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Sample GSM798954 Query DataSets for GSM798954
Status Public on Sep 19, 2012
Title Patient 2, 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 05PB3095
Organism Homo sapiens
Characteristics cell type: acute myeloid leukemia peripheral blood
time: 48 h
individual: Patient 2
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/2005-11/65513.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
1 320 259 140 306 180 -47 333 249 141 310 193 -57 0 0 66 71 19 64 100 12 100 0 133 136 null null null .288 .405 5.46 32 236 -.731 -.45 70 2020 6050 61 68 42 49 0 238 281 -43 null 229 -52 null null null null
2 3226 359 156 315 3070 44 3416 331 167 316 3260 16 0 0 632 58 58 61 100 41 100 16 3114 3276 69.773 .014 .005 .008 .018 5.284 12 104 .009 .2 50 2160 6050 62 67 57 62 0 330 289 40 .013 304 15 75.924 .005 -6.246 -7.793
3 3084 2807 139 302 2945 2505 3225 3184 141 305 3086 2882 0 0 1324 1387 22 63 100 93 100 87 5450 5968 1.176 .851 .934 .639 .835 2.259 32 176 .888 .94 60 2310 6050 62 68 72 78 0 2580 278 2302 .782 2926 2649 1.279 .858 -.355 -.221
4 911 418 145 305 766 113 1032 406 145 308 887 101 0 0 349 78 21 58 100 78 100 37 879 988 6.779 .148 .114 .142 .146 2.599 32 176 .108 .51 60 2460 6050 62 68 87 93 0 384 280 104 .136 373 93 7.376 .105 -2.883 -3.256
5 817 197 143 316 674 -119 805 181 143 315 662 -135 0 0 72 45 22 59 100 0 100 0 555 527 null null null 0 0 1 12 104 -.172 -.63 50 2600 6050 62 67 101 106 0 181 290 -109 null 166 -124 null null null null
6 279 275 133 295 146 -20 301 230 133 295 168 -65 0 0 96 118 21 58 90 18 84 12 126 103 null null null .894 .65 4.401 32 236 -1 -1 70 2750 6060 62 69 115 122 0 253 271 -18 null 211 -60 null null null null
7 1671 312 139 287 1532 25 1747 310 142 292 1608 23 0 0 274 61 26 56 100 25 100 8 1557 1631 61.28 .016 .014 .025 .03 2.49 12 104 .017 .16 50 2890 6050 62 67 130 135 0 287 264 23 .015 285 21 66.682 .013 -6.059 -6.249
8 538 502 131 278 407 224 562 504 135 282 431 226 0 0 86 94 23 65 100 100 100 75 631 657 1.817 .55 .524 .514 .564 1.599 12 104 .554 .77 50 3040 6040 61 66 145 150 0 461 255 206 .506 463 208 1.977 .482 -.983 -1.053
9 757 447 135 297 622 150 845 443 137 302 710 146 0 0 303 96 19 62 100 78 100 62 772 856 4.147 .241 .206 .262 .258 2.482 32 176 .186 .59 60 3190 6060 63 69 160 166 0 411 273 138 .222 407 134 4.512 .189 -2.174 -2.404
10 1349 1279 137 294 1212 985 1414 1364 139 298 1277 1070 0 0 372 412 23 64 100 100 100 96 2197 2347 1.23 .813 .838 .708 .844 1.843 32 232 .839 .93 70 3330 6060 62 69 173 180 0 1175 270 905 .747 1253 983 1.339 .77 -.421 -.377
11 2649 568 159 280 2490 288 2876 620 160 280 2717 340 0 0 660 141 28 46 100 100 100 75 2778 3057 8.646 .116 .125 .099 .12 1.652 12 104 .12 .86 50 3470 6060 63 68 188 193 0 522 257 265 .106 570 312 9.408 .115 -3.234 -3.12
12 5122 5469 147 298 4975 5171 5315 5573 149 311 5168 5275 0 0 2546 2598 29 86 100 100 100 100 10146 10443 .962 1.039 1.021 1.091 1.063 2.022 32 176 1.031 .94 60 3630 6050 62 68 204 210 0 5026 274 4752 .955 5122 4848 1.047 .938 -.066 -.092
13 854 1869 132 277 722 1592 932 2073 133 273 800 1796 0 0 364 902 19 61 100 93 100 87 2314 2596 .454 2.205 2.245 1.861 2.393 2.68 32 176 2.394 .92 60 3770 6050 62 68 218 224 0 1718 255 1463 2.026 1905 1650 .493 2.063 1.019 1.045
14 285 417 121 264 164 153 293 412 123 260 172 148 0 0 53 87 18 54 100 90 96 75 317 320 1.072 .933 .86 .885 .886 1.696 32 176 1.223 .75 60 3920 6060 63 69 233 239 0 383 243 141 .857 379 136 1.166 .791 -.222 -.339
15 382 13155 122 267 260 12888 380 15431 126 275 258 15164 0 0 75 4877 21 73 100 100 100 100 13148 15422 .02 49.569 58.775 45.17 50.299 1.703 32 228 54.321 .94 70 4060 6060 62 69 246 253 0 12089 245 11844 45.553 14181 13936 .022 54.014 5.509 5.755
16 4037 12564 132 270 3905 12294 4618 14154 137 290 4486 13884 0 0 1350 4635 31 98 100 100 100 100 16199 18370 .318 3.148 3.095 3.11 3.236 1.592 32 236 3.294 .95 70 4210 6050 61 68 261 268 0 11546 248 11298 2.893 13007 12759 .346 2.844 1.533 1.508
17 3227 4513 144 283 3083 4230 3147 4790 147 313 3003 4507 0 0 262 994 27 141 100 100 100 100 7313 7510 .729 1.372 1.501 1.326 1.474 1.326 12 104 1.517 .92 50 4350 6060 63 68 276 281 0 4147 260 3887 1.261 4402 4142 .793 1.379 .334 .464
18 558 317 127 248 431 69 570 303 126 250 443 55 0 0 70 55 20 55 100 50 100 25 500 498 6.246 .16 .124 .151 .15 1.776 12 104 .102 .23 50 4500 6050 62 67 291 296 0 291 228 63 .147 278 51 6.797 .114 -2.765 -3.132
19 3820 3301 145 288 3675 3013 3789 3386 157 307 3644 3098 0 0 362 621 79 121 100 100 100 100 6688 6742 1.22 .82 .85 .803 .864 1.247 12 104 .841 .93 50 4640 6070 64 69 305 310 0 3034 265 2769 .753 3112 2847 1.327 .781 -.408 -.356
20 3705 4986 132 256 3573 4730 3740 5484 132 264 3608 5228 0 0 368 1324 19 54 100 100 100 100 8303 8836 .755 1.324 1.449 1.272 1.4 1.311 12 104 1.512 .93 50 4790 6060 63 68 320 325 0 4582 235 4347 1.217 5040 4804 .822 1.332 .283 .413

Total number of rows: 41472

Table truncated, full table size 9264 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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