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Sample GSM516043 Query DataSets for GSM516043
Status Public on Jul 11, 2010
Title shfe186 | t(9;11)
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 02PB1189
Organism Homo sapiens
Characteristics source: 02PB1189
age: 28.20533881 years
overall survival time: 1044 days
overall survival status: alive
genotype: t(9;11)
gender: male
runx1 mutation: 0 (wt)
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/2005-06/61979.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 GPL10106
Series (4)
GSE16432 Musashi-2 regulates normal hematopoiesis and promotes aggressive myeloid leukemia
GSE22778 Musashi 2 regulates normal hematopoiesis and accelerates leukemogenesis
GSE23312 RUNX1 mutated cases in acute myeloid leukemia share a distinct biological subgroup and are associated with inferior outcome. Results of the AML Study Group (AMLSG).

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
1 583 221 281 327 302 -106 634 221 317 362 353 -106 0 0 117 56 326 274 61 0 0 0 196 247 null null null .789 .789 1 52 296 .416 .06 80 1920 6080 36 44 40 48 0 198 293 -95 null 198 -95 null null null null
2 3344 364 240 329 3104 35 3631 356 247 330 3391 27 0 0 992 69 40 76 100 26 100 7 3139 3418 88.686 .011 .008 .016 .016 2.763 80 348 .017 .33 100 2080 6090 36 46 55 65 0 327 295 31 .01 319 24 98.855 .007 -6.627 -7.129
3 1450 1250 221 339 1229 911 1327 1209 225 339 1106 870 0 0 686 428 34 78 100 100 100 100 2140 1976 1.349 .741 .787 .81 .828 1.648 52 253 .683 .91 80 2220 6080 36 44 70 78 0 1121 304 817 .665 1085 781 1.504 .706 -.589 -.503
4 526 370 208 336 318 34 528 355 214 338 320 19 0 0 91 103 33 72 100 34 100 15 352 339 9.353 .107 .059 .277 .313 2.156 52 264 .171 .19 80 2370 6090 37 45 85 93 0 332 301 31 .096 318 17 10.425 .053 -3.382 -4.231
5 630 334 212 344 418 -10 631 324 213 344 419 -20 0 0 85 70 25 72 100 13 100 3 408 399 null null null .089 .102 3.246 52 231 -.03 -.06 80 2520 6090 37 45 100 108 0 300 309 -9 null 291 -18 null null null null
6 388 161 209 336 179 -175 420 155 209 341 211 -181 0 0 78 51 24 72 100 0 94 0 4 30 null null null 0 0 1 52 241 -.978 -.67 80 2650 6080 36 44 113 121 0 144 301 -157 null 139 -162 null null null null
7 941 737 217 333 724 404 894 305 222 333 677 -28 0 0 201 1243 48 73 100 21 100 15 1128 649 1.792 .558 null .25 .165 9.686 32 225 5.852 .25 70 2800 6080 36 43 128 135 -100 661 299 362 .501 274 -25 1.998 null -.998 null
8 705 195 217 314 488 -119 717 198 221 320 500 -116 0 0 87 49 37 74 100 0 100 0 369 384 null null null 0 0 1 32 187 -.286 -.63 70 2960 6090 37 44 144 151 0 175 282 -107 null 178 -104 null null null null
9 678 412 215 347 463 65 676 414 219 348 461 67 0 0 61 72 31 71 100 47 100 10 528 528 7.123 .14 .145 .137 .204 2.895 80 336 .131 .34 110 3090 6090 35 46 155 166 0 370 311 58 .126 371 60 7.94 .13 -2.989 -2.939
10 1635 2717 216 349 1419 2368 1763 2897 219 358 1547 2548 0 0 513 1052 30 74 100 99 98 97 3787 4095 .599 1.669 1.647 1.521 1.683 2.265 120 344 1.857 .9 120 3240 6090 35 47 170 182 0 2437 313 2124 1.497 2599 2286 .668 1.478 .582 .563
11 2302 910 217 362 2085 548 2380 945 220 368 2163 583 0 0 540 232 32 79 100 94 100 92 2633 2746 3.805 .263 .27 .254 .271 1.804 120 339 .244 .84 120 3390 6090 35 47 185 197 0 816 325 492 .236 848 523 4.241 .242 -2.084 -2.048
12 13728 15226 224 375 13504 14851 15888 17354 226 383 15664 16979 0 0 4800 4694 36 81 100 100 100 100 28355 32643 .909 1.1 1.084 1.19 1.104 1.797 120 421 1.086 .94 130 3530 6090 34 47 198 211 0 13660 336 13323 .987 15569 15232 1.014 .972 -.019 -.04
13 1465 4491 222 384 1243 4107 1594 4754 227 391 1372 4370 0 0 429 1092 43 82 99 100 99 100 5350 5742 .303 3.304 3.185 3.561 3.22 1.897 120 422 3.422 .91 120 3680 6080 34 46 214 226 0 4029 344 3685 2.964 4265 3920 .337 2.857 1.568 1.515
14 450 740 222 386 228 354 445 744 225 393 223 358 0 0 62 120 37 83 100 100 100 95 582 581 .644 1.553 1.605 1.513 1.646 1.547 80 284 1.758 .69 100 3820 6090 36 46 229 239 0 664 346 318 1.393 667 321 .718 1.44 .478 .526
15 408 26104 224 403 184 25701 415 28154 225 405 191 27751 0 0 74 6318 29 80 96 100 94 100 25885 27942 .007 139.679 145.293 147.38 144.61 1.665 120 404 149.471 .85 120 3970 6080 34 46 243 255 0 23419 362 23057 125.31 25258 24896 .008 130.346 6.969 7.026
16 9737 13673 220 411 9517 13262 10570 14604 221 411 10350 14193 0 0 3872 4813 27 80 100 100 100 100 22779 24543 .718 1.394 1.371 1.438 1.373 1.794 120 366 1.383 .94 120 4120 6080 34 46 258 270 0 12266 369 11898 1.25 13102 12733 .8 1.23 .322 .299
17 1814 16545 215 412 1599 16133 2031 17713 215 411 1816 17301 0 0 611 4497 26 79 99 100 98 100 17732 19117 .099 10.089 9.527 11.853 10.115 2.059 120 381 10.381 .93 120 4260 6080 34 46 272 284 0 14843 370 14473 9.052 15891 15521 .11 8.547 3.178 3.095
18 641 420 208 397 433 23 639 421 210 403 431 24 0 0 69 79 31 82 100 21 100 5 456 455 18.826 .053 .056 .113 .112 2.691 80 326 .032 .07 110 4410 6080 34 45 287 298 0 377 356 21 .048 378 22 20.985 .05 -4.391 -4.323
19 5970 3544 204 403 5766 3141 6074 3784 207 405 5870 3381 0 0 1770 1337 34 81 100 99 100 98 8907 9251 1.836 .545 .576 .464 .545 2.123 120 351 .556 .93 120 4560 6090 35 47 302 314 0 3179 362 2818 .489 3395 3033 2.046 .517 -1.033 -.953
20 6835 7680 205 403 6630 7277 7397 7769 207 405 7192 7366 0 0 1923 1643 32 79 100 100 100 100 13907 14558 .911 1.098 1.024 1.178 1.091 1.687 120 415 1.067 .92 130 4700 6080 33 46 315 328 0 6890 362 6528 .985 6970 6608 1.016 .919 -.022 -.122

Total number of rows: 41472

Table truncated, full table size 9310 Kbytes.




Supplementary data files not provided
Raw data included within Sample table
Processed data included within Sample table

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