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Sample GSM516071 Query DataSets for GSM516071
Status Public on Jul 11, 2010
Title shdj089 | t(8;21)
Sample type RNA
 
Channel 1
Source name Stratagene common reference
Organism Homo sapiens
Characteristics reference: Stratagene common reference
Extracted molecule total RNA
Extraction protocol not provided
Label Cy3
Label protocol A universal reference RNA (pooled from 11 cell lines) was labeled identically but with Cy3-dUTP
 
Channel 2
Source name AML 23; Sample source=BM; CBF group=t(8;21)
Organism Homo sapiens
Characteristics source: AML 23; Sample source=BM; CBF group=t(8;21)
age: 73.08692676 years
overall survival time: 29 days
overall survival status: dead
genotype: t(8;21)
gender: male
Extracted molecule total RNA
Extraction protocol Normal karyotype acute myeloid leukemia (NK-AML) specimens comprise Ficoll gradient purified mononuclear cells (>80% blasts) from diagnostic peripheral blood or bone marrow. Total RNA was isolated from stored, frozen mononuclear AML-cell pellets using Trizol reagent, and RNA quality assessed by gel electrophoresis.; Protocol Type = Extract preparation
Label Cy5
Label protocol RNA from AML specimens was labeled with Cy5-dUTP using an anchored poly(dT) primer during first strand reverse transcription (Superscript II). A universal reference RNA (pooled from 11 cell lines) was labeled identically but with Cy3-dUTP
 
 
Hybridization protocol not provided
Scan protocol GenePix 4000B
Description Simple annotation: Myeloid Leukemias, Acute Myeloid Leukemia
Image: http://smd.stanford.edu/MicroArray/gifs/2002-09/33367.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 Feb 25, 2010
Last update date Aug 02, 2010
Contact name Lars Bullinger
E-mail(s) lars.bullinger@charite.de
Phone +49-30-450-553111
Organization name Charité
Department Hematology, Oncology and Tumorimmunology
Street address Augustenburger Platz 1
City Berlin
ZIP/Postal code 13353
Country Germany
 
Platform ID GPL8652
Series (3)
GSE16432 Musashi-2 regulates normal hematopoiesis and promotes aggressive myeloid leukemia
GSE22778 Musashi 2 regulates normal hematopoiesis and accelerates leukemogenesis
GSE23143 Common and overlapping oncogenic pathways contribute to the evolution of acute myeloid leukemias.

