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Sample GSM798944 Query DataSets for GSM798944
Status Public on Sep 19, 2012
Title Patient 18, 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 05PB4025
Organism Homo sapiens
Characteristics cell type: acute myeloid leukemia peripheral blood
time: 48 h
individual: Patient 18
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/2005-11/65547.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
1 812 558 225 374 587 184 855 556 226 382 630 182 0 0 371 116 28 66 100 84 96 65 771 812 3.19 .313 .289 .329 .329 2.693 32 176 .282 .78 60 2110 6640 25 31 24 30 0 624 418 206 .35 621 203 2.854 .323 -1.513 -1.631
2 8120 2387 232 396 7888 1991 8339 2568 319 415 8107 2172 0 0 3239 1007 509 148 100 100 100 100 9879 10279 3.962 .252 .268 .236 .263 1.531 12 104 .251 .93 50 2250 6620 23 28 38 43 0 2668 443 2226 .282 2870 2428 3.544 .299 -1.826 -1.74
3 7678 4975 216 375 7462 4600 7560 4791 219 373 7344 4416 0 0 5288 3100 29 62 100 100 100 100 12062 11760 1.622 .616 .601 .826 .648 2.671 32 176 .586 .93 60 2410 6620 23 29 54 60 0 5561 419 5142 .689 5355 4936 1.451 .672 -.537 -.573
4 2180 489 217 362 1963 127 2120 449 218 370 1903 87 0 0 1334 133 31 104 100 46 100 25 2090 1990 15.457 .065 .046 .063 .053 2.202 32 176 .058 .38 60 2550 6640 25 31 68 74 0 547 405 142 .072 502 97 13.828 .051 -3.79 -4.29
5 2549 357 219 348 2330 9 3026 335 222 354 2807 -13 0 0 845 65 29 55 100 33 100 0 2339 2794 258.889 .004 null .04 .027 2.277 12 104 -.009 -.15 50 2680 6630 24 29 81 86 0 399 389 10 .004 374 -15 231.609 null -7.856 null
6 1043 460 214 346 829 114 1086 442 220 352 872 96 0 0 240 61 30 62 100 83 100 33 943 968 7.272 .138 .11 .122 .123 2.001 12 68 .11 .55 40 2830 6620 24 28 97 101 0 514 387 127 .154 494 107 6.506 .123 -2.702 -3.023
7 3549 686 228 353 3321 333 4003 682 237 367 3775 329 0 0 1359 209 56 62 100 83 100 83 3654 4104 9.973 .1 .087 .098 .109 1.427 12 68 .102 .83 40 2980 6640 26 30 112 116 0 767 395 372 .112 762 368 8.922 .097 -3.157 -3.36
8 1622 329 223 348 1399 -19 1758 349 233 351 1535 1 0 0 429 65 53 59 100 16 100 0 1380 1536 null null .001 .019 .026 2.573 12 104 -.03 -.32 50 3130 6620 23 28 126 131 0 368 389 -21 null 390 1 null .001 null -10.423
9 1485 8960 221 386 1264 8574 1502 10069 231 443 1281 9683 0 0 408 3392 80 381 100 100 100 100 9838 10964 .147 6.783 7.559 6.489 6.962 1.357 12 104 7.449 .92 50 3270 6630 24 29 140 145 0 10015 431 9584 7.582 11255 10824 .132 8.449 2.923 3.079
10 2690 2137 215 349 2475 1788 3269 2158 215 354 3054 1809 0 0 1384 1048 26 66 100 96 100 87 4263 4863 1.384 .722 .592 .608 .742 2.873 32 176 .719 .95 60 3420 6640 25 31 155 161 0 2389 390 1999 .808 2412 2022 1.238 .662 -.308 -.595
11 5378 641 237 346 5141 295 5264 692 323 352 5027 346 0 0 1716 169 467 60 100 83 100 83 5436 5373 17.427 .057 .069 .055 .059 1.644 12 104 .059 .89 50 3560 6630 24 29 169 174 0 717 387 330 .064 774 387 15.591 .077 -3.963 -3.7
12 10955 7609 221 347 10734 7262 13471 8434 226 357 13250 8087 0 0 6039 4022 35 66 100 100 100 100 17996 21337 1.478 .677 .61 .653 .672 2.605 32 176 .649 .94 60 3710 6630 24 30 184 190 0 8505 388 8117 .756 9427 9040 1.322 .682 -.403 -.552
13 1592 2560 211 346 1381 2214 1595 2644 211 356 1384 2298 0 0 300 798 26 61 100 100 100 100 3595 3682 .624 1.603 1.66 1.529 1.637 1.39 12 104 1.753 .93 50 3860 6650 26 31 199 204 0 2862 387 2475 1.792 2955 2569 .558 1.856 .842 .892
14 1074 950 223 363 851 587 1108 991 244 380 885 628 0 0 277 253 105 113 100 100 100 91 1438 1513 1.45 .69 .71 .648 .705 1.428 12 104 .746 .94 50 4000 6630 24 29 213 218 0 1062 406 656 .771 1108 702 1.297 .793 -.375 -.334
15 500 14276 218 426 282 13850 530 16394 222 751 312 15968 0 0 109 5282 45 1514 100 100 100 100 14132 16280 .02 49.113 51.179 49.082 49.14 1.299 12 104 49.007 .93 50 4150 6630 24 29 228 233 0 15957 476 15481 54.898 18325 17849 .018 57.208 5.779 5.838
16 8829 17501 219 368 8610 17133 9813 19421 224 374 9594 19053 0 0 3178 5857 34 76 100 100 100 100 25743 28647 .503 1.99 1.986 2.064 2.049 1.699 32 232 2.027 .94 70 4300 6640 24 31 242 249 0 19562 411 19151 2.224 21708 21297 .45 2.22 1.153 1.15
17 3781 7809 213 351 3568 7458 4410 8212 217 366 4197 7861 0 0 2132 4433 29 82 100 100 100 90 11026 12058 .478 2.09 1.873 1.847 2.094 1.891 32 232 2.171 .95 70 4440 6640 24 31 256 263 0 8729 392 8336 2.336 9179 8787 .428 2.094 1.224 1.066
18 1298 489 209 335 1089 154 1335 455 212 339 1126 120 0 0 314 114 32 60 100 83 100 50 1243 1246 7.071 .141 .107 .116 .094 1.878 12 104 .155 .69 50 4580 6630 24 29 271 276 0 547 374 172 .158 509 134 6.326 .119 -2.661 -3.069
19 4592 3727 216 363 4376 3364 4223 3713 217 362 4007 3350 0 0 2746 2107 27 64 100 100 100 100 7740 7357 1.301 .769 .836 .741 .761 2.15 32 176 .761 .96 60 4740 6660 27 33 287 293 0 4166 406 3760 .859 4150 3745 1.164 .935 -.219 -.098
20 4347 4914 224 383 4123 4531 4448 4776 222 386 4224 4393 0 0 2715 3593 30 78 100 100 100 91 8654 8617 .91 1.099 1.04 .809 .939 2.05 12 104 1.241 .93 50 4880 6650 26 31 301 306 0 5493 428 5065 1.228 5339 4910 .814 1.163 .297 .217

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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