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Sample GSM798957 Query DataSets for GSM798957
Status Public on Sep 19, 2012
Title Patient 16, 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 05PB4338
Organism Homo sapiens
Characteristics cell type: acute myeloid leukemia peripheral blood
time: 48 h
individual: Patient 16
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/2005-11/65548.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 1518 475 257 304 1261 171 1577 460 256 297 1320 156 0 0 189 76 33 51 100 91 100 83 1432 1476 7.374 .136 .118 .123 .121 1.619 12 104 .14 .7 50 2140 6100 27 32 31 36 0 611 391 220 .174 592 201 5.732 .152 -2.519 -2.718
2 12657 1950 263 321 12394 1629 13231 2087 331 325 12968 1766 0 0 4975 696 356 70 100 100 100 100 14023 14734 7.608 .131 .136 .128 .13 1.465 12 104 .12 .93 50 2280 6090 26 31 45 50 0 2509 413 2096 .169 2685 2272 5.914 .175 -2.564 -2.513
3 8405 11001 247 331 8158 10670 8492 10791 250 332 8245 10460 0 0 6181 7653 35 60 100 100 100 96 18828 18705 .765 1.308 1.269 1.283 1.368 2.12 32 176 1.285 .94 60 2440 6100 27 33 61 67 0 14152 426 13726 1.683 13882 13456 .594 1.632 .751 .707
4 3817 928 272 344 3545 584 3885 868 389 357 3613 524 0 0 1588 238 496 108 100 100 100 91 4129 4137 6.07 .165 .145 .167 .163 1.454 12 104 .136 .9 50 2570 6080 25 30 74 79 0 1194 443 751 .212 1117 674 4.719 .187 -2.238 -2.422
5 3167 640 256 338 2911 302 3506 662 261 341 3250 324 0 0 800 142 40 57 100 91 100 83 3213 3574 9.639 .104 .1 .09 .11 1.859 12 104 .097 .82 50 2720 6100 27 32 89 94 0 823 435 389 .133 852 417 7.493 .128 -2.905 -2.963
6 1220 416 248 329 972 87 1329 446 255 330 1081 117 0 0 260 70 38 53 100 66 100 58 1059 1198 11.172 .09 .108 .06 .107 4.289 12 104 .138 .68 50 2860 6080 25 30 103 108 0 535 423 112 .115 574 151 8.685 .139 -3.118 -2.844
7 4370 1001 251 323 4119 678 4807 1010 265 337 4556 687 0 0 1828 243 55 60 100 100 100 100 4797 5243 6.075 .165 .151 .177 .167 1.342 12 104 .146 .95 50 3010 6090 26 31 118 123 0 1288 416 872 .212 1299 884 4.722 .194 -2.24 -2.366
8 1434 1140 240 302 1194 838 1591 1108 241 308 1351 806 0 0 768 536 31 53 100 87 100 87 2032 2157 1.425 .702 .597 .588 .643 2.808 32 176 .693 .94 60 3160 6090 26 32 133 139 0 1467 389 1078 .903 1425 1037 1.108 .767 -.147 -.382
9 1372 765 242 312 1130 453 1370 746 256 314 1128 434 0 0 394 197 101 57 100 100 100 100 1583 1562 2.494 .401 .385 .382 .453 1.621 12 104 .36 .89 50 3300 6080 25 30 147 152 0 984 401 583 .516 960 558 1.939 .495 -.955 -1.015
10 4113 2788 249 311 3864 2477 4455 3114 262 311 4206 2803 0 0 1013 718 78 58 100 100 100 100 6341 7009 1.56 .641 .666 .635 .623 1.159 12 104 .6 .96 50 3450 6100 27 32 162 167 0 3587 400 3187 .825 4006 3606 1.213 .857 -.278 -.222
11 5715 505 252 306 5463 199 5786 520 263 307 5534 214 0 0 1746 114 74 53 100 91 100 75 5662 5748 27.452 .036 .039 .035 .035 1.39 12 104 .033 .76 50 3590 6100 27 32 176 181 0 650 394 256 .047 669 275 21.339 .05 -4.415 -4.329
12 6925 10674 238 301 6687 10373 8148 12285 245 310 7910 11984 0 0 4061 6223 51 79 100 100 100 100 17060 19894 .645 1.551 1.515 1.504 1.599 2.404 32 176 1.57 .95 60 3740 6100 27 33 191 197 0 13732 387 13344 1.996 15804 15417 .501 1.949 .997 .963
13 1483 2674 226 287 1257 2387 1462 2780 230 291 1236 2493 0 0 285 781 29 57 100 100 100 100 3644 3729 .527 1.899 2.017 1.817 2.052 1.445 12 104 2.025 .92 50 3880 6090 26 31 205 210 0 3440 369 3071 2.443 3576 3207 .409 2.595 1.289 1.376
14 1216 1200 235 276 981 924 1243 1177 253 288 1008 901 0 0 218 332 87 64 100 100 100 100 1905 1909 1.062 .942 .894 .904 .997 1.471 12 104 .962 .91 50 4030 6090 26 31 220 225 0 1544 355 1189 1.212 1514 1159 .825 1.15 .277 .202
15 534 19632 227 283 307 19349 501 20931 226 292 274 20648 0 0 141 10459 31 67 100 100 96 100 19656 20922 .016 63.026 75.358 55.681 61.655 1.711 32 233 69.345 .93 70 4190 6120 28 35 235 242 0 25256 364 24892 81.08 26927 26563 .012 96.944 6.341 6.599
16 7794 13872 232 283 7562 13589 8402 14638 234 289 8170 14355 0 0 3668 4828 35 60 100 100 100 100 21151 22525 .556 1.797 1.757 2.1 1.824 1.632 32 233 1.713 .96 70 4330 6100 26 33 249 256 0 17846 364 17482 2.312 18831 18467 .433 2.26 1.209 1.177
17 3792 5326 231 294 3561 5032 4440 5526 232 291 4209 5232 0 0 2077 2268 32 57 100 100 100 100 8593 9441 .708 1.413 1.243 1.92 1.417 2.232 32 176 1.332 .96 60 4480 6110 28 34 265 271 0 6852 378 6473 1.818 7109 6731 .55 1.599 .862 .677
18 1516 417 229 280 1287 137 1575 416 231 278 1346 136 0 0 311 52 30 46 100 100 100 75 1424 1482 9.394 .106 .101 .102 .118 1.675 12 104 .093 .65 50 4610 6110 28 33 278 283 0 536 360 176 .137 535 175 7.302 .13 -2.868 -2.944
19 3823 2341 233 296 3590 2045 3354 2483 424 360 3121 2187 0 0 2288 951 834 316 75 100 75 100 5635 5308 1.756 .57 .701 .714 .609 2.127 12 104 .468 .93 50 4760 6080 25 30 293 298 0 3012 381 2631 .733 3194 2813 1.365 .901 -.448 -.15
20 3928 3135 234 267 3694 2868 3403 3423 237 277 3169 3156 0 0 2715 1615 39 54 100 100 100 100 6562 6325 1.288 .776 .996 .996 .832 2.032 12 104 .661 .94 50 4910 6100 27 32 308 313 0 4033 343 3690 .999 4404 4060 1.001 1.281 -.002 .357

Total number of rows: 41472

Table truncated, full table size 9364 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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