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
1 689 2347 137 135 552 2212 671 2268 138 138 534 2133 0 0 239 799 30 43 100 100 100 100 2764 2667 .25 4.007 3.994 4.19 3.897 1.411 52 332 4.042 .96 90 1790 8420 21 30 18 27 0 2637 152 2485 4.503 2548 2397 .222 4.488 2.171 2.166
2 6144 1326 138 132 6006 1194 6441 1284 137 135 6303 1152 0 0 1906 457 32 42 100 100 100 100 7200 7455 5.03 .199 .183 .195 .19 1.274 52 304 .195 .97 90 1940 8420 21 30 33 42 0 1490 148 1342 .223 1443 1294 4.477 .205 -2.162 -2.284
3 1981 1468 137 132 1844 1336 1834 1416 137 133 1697 1284 0 0 813 571 32 39 100 100 100 100 3180 2981 1.38 .725 .757 .728 .718 1.209 32 198 .716 .98 70 2080 8420 22 29 48 55 0 1649 148 1501 .814 1591 1443 1.228 .85 -.297 -.234
4 987 1024 133 136 854 888 982 1048 134 141 849 912 0 0 363 380 30 44 100 100 100 100 1742 1761 .962 1.04 1.074 1.041 1.089 1.318 52 253 1.039 .95 80 2230 8420 22 30 63 71 0 1151 153 998 1.168 1178 1025 .856 1.207 .224 .271
5 1882 2764 136 136 1746 2628 1908 2733 137 141 1772 2597 0 0 617 924 31 47 100 100 100 100 4374 4369 .664 1.505 1.466 1.524 1.536 1.251 52 311 1.526 .97 90 2370 8410 20 29 76 85 0 3106 153 2953 1.691 3071 2918 .591 1.647 .758 .72
6 1066 812 132 135 934 677 1063 821 135 137 931 686 0 0 423 301 29 42 100 100 100 100 1611 1617 1.38 .725 .737 .737 .726 1.439 52 264 .711 .95 80 2530 8420 22 30 93 101 0 912 152 761 .814 922 771 1.228 .828 -.296 -.272
7 2047 3764 130 135 1917 3629 2156 3589 130 137 2026 3454 0 0 966 1924 29 38 100 100 100 100 5546 5480 .528 1.893 1.705 1.862 1.979 1.45 52 291 1.952 .96 90 2670 8410 20 29 106 115 0 4229 152 4078 2.127 4033 3881 .47 1.916 1.089 .938
8 969 745 130 131 839 614 986 737 132 134 856 606 0 0 329 252 29 38 100 100 100 100 1453 1462 1.366 .732 .708 .724 .755 1.326 52 244 .73 .95 80 2810 8420 22 30 121 129 0 837 147 690 .822 828 681 1.216 .795 -.282 -.33
9 711 506 135 127 576 379 729 511 136 132 594 384 0 0 209 160 29 38 100 100 100 97 955 978 1.52 .658 .646 .634 .65 1.455 80 369 .648 .92 100 2960 8410 20 30 135 145 0 569 143 426 .739 574 431 1.353 .726 -.436 -.461
10 612 422 129 134 483 288 607 427 129 137 478 293 0 0 191 107 27 47 100 96 100 96 771 771 1.677 .596 .613 .6 .568 1.571 32 192 .58 .88 70 3100 8410 21 28 150 157 0 474 151 324 .67 480 329 1.493 .689 -.578 -.538
11 5394 1080 131 137 5263 943 5771 1045 132 140 5640 908 0 0 2076 418 29 42 100 100 100 100 6206 6548 5.581 .179 .161 .178 .185 1.338 80 369 .175 .96 100 3250 8420 21 31 164 174 0 1213 154 1060 .201 1174 1020 4.967 .181 -2.312 -2.467
12 9918 8585 136 137 9782 8448 9571 8245 136 142 9435 8108 0 0 4629 4114 31 41 100 100 100 100 18230 17543 1.158 .864 .859 .843 .894 1.334 80 343 .866 .99 100 3390 8420 21 31 178 188 0 9646 154 9492 .97 9264 9110 1.031 .966 -.043 -.051
13 1446 2226 134 131 1312 2095 1428 2081 136 138 1294 1950 0 0 502 1025 30 43 100 100 100 100 3407 3244 .626 1.597 1.507 1.508 1.539 1.358 80 343 1.706 .96 100 3540 8420 21 31 193 203 0 2501 147 2354 1.794 2338 2191 .557 1.693 .843 .76
14 599 831 135 126 464 705 600 835 136 132 465 709 0 0 135 172 30 40 100 100 100 100 1169 1174 .658 1.519 1.525 1.539 1.493 1.327 80 361 1.529 .94 110 3680 8420 20 31 206 217 0 934 142 792 1.707 938 797 .586 1.713 .772 .777
15 973 12341 134 136 839 12205 1020 13285 136 142 886 13149 0 0 279 3380 32 52 100 100 100 100 13044 14035 .069 14.547 14.841 15.069 14.364 1.251 80 364 14.58 .97 110 3830 8420 20 31 221 232 0 13866 153 13713 16.345 14927 14774 .061 16.675 4.031 4.06
16 6220 16302 129 137 6091 16165 6598 18072 133 144 6469 17935 0 0 3201 8060 33 51 97 100 97 100 22256 24404 .377 2.654 2.772 2.916 2.627 1.633 120 426 2.637 .99 120 3980 8420 20 32 236 248 0 18317 154 18163 2.982 20306 20152 .335 3.115 1.576 1.639
17 2275 33498 129 137 2146 33361 2578 38657 132 140 2449 38520 0 0 877 12972 30 40 98 100 97 100 35507 40969 .064 15.546 15.729 16.392 15.575 1.359 120 371 15.505 .99 120 4130 8420 20 32 251 263 0 37638 154 37484 17.467 43435 43281 .057 17.673 4.127 4.143
18 198 192 129 128 69 64 145 153 132 132 16 25 0 0 165 139 30 43 35 36 25 22 133 41 1.078 .928 1.563 1.534 1.103 3.754 80 294 .87 .79 100 4270 8410 20 30 266 276 -50 216 144 72 1.042 172 28 .96 1.756 .06 .812
19 4520 1969 128 125 4392 1844 4629 2008 131 127 4501 1883 0 0 1109 452 29 40 100 100 100 100 6236 6384 2.382 .42 .418 .422 .425 1.175 80 311 .412 .98 100 4420 8420 21 31 281 291 0 2212 140 2072 .472 2256 2116 2.12 .47 -1.084 -1.089
20 2863 2461 128 128 2735 2333 2892 2530 130 131 2764 2402 0 0 608 552 29 37 100 100 100 100 5068 5166 1.172 .853 .869 .848 .831 1.169 80 386 .848 .98 110 4560 8410 19 30 294 305 0 2765 144 2621 .958 2843 2699 1.043 .976 -.061 -.034

Total number of rows: 43008

Table truncated, full table size 9517 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
Processed data are available on Series record
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