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Sample GSM798941 Query DataSets for GSM798941
Status Public on Sep 19, 2012
Title Patient 3, 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 05PB2492
Organism Homo sapiens
Characteristics cell type: acute myeloid leukemia peripheral blood
time: 0 h
individual: Patient 3
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/2005-11/65526.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
1 444 187 150 214 294 -27 488 171 153 213 338 -43 0 0 154 43 25 47 90 3 87 0 267 295 null null null .145 .104 3.873 32 176 -.051 -.14 60 2020 5910 64 70 51 57 0 215 246 -31 null 197 -50 null null null null
2 3789 1724 162 251 3627 1473 3900 1559 236 561 3738 1308 0 0 2090 1239 751 2734 90 18 78 0 5100 5046 2.462 .406 .35 .3 .37 2.29 32 176 .444 .88 60 2170 5910 64 70 66 72 0 1986 289 1697 .468 1796 1507 2.138 .403 -1.096 -1.311
3 3866 6093 174 280 3692 5813 4027 6736 177 285 3853 6456 0 0 2068 3069 35 90 100 96 100 93 9505 10309 .635 1.574 1.676 1.339 1.523 2.407 32 176 1.564 .87 60 2320 5910 64 70 81 87 0 7018 323 6695 1.814 7759 7436 .551 1.93 .859 .949
4 1548 285 191 267 1357 18 1532 299 203 276 1341 32 0 0 390 81 87 66 100 16 100 16 1375 1373 75.389 .013 .024 .041 .036 1.902 12 104 .016 .13 50 2460 5900 63 68 95 100 0 328 308 21 .015 344 37 65.452 .027 -6.032 -5.185
5 1125 159 189 268 936 -109 1104 160 186 268 915 -108 0 0 58 44 30 66 100 0 100 0 827 807 null null null 0 0 1 12 104 -.117 -.57 50 2610 5910 64 69 110 115 0 183 309 -126 null 184 -124 null null null null
6 521 221 181 280 340 -59 545 213 182 291 364 -67 0 0 83 39 30 57 100 0 100 0 281 297 null null null .07 .07 1 12 68 -.186 -.37 40 2750 5900 64 68 125 129 0 255 323 -68 null 245 -77 null null null null
7 2249 584 191 296 2058 288 2173 561 250 559 1982 265 0 0 316 163 379 2336 100 0 100 0 2346 2247 7.146 .14 .134 .092 .137 4.269 12 104 .17 .74 50 2900 5910 64 69 139 144 0 673 341 332 .161 646 305 6.204 .154 -2.633 -2.699
8 845 169 173 250 672 -81 840 158 216 248 667 -92 0 0 98 55 402 47 100 0 8 0 591 575 null null null .034 .034 1 12 104 -.035 -.3 50 3050 5910 64 69 154 159 0 195 288 -93 null 182 -106 null null null null
9 808 909 162 254 646 655 791 900 325 276 629 646 0 0 215 133 1598 189 0 100 0 100 1301 1275 .986 1.014 1.027 1.051 1.231 1.377 12 104 .021 .08 50 3190 5910 64 69 168 173 0 1047 293 754 1.168 1037 744 .856 1.183 .224 .242
10 1734 1184 165 247 1569 937 1664 1264 172 243 1499 1017 0 0 404 440 48 47 100 100 100 100 2506 2516 1.674 .597 .678 .53 .594 1.713 32 176 .624 .9 60 3340 5920 65 71 183 189 0 1364 284 1079 .688 1456 1171 1.454 .781 -.54 -.356
11 2607 280 178 243 2429 37 2826 288 183 248 2648 45 0 0 916 51 35 51 100 34 100 9 2466 2693 65.649 .015 .017 .021 .026 2.279 32 176 .014 .31 60 3480 5910 64 70 197 203 0 323 280 43 .018 332 52 56.996 .02 -5.833 -5.675
12 4798 5163 186 265 4612 4898 5998 5893 190 266 5812 5628 0 0 2510 2317 35 58 100 100 100 100 9510 11440 .942 1.062 .968 1.153 1.07 2.361 32 176 .983 .89 60 3630 5920 65 71 212 218 0 5947 305 5642 1.223 6788 6482 .818 1.115 .291 .157
13 858 564 181 244 677 320 885 579 181 251 704 335 0 0 309 182 27 53 100 93 96 87 997 1039 2.116 .473 .476 .459 .477 1.981 32 176 .468 .79 60 3780 5910 64 70 227 233 0 650 281 369 .544 667 386 1.837 .548 -.877 -.868
14 453 359 179 239 274 120 452 373 182 253 273 134 0 0 38 137 25 56 100 58 100 50 394 407 2.283 .438 .491 .466 .697 2.716 12 68 1.02 .33 40 3920 5920 66 70 242 246 0 414 275 138 .504 430 154 1.982 .565 -.987 -.823
15 357 1447 175 252 182 1195 363 1536 190 264 188 1284 0 0 51 273 105 109 87 100 31 100 1377 1472 .152 6.566 6.83 6.675 6.581 1.309 32 176 7.346 .83 60 4070 5920 65 71 256 262 0 1667 290 1376 7.563 1769 1479 .132 7.867 2.919 2.976
16 6964 8615 182 280 6782 8335 7610 10182 191 309 7428 9902 0 0 2220 3923 46 263 100 100 100 96 15117 17330 .814 1.229 1.333 1.04 1.307 1.701 32 232 1.447 .92 70 4210 5910 63 70 269 276 0 9923 323 9600 1.416 11728 11405 .706 1.535 .501 .619
17 2228 4188 186 279 2042 3909 2295 4462 190 285 2109 4183 0 0 557 1566 42 71 100 100 100 100 5951 6292 .522 1.914 1.983 1.77 1.863 1.469 32 236 2.188 .93 70 4360 5910 63 70 284 291 0 4824 321 4502 2.205 5139 4818 .454 2.285 1.141 1.192
18 619 167 180 265 439 -98 614 156 195 261 434 -109 0 0 69 45 70 56 100 0 100 0 341 325 null null null 0 0 1 12 104 -.191 -.6 50 4500 5900 63 68 299 304 0 192 305 -113 null 180 -126 null null null null
19 3153 2521 190 275 2963 2246 3364 2705 191 279 3174 2430 0 0 756 829 34 58 100 100 100 100 5209 5604 1.319 .758 .766 .703 .763 1.536 32 232 .767 .9 70 4650 5920 64 71 313 320 0 2904 317 2587 .873 3116 2799 1.145 .882 -.196 -.181
20 3116 3141 189 274 2927 2867 3430 3708 189 281 3241 3434 0 0 1482 1605 34 57 100 100 100 100 5794 6675 1.021 .98 1.06 .874 .961 2.137 32 176 1.002 .89 60 4800 5920 65 71 329 335 0 3618 316 3302 1.128 4271 3955 .886 1.22 .174 .287

Total number of rows: 41472

Table truncated, full table size 9209 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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