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Sample GSM798926 Query DataSets for GSM798926
Status Public on Sep 19, 2012
Title Patient 14, 0 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 05PB4266
Organism Homo sapiens
Characteristics cell type: acute myeloid leukemia peripheral blood
time: 0 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/2005-11/65553.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
1 786 7302 181 247 605 7055 946 8534 185 245 765 8287 0 0 346 4389 33 51 100 100 100 100 7660 9052 .086 11.661 10.833 10.565 11.334 2.103 32 176 12.83 .93 60 2210 6140 27 33 26 32 0 7292 247 7045 11.645 8522 8276 .086 10.818 3.542 3.435
2 8167 962 183 237 7984 725 8626 996 191 240 8443 759 0 0 4810 387 42 51 100 100 100 100 8709 9202 11.012 .091 .09 .113 .093 2.334 32 176 .081 .92 60 2360 6150 28 34 41 47 0 961 237 724 .091 995 758 11.027 .09 -3.463 -3.478
3 7403 9855 174 236 7229 9619 8521 10778 179 233 8347 10542 0 0 4915 6005 33 53 100 100 100 100 16848 18889 .752 1.331 1.263 1.62 1.389 2.377 32 176 1.314 .94 60 2510 6140 27 33 56 62 0 9842 236 9606 1.329 10763 10528 .753 1.261 .41 .335
4 3003 686 175 226 2828 460 3511 678 176 234 3336 452 0 0 1466 270 30 55 100 93 100 84 3288 3788 6.148 .163 .135 .15 .153 1.969 32 176 .152 .89 60 2650 6160 29 35 70 76 0 685 226 459 .162 677 451 6.156 .135 -2.622 -2.886
5 2748 355 190 232 2558 123 2814 361 196 238 2624 129 0 0 461 48 39 54 100 83 100 66 2681 2753 20.797 .048 .049 .044 .054 1.582 12 104 .043 .69 50 2790 6140 27 32 84 89 0 355 232 123 .048 361 129 20.825 .049 -4.38 -4.348
6 1025 325 182 250 843 75 1043 317 182 255 861 67 0 0 258 62 29 58 100 50 100 33 918 928 11.24 .089 .078 .06 .075 4.281 12 104 .101 .55 50 2930 6140 27 32 98 103 0 325 250 75 .089 317 67 11.255 .078 -3.493 -3.686
7 3988 594 182 239 3806 355 3985 617 190 241 3803 378 0 0 616 132 37 58 100 100 100 100 4161 4181 10.721 .093 .099 .088 .098 1.43 12 104 .085 .83 50 3080 6140 27 32 113 118 0 593 239 355 .093 616 377 10.736 .099 -3.424 -3.333
8 1268 1868 175 239 1093 1629 1567 2151 181 240 1392 1912 0 0 643 826 34 52 100 96 100 96 2722 3304 .671 1.49 1.374 1.681 1.44 1.966 32 176 1.474 .94 60 3230 6140 27 33 128 134 0 1865 239 1627 1.488 2148 1909 .672 1.372 .574 .456
9 1701 781 183 249 1518 532 1615 725 194 247 1432 476 0 0 517 212 66 55 100 100 100 100 2050 1908 2.853 .35 .332 .345 .343 1.271 12 104 .315 .92 50 3370 6140 27 32 142 147 0 780 249 531 .35 724 475 2.857 .332 -1.515 -1.591
10 3025 2113 174 238 2851 1875 3738 2165 178 240 3564 1927 0 0 1405 843 31 57 100 100 100 100 4726 5491 1.521 .658 .541 .705 .658 2.144 32 176 .616 .93 60 3520 6150 28 34 157 163 0 2110 238 1872 .657 2162 1924 1.523 .54 -.607 -.889
11 5407 518 202 238 5205 280 5089 550 231 244 4887 312 0 0 920 97 155 68 100 100 100 91 5485 5199 18.589 .054 .064 .051 .06 1.499 12 104 .047 .8 50 3660 6140 27 32 171 176 0 517 238 280 .054 549 312 18.614 .064 -4.218 -3.971
12 7690 12789 182 258 7508 12531 8685 15228 187 266 8503 14970 0 0 3898 6566 34 63 100 100 100 100 20039 23473 .599 1.669 1.761 1.934 1.857 2.414 32 232 1.758 .91 70 3820 6150 27 34 186 193 0 12772 258 12514 1.667 15207 14950 .6 1.758 .737 .814
13 1285 2562 174 253 1111 2309 1293 2709 178 257 1119 2456 0 0 562 1256 30 54 93 96 93 96 3420 3575 .481 2.078 2.195 2.415 2 2.552 32 176 2.251 .92 60 3960 6150 28 34 201 207 0 2559 253 2306 2.075 2705 2453 .482 2.192 1.053 1.132
14 969 1152 192 242 777 910 1000 1172 220 257 808 930 0 0 161 189 114 97 100 100 100 100 1687 1738 .854 1.171 1.151 1.175 1.175 1.252 12 104 1.219 .94 50 4100 6140 27 32 215 220 0 1150 242 909 1.17 1170 929 .855 1.149 .226 .201
15 497 19594 177 253 320 19341 532 17677 182 262 355 17424 0 0 265 16535 33 78 82 100 69 100 19661 17779 .017 60.441 49.082 53.939 61.495 2.205 52 320 65.536 .93 80 4250 6150 27 35 229 237 0 19568 253 19315 60.359 17653 17400 .017 49.015 5.915 5.615
16 8496 14356 186 261 8310 14095 8785 14422 200 272 8599 14161 0 0 2453 2645 62 71 100 100 100 100 22405 22760 .59 1.696 1.647 1.805 1.71 1.49 32 176 1.652 .93 60 4400 6150 28 34 245 251 0 14337 261 14076 1.694 14403 14142 .59 1.645 .76 .718
17 4701 6602 179 264 4522 6338 5262 7566 182 265 5083 7302 0 0 1763 2747 32 70 100 100 100 100 10860 12385 .713 1.402 1.437 1.257 1.43 1.556 32 232 1.423 .95 70 4540 6150 27 34 258 265 0 6593 264 6329 1.4 7556 7292 .714 1.435 .485 .521
18 1681 537 177 237 1504 300 1612 531 181 241 1435 294 0 0 177 112 32 52 100 100 100 91 1804 1729 5.013 .199 .205 .184 .201 1.597 12 104 .198 .85 50 4680 6150 28 33 273 278 0 536 237 300 .199 530 294 5.02 .205 -2.328 -2.289
19 4928 3386 180 246 4748 3140 5331 3902 185 249 5151 3656 0 0 2094 1617 32 56 100 100 100 100 7888 8807 1.512 .661 .71 .557 .65 1.896 32 236 .666 .92 70 4830 6160 28 35 287 294 0 3381 246 3136 .66 3897 3651 1.514 .709 -.599 -.497
20 3757 3442 183 253 3574 3189 3976 2960 183 254 3793 2707 0 0 2943 2694 31 58 100 93 100 84 6763 6500 1.121 .892 .714 .693 .84 3.235 32 176 .896 .93 60 4980 6150 28 34 303 309 0 3437 253 3185 .891 2956 2703 1.122 .713 -.166 -.489

Total number of rows: 41472

Table truncated, full table size 9346 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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