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Sample GSM516447 Query DataSets for GSM516447
Status Public on Jul 11, 2010
Title shcz085 | inv(16)
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 34; Sample source=BM; CBF group=inv(16)
Organism Homo sapiens
Characteristics source: AML 34; Sample source=BM; CBF group=inv(16)
age: 41.5633128 years
overall survival time: 1500 days
overall survival status: alive
genotype: inv(16)
gender: female
tet2 mutation status: wt
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/2002-09/32810.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 26, 2010
Last update date Sep 20, 2011
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 GPL8651
Series (4)
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
1 607 1410 117 124 490 1286 657 1562 120 132 540 1438 0 0 386 869 34 47 82 94 80 92 1776 1978 .381 2.624 2.663 2.26 2.541 2.461 52 357 2.595 .92 90 1990 7640 47 56 26 35 0 2074 182 1891 3.86 2297 2115 .259 3.916 1.948 1.969
2 4498 8209 119 128 4379 8081 4469 7211 127 133 4350 7083 0 0 3230 5351 39 45 100 100 100 100 12460 11433 .542 1.845 1.628 2.191 1.89 1.794 52 300 1.805 .96 90 2130 7640 47 56 40 49 0 12072 188 11884 2.714 10604 10416 .368 2.395 1.44 1.26
3 3052 2508 122 131 2930 2377 2812 2375 129 140 2690 2244 0 0 2176 1449 38 57 100 100 98 100 5307 4934 1.233 .811 .834 .994 .818 1.816 52 331 .746 .96 90 2270 7640 47 56 54 63 0 3688 193 3496 1.193 3493 3300 .838 1.227 .255 .295
4 1283 1819 130 138 1153 1681 1305 1709 137 151 1175 1571 0 0 424 632 48 68 100 100 100 100 2834 2746 .686 1.458 1.337 1.484 1.433 1.465 32 218 1.469 .95 70 2410 7640 48 55 69 76 0 2675 203 2472 2.144 2513 2310 .466 1.966 1.1 .975
5 1164 1035 133 145 1031 890 1086 911 149 217 953 766 0 0 722 670 73 345 96 73 94 55 1921 1719 1.158 .863 .804 .838 .788 1.712 52 284 1.048 .85 80 2560 7640 48 56 84 92 0 1522 213 1309 1.269 1340 1126 .788 1.182 .344 .241
6 1101 1009 122 129 979 880 1133 922 132 182 1011 793 0 0 499 419 50 341 100 90 100 68 1859 1804 1.113 .899 .784 .94 .96 1.706 32 226 .88 .94 70 2710 7640 48 55 99 106 0 1484 190 1294 1.322 1356 1166 .757 1.153 .403 .206
7 1895 2610 124 123 1771 2487 1947 2662 133 133 1823 2539 0 0 838 967 47 57 96 100 96 100 4258 4362 .712 1.404 1.393 1.487 1.322 1.796 32 227 1.369 .93 70 2850 7640 48 55 113 120 0 3838 181 3657 2.065 3915 3734 .484 2.048 1.046 1.034
8 1126 366 124 129 1002 237 1190 378 138 134 1066 249 0 0 427 117 78 44 100 93 90 87 1239 1315 4.228 .237 .234 .235 .235 1.714 32 232 .223 .85 70 3000 7640 48 55 128 135 0 538 190 349 .348 556 366 2.875 .344 -1.524 -1.542
9 726 1007 115 127 611 880 784 1015 123 132 669 888 0 0 300 395 33 43 90 100 90 96 1491 1557 .694 1.44 1.327 1.582 1.491 1.983 32 176 1.461 .88 60 3150 7640 49 55 144 150 0 1481 187 1294 2.118 1493 1306 .472 1.952 1.083 .965
10 883 265 122 133 761 132 950 259 140 138 828 126 0 0 282 92 76 48 93 81 93 62 893 954 5.765 .173 .152 .153 .15 1.75 32 227 .175 .74 70 3290 7640 48 55 157 164 0 390 196 194 .255 381 185 3.92 .224 -1.971 -2.16
11 3314 881 121 125 3193 756 2953 807 125 131 2832 682 0 0 2349 479 34 41 100 100 100 93 3949 3514 4.224 .237 .241 .282 .251 2.199 32 172 .21 .93 60 3450 7640 49 55 174 180 0 1296 184 1112 .348 1187 1003 2.872 .354 -1.522 -1.498
12 4261 3573 127 123 4134 3450 4268 3461 141 138 4141 3338 0 0 2918 2213 79 59 96 100 90 100 7584 7479 1.198 .835 .806 1.077 .869 2.529 32 172 .779 .94 60 3580 7640 49 55 187 193 0 5254 181 5074 1.227 5090 4909 .815 1.185 .295 .245
13 1204 1513 123 130 1081 1383 1159 1425 123 132 1036 1295 0 0 526 681 32 37 96 100 96 100 2464 2331 .782 1.279 1.25 1.258 1.179 1.804 32 176 1.267 .85 60 3730 7640 49 55 202 208 0 2225 191 2034 1.881 2096 1904 .532 1.838 .912 .878
14 414 401 117 131 297 270 400 359 124 134 283 228 0 0 196 147 32 35 90 96 87 96 567 511 1.1 .909 .806 .792 .776 2.395 32 170 .848 .84 60 3880 7640 49 55 217 223 0 590 193 397 1.337 528 335 .748 1.185 .419 .245
15 678 14187 118 130 560 14057 693 13488 122 141 575 13358 0 0 380 8950 31 105 92 100 90 100 14617 13933 .04 25.102 23.231 22.563 23.313 1.514 52 342 26.333 .93 90 4020 7640 47 56 229 238 0 20863 191 20672 36.914 19835 19644 .027 34.164 5.206 5.094
16 6152 14348 118 127 6034 14221 7526 16319 127 139 7408 16192 0 0 3778 7616 107 106 96 100 96 100 20255 23600 .424 2.357 2.186 2.659 2.291 1.714 52 337 2.294 .95 90 4170 7640 47 56 244 253 0 21100 187 20913 3.466 23999 23812 .289 3.214 1.793 1.685
17 1180 9502 115 122 1065 9380 982 8790 118 127 867 8668 0 0 902 6646 32 42 90 100 85 100 10445 9535 .114 8.808 9.998 9.871 8.388 2.07 80 404 8.59 .94 100 4330 7640 47 57 260 270 0 13974 179 13794 12.952 12926 12747 .077 14.702 3.695 3.878
18 783 293 124 121 659 172 788 293 132 128 664 172 0 0 190 51 54 41 100 100 100 91 831 836 3.831 .261 .259 .259 .246 1.395 12 92 .215 .78 50 4450 7640 49 54 274 279 0 431 178 253 .384 431 253 2.605 .381 -1.381 -1.392
19 2825 1269 122 131 2703 1138 2740 1389 135 136 2618 1258 0 0 1668 676 91 50 93 100 93 96 3841 3876 2.375 .421 .481 .474 .397 2.37 32 228 .395 .94 70 4620 7640 48 55 290 297 0 1866 193 1674 .619 2043 1850 1.615 .707 -.692 -.501
20 2410 1883 122 128 2288 1755 2608 1957 127 132 2486 1829 0 0 1307 921 37 45 100 100 100 100 4043 4315 1.304 .767 .736 .794 .749 1.626 32 212 .728 .97 70 4760 7640 48 55 304 311 0 2769 188 2581 1.128 2878 2690 .887 1.082 .174 .114

Total number of rows: 43008

Table truncated, full table size 9423 Kbytes.




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