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Sample GSM798937 Query DataSets for GSM798937
Status Public on Sep 19, 2012
Title Patient 11, 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 05PB3616
Organism Homo sapiens
Characteristics cell type: acute myeloid leukemia peripheral blood
time: 48 h
individual: Patient 11
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/2005-11/65487.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
1 824 541 248 540 576 1 858 531 278 535 610 -9 0 0 210 130 110 94 100 33 91 16 577 601 576 .002 null .155 .412 10.533 12 104 -.072 -.18 50 2110 5920 25 30 40 45 0 625 624 1 .002 614 -10 498.372 null -8.961 null
2 8218 807 238 528 7980 279 8236 797 244 525 7998 269 0 0 3456 146 43 92 100 93 100 78 8259 8267 28.602 .035 .034 .036 .035 1.531 32 176 .034 .81 60 2260 5940 27 33 55 61 0 933 610 322 .04 921 311 24.747 .039 -4.629 -4.685
3 7798 4376 226 524 7572 3852 7542 4527 228 539 7316 4003 0 0 5650 3180 32 158 100 82 100 78 11424 11319 1.966 .509 .547 .394 .497 3.612 52 310 .496 .88 80 2420 5930 25 33 70 78 0 5058 606 4452 .588 5232 4627 1.701 .632 -.766 -.661
4 2650 752 242 507 2408 245 2866 741 325 538 2624 234 0 0 586 120 386 130 100 83 100 41 2653 2858 9.829 .102 .089 .091 .098 1.713 12 98 .111 .78 50 2540 5930 26 31 83 88 0 869 586 283 .118 856 270 8.504 .103 -3.088 -3.278
5 1939 445 231 517 1708 -72 2264 440 232 524 2033 -77 0 0 790 110 32 88 100 12 100 0 1636 1956 null null null .184 .104 3.534 32 176 -.061 -.49 60 2700 5940 27 33 99 105 0 514 598 -83 null 509 -89 null null null null
6 999 631 231 503 768 128 1028 590 236 503 797 87 0 0 99 142 35 90 100 50 100 33 896 884 6 .167 .109 .124 .139 2.948 12 104 .175 .41 50 2840 5930 26 31 113 118 0 729 581 148 .193 682 101 5.191 .126 -2.376 -2.987
7 2739 869 228 505 2511 364 3118 890 230 508 2890 385 0 0 1316 214 37 87 100 87 100 75 2875 3275 6.898 .145 .133 .148 .133 3.376 32 176 .121 .73 60 2990 5940 27 33 128 134 0 1004 584 421 .168 1029 445 5.969 .154 -2.577 -2.699
8 1448 403 230 497 1218 -94 1620 389 230 493 1390 -108 0 0 436 100 33 81 100 3 100 3 1124 1282 null null null .025 .026 8.968 32 176 -.071 -.4 60 3130 5940 27 33 142 148 0 466 574 -109 null 450 -125 null null null null
9 1421 3134 223 534 1198 2600 1370 3342 223 532 1147 2808 0 0 454 805 31 89 100 100 100 100 3798 3955 .461 2.17 2.448 2.236 2.107 1.769 32 176 2.257 .88 60 3280 5950 28 34 157 163 0 3622 617 3005 2.508 3863 3245 .399 2.829 1.327 1.501
10 3809 1733 220 503 3589 1230 4097 1887 223 503 3877 1384 0 0 940 583 32 93 100 100 100 96 4819 5261 2.918 .343 .357 .3 .353 1.681 32 232 .363 .91 70 3420 5950 27 34 170 177 0 2003 581 1422 .396 2181 1600 2.525 .413 -1.336 -1.277
11 4194 1016 240 514 3954 502 4343 1052 244 517 4103 538 0 0 1611 303 46 92 100 87 100 87 4456 4641 7.876 .127 .131 .121 .132 1.984 32 176 .122 .81 60 3570 5940 27 33 186 192 0 1174 594 580 .147 1216 622 6.815 .152 -2.769 -2.722
12 11906 5161 241 524 11665 4637 12812 6179 251 548 12571 5655 0 0 4073 2791 63 175 100 93 100 87 16302 18226 2.516 .398 .45 .275 .407 2.424 32 232 .458 .9 70 3720 5930 25 32 200 207 0 5965 606 5359 .459 7141 6536 2.177 .52 -1.122 -.944
13 1382 2201 222 516 1160 1685 1430 2337 228 524 1208 1821 0 0 452 925 35 103 100 93 100 93 2845 3029 .688 1.453 1.507 1.284 1.458 2.15 32 176 1.832 .84 60 3860 5940 27 33 215 221 0 2544 596 1947 1.679 2701 2105 .596 1.742 .747 .801
14 1078 887 226 505 852 382 1089 906 227 508 863 401 0 0 188 169 35 93 100 93 100 87 1234 1264 2.23 .448 .465 .386 .449 2.12 32 176 .481 .78 60 4010 5950 28 34 230 236 0 1025 584 442 .518 1047 463 1.93 .537 -.948 -.897
15 526 8977 225 528 301 8449 584 10031 265 552 359 9503 0 0 146 2559 251 153 62 100 0 100 8750 9862 .036 28.07 26.471 35.287 25.739 2.521 32 220 29.722 .41 70 4160 5960 28 35 244 251 0 10375 610 9765 32.442 11593 10983 .031 30.594 5.02 4.935
16 9730 20031 227 502 9503 19529 11659 23033 258 533 11432 22531 0 0 4941 7175 228 159 100 100 90 100 29032 33963 .487 2.055 1.971 2.595 1.899 2.078 52 268 1.953 .92 80 4310 5960 28 36 259 267 0 23151 580 22571 2.375 26621 26040 .421 2.278 1.248 1.188
17 3516 5704 219 504 3297 5200 4281 6867 222 507 4062 6363 0 0 1834 2859 33 97 100 100 100 96 8497 10425 .634 1.577 1.566 1.561 1.487 2.649 52 276 1.661 .9 80 4450 5950 27 35 273 281 0 6592 583 6010 1.823 7937 7354 .549 1.81 .866 .856
18 1084 506 215 510 869 -4 1177 489 222 515 962 -21 0 0 235 90 40 114 100 9 100 0 865 941 null null null .094 .087 2.483 32 170 -.015 -.05 60 4590 5950 28 34 288 294 0 585 589 -5 null 565 -24 null null null null
19 5193 4542 220 499 4973 4043 5557 4580 229 516 5337 4081 0 0 1492 1153 48 114 100 100 100 100 9016 9418 1.23 .813 .765 .824 .796 1.5 32 232 .797 .89 70 4740 5950 27 34 302 309 0 5249 577 4673 .94 5293 4717 1.064 .884 -.09 -.178
20 4723 3256 221 497 4502 2759 4416 3001 226 511 4195 2504 0 0 2919 2054 47 113 100 93 100 87 7261 6699 1.632 .613 .597 .518 .584 2.3 32 232 .641 .9 70 4880 5940 26 33 316 323 0 3763 574 3189 .708 3468 2894 1.412 .69 -.498 -.536

Total number of rows: 41472

Table truncated, full table size 9342 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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