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Sample GSM515724 Query DataSets for GSM515724
Status Public on Jul 11, 2010
Title shet136 | normal karyotype
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 98KM585
Organism Homo sapiens
Characteristics source: 98KM585
age: 36.63791923 years
overall survival time: 1008 days
overall survival status: dead
genotype: normal karyotype
npm1 mutation status: WT
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/2003-12/47463.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 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 GPL8654
Series (5)
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
1 385 371 175 171 210 200 386 365 179 173 211 194 0 0 55 100 33 60 100 86 100 80 410 405 1.05 .952 .919 .819 .931 1.927 52 264 1.157 .452 80 1800 4940 26 34 24 32 0 379 175 204 .973 373 198 1.028 .939 -.039 -.09
2 752 323 179 159 573 164 784 303 182 165 605 144 0 0 193 106 39 62 100 84 100 67 737 749 3.494 .286 .238 .249 .299 2.162 52 255 .286 .499 80 1950 4940 26 34 39 47 0 330 162 168 .292 310 147 3.42 .243 -1.774 -2.04
3 1957 1046 171 160 1786 886 2059 1058 175 165 1888 898 0 0 454 276 32 60 100 100 100 100 2672 2786 2.016 .496 .476 .491 .486 1.287 80 390 .493 .895 100 2100 4940 25 35 53 63 0 1069 163 905 .507 1081 917 1.973 .486 -.98 -1.041
4 380 304 173 177 207 127 378 309 183 179 205 132 0 0 41 91 38 57 100 81 100 59 334 337 1.63 .614 .644 .681 .644 1.649 32 132 1.095 .273 60 2240 4930 26 32 69 75 0 311 181 130 .627 316 135 1.595 .658 -.674 -.604
5 623 743 169 166 454 577 616 746 174 169 447 580 0 0 118 199 42 57 100 100 100 100 1031 1027 .787 1.271 1.298 1.229 1.309 1.412 80 433 1.362 .782 100 2390 4950 26 36 82 92 0 759 170 590 1.298 762 593 .77 1.326 .377 .407
6 328 253 178 166 150 87 311 240 179 168 133 74 0 0 53 72 36 58 100 59 96 31 237 207 1.724 .58 .556 .551 .607 2.37 32 198 .98 .106 70 2540 4950 27 34 98 105 0 258 170 89 .593 245 76 1.688 .568 -.755 -.815
7 731 1008 164 166 567 842 740 1025 167 169 576 859 0 0 186 267 32 60 100 100 100 100 1409 1435 .673 1.485 1.491 1.49 1.525 1.344 52 266 1.585 .836 80 2670 4940 26 34 111 119 0 1030 170 860 1.517 1047 878 .659 1.524 .601 .608
8 542 301 159 172 383 129 531 299 161 175 372 127 0 0 67 82 30 62 100 76 100 51 512 499 2.969 .337 .341 .274 .324 2.327 52 322 .369 .382 90 2830 4950 26 35 126 135 0 308 176 132 .344 305 130 2.906 .349 -1.539 -1.52
9 428 415 159 167 269 248 425 415 161 175 266 248 0 0 59 110 32 64 100 94 100 88 517 514 1.085 .922 .932 .816 .902 1.921 52 325 .995 .55 90 2970 4950 26 35 140 149 0 424 171 253 .942 424 253 1.062 .953 -.086 -.07
10 382 295 164 168 218 127 384 284 169 175 220 116 0 0 53 81 37 64 100 80 100 44 345 336 1.717 .583 .527 .6 .608 1.749 52 324 .733 .221 90 3120 4950 26 35 155 164 0 301 172 130 .595 290 119 1.68 .539 -.749 -.892
11 2740 577 172 169 2568 408 2690 567 188 170 2518 398 0 0 485 154 105 58 100 100 100 98 2976 2916 6.294 .159 .158 .148 .159 1.548 52 314 .152 .764 90 3270 4960 27 36 170 179 0 590 173 417 .162 579 407 6.161 .161 -2.623 -2.63
12 6569 3852 165 174 6404 3678 7283 4230 183 173 7118 4056 0 0 2261 1377 131 58 100 100 100 100 10082 11174 1.741 .574 .57 .569 .585 1.214 80 375 .564 .944 100 3410 4940 25 35 184 194 0 3936 178 3758 .587 4322 4144 1.704 .582 -.769 -.78
13 548 987 167 167 381 820 538 976 169 171 371 809 0 0 83 215 34 61 100 100 100 100 1201 1180 .465 2.152 2.181 2.131 2.067 1.381 52 240 2.373 .781 80 3550 4940 26 34 199 207 0 1008 171 838 2.199 997 827 .455 2.228 1.137 1.156
14 346 333 166 166 180 167 352 330 168 173 186 164 0 0 39 88 30 65 100 88 100 65 347 350 1.078 .928 .882 .846 .878 2.038 80 383 1.343 .442 100 3700 4950 26 36 213 223 0 340 170 171 .948 337 168 1.055 .901 -.077 -.151
15 512 8059 163 170 349 7889 535 8656 166 177 372 8486 0 0 120 2772 34 63 100 100 97 100 8238 8858 .044 22.605 22.812 22.695 22.36 1.289 80 369 23.355 .906 100 3840 4940 25 35 227 237 0 8234 174 8060 23.095 8844 8670 .043 23.306 4.529 4.543
16 3955 5384 163 168 3792 5216 3932 5482 168 177 3769 5314 0 0 355 619 34 68 100 100 100 100 9008 9083 .727 1.376 1.41 1.372 1.355 1.15 52 306 1.371 .945 90 3990 4950 26 35 242 251 0 5501 172 5329 1.405 5601 5429 .712 1.44 .491 .527
17 659 4613 162 173 497 4440 656 4539 166 195 494 4366 0 0 131 1175 33 121 100 100 100 100 4937 4860 .112 8.934 8.838 8.933 8.893 1.276 52 276 9.318 .865 80 4130 4940 26 34 257 265 0 4713 177 4536 9.127 4637 4461 .11 9.03 3.19 3.175
18 350 272 164 177 186 95 350 282 166 193 186 105 0 0 39 83 35 111 100 46 100 7 281 291 1.958 .511 .565 .498 .647 2.488 52 248 .861 .202 80 4300 4950 27 35 274 282 0 278 181 97 .522 288 107 1.916 .577 -.938 -.794
19 1611 671 159 172 1452 499 1670 635 167 179 1511 463 0 0 355 172 56 66 100 100 100 100 1951 1974 2.91 .344 .306 .336 .344 1.397 80 354 .329 .781 100 4430 4940 25 35 286 296 0 686 176 510 .351 649 473 2.848 .313 -1.51 -1.675
20 962 617 162 163 800 454 944 598 170 170 782 435 0 0 191 166 43 62 100 100 100 98 1254 1217 1.762 .568 .556 .543 .574 1.475 80 355 .569 .765 100 4580 4940 25 35 301 311 0 630 167 464 .58 611 444 1.725 .568 -.786 -.815

Total number of rows: 41472

Table truncated, full table size 9035 Kbytes.




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