646 .3 .719
10 1220 767 136 177 1084 590 1182 782 138 183 1046 605 0 0 905 492 24 53 82 75 78 69 1674 1651 1.837 .544 .578 .593 .533 2.163 52 264 .524 .94 80 3330 6120 32 40 161 169 0 803 185 617 .57 818 633 1.756 .605 -.812 -.725
11 195 281 135 183 60 98 176 244 136 186 41 61 0 0 61 117 21 53 57 51 50 38 158 102 .612 1.633 1.488 1.542 1.693 3.568 52 286 2.585 .67 80 3480 6120 32 40 176 184 0 294 191 103 1.709 255 64 .585 1.557 .773 .639
12 3112 3522 135 187 2977 3335 3605 4099 137 191 3470 3912 0 0 2117 2542 21 52 96 93 93 90 6312 7382 .893 1.12 1.127 1.202 1.128 1.905 32 220 1.176 .97 70 3630 6100 30 37 191 198 0 3685 196 3490 1.172 4289 4093 .853 1.18 .229 .238
13 424 412 135 184 289 228 327 349 137 188 192 165 0 0 292 238 23 55 73 69 63 59 517 357 1.268 .789 .859 .961 .842 3.099 52 287 .812 .88 80 3770 6110 31 39 205 213 0 431 193 239 .825 365 173 1.211 .899 -.277 -.153
14 407 243 134 182 273 61 426 244 136 184 292 62 0 0 120 65 21 52 100 56 96 15 334 354 4.475 .223 .212 .24 .243 2.864 32 224 .419 .38 70 3920 6110 31 38 220 227 0 254 190 64 .234 255 65 4.277 .222 -2.097 -2.17
15 377 1504 133 189 244 1315 386 1662 135 186 253 1473 0 0 96 512 22 51 100 100 93 100 1559 1726 .186 5.389 5.822 5.535 5.458 1.564 32 226 5.794 .94 70 4070 6110 31 38 235 242 0 1574 198 1376 5.639 1739 1541 .177 6.092 2.495 2.607
16 8604 2981 140 181 8464 2800 9746 3545 150 187 9606 3364 0 0 3736 1313 41 53 100 96 100 96 11264 12970 3.023 .331 .35 .319 .353 1.704 32 226 .334 .96 70 4210 6110 31 38 249 256 0 3119 189 2930 .346 3709 3520 2.889 .366 -1.531 -1.448
17 1633 2365 139 188 1494 2177 2067 2756 142 197 1928 2568 0 0 978 1442 27 59 84 93 84 87 3671 4496 .686 1.457 1.332 1.896 1.542 1.847 32 225 1.464 .97 70 4360 6100 30 37 264 271 0 2475 197 2278 1.525 2884 2687 .656 1.394 .609 .479
18 143 178 136 187 7 -9 146 177 138 189 10 -10 0 0 28 45 24 53 30 7 9 0 -2 0 null null null 1.315 1.344 4.256 52 268 21.491 .08 80 4500 6120 32 40 278 286 0 186 196 -9 null 185 -10 null null null null
19 1281 795 135 185 1146 610 1205 780 135 185 1070 595 0 0 1083 570 21 47 78 76 71 67 1756 1665 1.879 .532 .556 .893 .574 2.929 52 274 .524 .98 80 4650 6110 31 39 293 301 0 832 194 638 .557 816 623 1.795 .582 -.844 -.781
20 743 823 136 182 607 641 372 473 137 185 236 291 0 0 722 717 22 49 65 67 61 61 1248 527 .947 1.056 1.233 1.545 1.089 3.216 52 264 1.016 .96 80 4800 6110 31 39 308 316 0 861 190 671 1.105 495 304 .905 1.29 .144 .368

Total number of rows: 41472

Table truncated, full table size 9104 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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