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Sample GSM798943 Query DataSets for GSM798943
Status Public on Sep 19, 2012
Title Patient 15, 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 05PB4358
Organism Homo sapiens
Characteristics cell type: acute myeloid leukemia peripheral blood
time: 0 h
individual: Patient 15
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/2005-11/65542.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 1102 294 253 490 849 -196 1120 288 257 495 867 -202 0 0 57 73 44 76 100 0 100 0 653 665 null null null 0 0 1 12 104 -.242 -.64 50 2330 6190 28 33 34 39 0 410 684 -273 null 402 -282 null null null null
2 8130 693 239 471 7891 222 9174 698 244 470 8935 227 0 0 3711 128 50 80 100 87 100 65 8113 9162 35.545 .028 .025 .028 .027 2.143 32 176 .027 .77 60 2480 6200 29 35 49 55 0 967 657 310 .039 974 317 25.477 .035 -4.671 -4.818
3 9291 3856 226 462 9065 3394 10121 4303 238 466 9895 3841 0 0 4539 2137 60 110 100 93 100 84 12459 13736 2.671 .374 .388 .279 .359 1.985 32 232 .399 .96 70 2630 6200 28 35 63 70 0 5380 645 4735 .522 6003 5359 1.914 .542 -.937 -.885
4 2495 388 221 421 2274 -33 2709 406 229 428 2488 -15 0 0 1139 62 42 69 100 0 96 0 2241 2473 null null null .018 .012 6.552 32 176 -.014 -.21 60 2770 6190 28 34 78 84 0 541 587 -46 null 566 -21 null null null null
5 1922 422 213 428 1709 -6 2137 381 223 441 1924 -47 0 0 861 166 49 90 100 18 100 15 1703 1877 null null null .105 .181 11.459 32 176 -.054 -.38 60 2910 6200 29 35 92 98 0 589 597 -8 null 532 -66 null null null null
6 1006 357 244 427 762 -70 1005 354 245 424 761 -73 0 0 135 77 44 69 100 0 100 0 692 688 null null null .066 .067 1.294 12 68 -.13 -.5 40 3060 6190 29 33 108 112 0 498 596 -98 null 494 -102 null null null null
7 3016 459 248 437 2768 22 3228 459 257 444 2980 22 0 0 1086 73 91 67 100 33 100 0 2790 3002 125.818 .008 .007 .015 .022 3.16 12 104 .009 .18 50 3200 6190 28 33 121 126 0 640 610 31 .011 640 31 90.181 .01 -6.495 -6.601
8 1472 298 221 438 1251 -140 1578 277 221 441 1357 -161 0 0 505 104 32 77 100 3 100 3 1111 1196 null null null .062 .089 5.247 32 176 -.122 -.66 60 3350 6200 29 35 136 142 0 416 611 -195 null 386 -225 null null null null
9 1690 687 214 428 1476 259 1732 689 214 433 1518 261 0 0 518 146 32 73 100 90 100 78 1735 1779 5.699 .175 .172 .168 .204 1.81 32 176 .169 .77 60 3500 6200 29 35 151 157 0 958 597 361 .245 961 364 4.085 .24 -2.03 -2.06
10 1718 993 221 421 1497 572 1884 951 227 426 1663 530 0 0 579 310 44 69 100 96 100 90 2069 2193 2.617 .382 .319 .353 .379 1.633 32 232 .405 .89 70 3640 6200 28 35 164 171 0 1385 587 798 .533 1327 739 1.876 .445 -.908 -1.169
11 4455 600 216 429 4239 171 4796 593 220 433 4580 164 0 0 1978 91 37 70 100 84 100 56 4410 4744 24.789 .04 .036 .041 .04 2.108 32 230 .033 .63 70 3790 6200 28 35 179 186 0 837 599 239 .056 827 229 17.768 .05 -4.151 -4.323
12 7579 4644 213 436 7366 4208 7010 4749 215 437 6797 4313 0 0 5785 3180 30 69 100 100 100 96 11574 11110 1.75 .571 .635 .649 .577 1.903 52 304 .551 .96 80 3940 6200 28 36 194 202 0 6479 608 5871 .797 6626 6017 1.255 .885 -.327 -.176
13 1418 1194 204 431 1214 763 1544 1267 206 438 1340 836 0 0 517 361 26 72 100 100 100 90 1977 2176 1.591 .629 .624 .603 .611 1.683 32 170 .626 .92 60 4080 6200 29 35 209 215 0 1666 601 1065 .877 1768 1166 1.14 .87 -.19 -.2
14 868 1095 212 440 656 655 945 1127 215 443 733 687 0 0 203 224 33 75 100 100 100 100 1311 1420 1.002 .998 .937 .996 1.042 1.37 32 232 1.054 .91 70 4230 6200 28 35 223 230 0 1528 614 914 1.393 1572 958 .718 1.308 .478 .387
15 516 8602 206 448 310 8154 500 9834 207 453 294 9386 0 0 105 2736 28 77 100 100 100 100 8464 9680 .038 26.303 31.925 25.989 25.581 1.383 32 227 28.479 .93 70 4370 6210 29 36 237 244 0 12001 625 11376 36.698 13720 13095 .027 44.541 5.198 5.477
16 8067 12290 211 441 7856 11849 9907 14675 212 444 9696 14234 0 0 3888 5188 31 82 100 100 100 100 19705 23930 .663 1.508 1.468 1.595 1.457 1.852 52 305 1.482 .96 80 4520 6200 28 36 252 260 0 17147 615 16531 2.104 20474 19859 .475 2.048 1.073 1.034
17 4128 8488 212 471 3916 8017 4680 8689 215 471 4468 8218 0 0 1386 2185 29 93 100 100 100 100 11933 12686 .488 2.047 1.839 2.156 2.069 1.36 32 226 2.019 .96 70 4670 6200 28 35 267 274 0 11842 657 11185 2.856 12123 11466 .35 2.566 1.514 1.36
18 1408 492 218 427 1190 65 1509 464 221 442 1291 37 0 0 228 89 41 68 100 33 100 33 1255 1328 18.308 .055 .029 .049 .054 3.938 12 104 .045 .33 50 4800 6200 29 34 281 286 0 686 596 91 .076 647 52 13.122 .04 -3.714 -4.644
19 5324 2280 209 428 5115 1852 5860 2417 213 427 5651 1989 0 0 1635 470 37 69 100 100 100 100 6967 7640 2.762 .362 .352 .374 .357 1.338 32 236 .342 .96 70 4960 6200 28 35 296 303 0 3181 597 2584 .505 3372 2775 1.98 .491 -.985 -1.026
20 4555 2681 210 410 4345 2271 4414 1890 212 413 4204 1480 0 0 2969 1595 27 68 100 100 100 100 6616 5684 1.913 .523 .352 .582 .569 1.738 32 176 .519 .97 60 5110 6200 29 35 312 318 0 3740 572 3168 .729 2637 2065 1.371 .491 -.456 -1.026

Total number of rows: 41472

Table truncated, full table size 9279 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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