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Sample GSM515954 Query DataSets for GSM515954
Status Public on Jul 11, 2010
Title shfs154 | complex 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 02KM2686
Organism Homo sapiens
Characteristics source: 02KM2686
age: 43.07734428 years
overall survival time: 176 days
overall survival status: dead
genotype: complex karyotype
gender: female
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/2005-06/61682.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 GPL10107
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
1 472 224 102 346 370 -122 515 228 106 379 413 -118 0 0 143 63 27 139 100 0 98 0 248 295 null null null .179 .191 1.667 52 265 -.407 -.51 80 2010 5600 32 40 33 41 0 209 323 -114 null 213 -110 null null null null
2 3223 1787 92 300 3131 1487 3702 1835 96 308 3610 1535 0 0 1367 642 23 70 100 100 100 100 4618 5145 2.106 .475 .425 .534 .48 2.274 52 244 .442 .91 80 2150 5590 31 39 47 55 0 1668 280 1388 .443 1713 1433 2.255 .397 -1.173 -1.333
3 3275 1784 88 280 3187 1504 3443 1792 91 287 3355 1512 0 0 1694 869 22 70 100 96 100 94 4691 4867 2.119 .472 .451 .457 .459 3.06 52 265 .451 .89 80 2290 5600 32 40 61 69 0 1666 261 1404 .441 1673 1412 2.27 .421 -1.182 -1.249
4 660 814 90 285 570 529 692 753 92 286 602 468 0 0 121 187 18 69 100 100 100 100 1099 1070 1.078 .928 .777 .895 .906 1.511 32 227 1.067 .78 70 2440 5600 32 39 76 83 0 760 266 494 .866 703 437 1.154 .726 -.207 -.462
5 693 149 93 279 600 -130 681 147 94 282 588 -132 0 0 101 45 19 63 100 0 100 0 470 456 null null null 0 0 1 32 225 -.225 -.66 70 2590 5590 31 38 91 98 0 139 260 -121 null 137 -123 null null null null
6 359 214 89 279 270 -65 426 204 91 288 337 -75 0 0 146 78 16 76 94 5 88 0 205 262 null null null .344 .212 9.294 52 296 -.29 -.38 80 2740 5600 32 40 106 114 0 200 260 -61 null 190 -70 null null null null
7 1077 428 87 283 990 145 1077 420 89 284 990 137 0 0 394 145 15 71 100 73 100 44 1135 1127 6.828 .146 .138 .144 .143 2.079 52 272 .167 .67 80 2890 5590 31 39 121 129 0 400 264 135 .137 392 128 7.313 .129 -2.87 -2.952
8 614 347 89 285 525 62 624 345 90 284 535 60 0 0 144 112 16 64 100 48 100 26 587 595 8.468 .118 .112 .196 .183 2.394 52 251 .145 .34 80 3030 5590 31 39 135 143 0 324 266 58 .11 322 56 9.069 .105 -3.181 -3.256
9 448 1496 88 280 360 1216 490 1565 88 278 402 1285 0 0 142 448 16 64 98 100 95 100 1576 1687 .296 3.378 3.197 3.712 3.325 2.091 80 362 3.648 .89 100 3170 5590 30 40 148 158 0 1397 261 1135 3.154 1461 1200 .317 2.984 1.657 1.577
10 3247 2654 89 273 3158 2381 3434 2816 89 276 3345 2543 0 0 1197 1007 17 61 100 100 100 98 5539 5888 1.326 .754 .76 .738 .773 1.988 80 408 .754 .91 110 3320 5590 29 40 162 173 0 2478 255 2223 .704 2629 2374 1.421 .71 -.506 -.495
11 2034 657 89 273 1945 384 2055 650 91 277 1966 377 0 0 505 143 21 62 100 98 100 98 2329 2343 5.065 .197 .192 .189 .192 1.7 52 302 .163 .75 90 3470 5600 31 40 178 187 0 613 255 359 .184 607 352 5.425 .179 -2.44 -2.482
12 7669 8956 88 269 7581 8687 9378 9077 90 269 9290 8808 0 0 4534 5428 20 65 100 98 100 98 16268 18098 .873 1.146 .948 1.12 1.208 3.55 80 392 1.182 .9 100 3620 5590 30 40 193 203 0 8362 251 8111 1.07 8475 8224 .935 .885 .097 -.176
13 1500 2816 88 273 1412 2543 1570 2781 90 274 1482 2508 0 0 541 397 28 64 100 100 100 100 3955 3990 .555 1.801 1.692 2.004 1.71 1.781 52 309 1.671 .85 90 3760 5590 30 39 207 216 0 2629 255 2374 1.682 2597 2342 .595 1.58 .75 .66
14 475 486 89 262 386 224 469 480 91 265 380 218 0 0 69 129 29 61 100 86 100 73 610 598 1.723 .58 .574 .486 .534 2.488 52 313 .666 .64 90 3900 5590 30 39 221 230 0 454 245 209 .542 448 204 1.846 .536 -.884 -.901
15 244 14462 88 257 156 14205 272 15305 89 262 184 15048 0 0 88 5932 16 65 90 100 83 100 14361 15232 .011 91.058 81.783 104.374 85.74 2.042 80 376 95.875 .87 100 4050 5590 30 40 236 246 0 13503 240 13263 85.017 14290 14050 .012 76.357 6.41 6.255
16 8655 9979 86 256 8569 9723 10130 11363 88 259 10044 11107 0 0 3987 4166 16 66 100 100 100 100 18292 21151 .881 1.135 1.106 1.296 1.097 3.182 80 367 1.124 .9 100 4200 5590 30 40 251 261 0 9317 239 9078 1.059 10609 10370 .944 1.032 .083 .046
17 1504 11533 87 252 1417 11281 1613 12711 90 258 1526 12459 0 0 610 3748 21 61 100 100 97 100 12698 13985 .126 7.961 8.164 9.005 8.126 2.439 80 362 8.508 .89 100 4340 5590 30 40 265 275 0 10768 235 10533 7.433 11868 11632 .135 7.623 2.894 2.93
18 544 268 86 246 458 22 537 266 88 252 451 20 0 0 72 61 19 59 100 26 100 3 480 471 20.818 .048 .044 .086 .107 2.716 52 290 .031 .09 90 4500 5600 31 40 281 290 0 250 230 21 .045 248 19 22.297 .041 -4.479 -4.594
19 4267 4819 85 246 4182 4573 4960 5403 86 249 4875 5157 0 0 1685 1410 16 59 100 100 100 100 8755 10032 .914 1.093 1.058 1.331 1.065 2.506 80 331 1.044 .92 100 4630 5590 30 40 294 304 0 4499 230 4270 1.021 5045 4815 .979 .988 .03 -.018
20 5914 5830 84 244 5830 5586 7528 7252 86 246 7444 7008 0 0 3091 2878 17 58 100 100 100 100 11416 14452 1.044 .958 .941 1.043 .943 2.833 120 477 .947 .93 120 4770 5590 29 41 307 319 0 5443 228 5215 .895 6771 6543 1.118 .879 -.161 -.186

Total number of rows: 41472

Table truncated, full table size 9167 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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