NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM515971 Query DataSets for GSM515971
Status Public on Jul 11, 2010
Title shee198 | 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 02PB717; Sample source=PB; CBF group=t(8;21)
Organism Homo sapiens
Characteristics source: 02PB717; Sample source=PB; CBF group=t(8;21)
age: 19.15674196 years
overall survival time: 782 days
overall survival status: alive
genotype: t(8;21)
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/2003-08/43819.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) [email protected]
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 GPL8653
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
1 698 322 340 162 358 160 699 308 343 169 359 146 0 0 115 93 48 48 100 94 100 71 518 505 2.238 .447 .407 .4 .377 1.846 52 336 .397 .63 90 1540 7800 35 44 33 42 0 293 148 146 .407 281 133 2.457 .37 -1.297 -1.433
2 1067 341 343 167 724 174 1054 348 354 172 711 181 0 0 232 93 88 53 100 94 100 76 898 892 4.161 .24 .255 .232 .255 2.093 52 329 .198 .68 90 1690 7790 34 43 48 57 0 311 152 158 .219 317 165 4.569 .232 -2.192 -2.109
3 751 381 337 161 414 220 706 377 339 166 369 216 0 0 236 127 51 50 100 84 90 78 634 585 1.882 .531 .585 .505 .541 1.792 32 164 .489 .82 60 1840 7800 37 43 65 71 0 347 147 200 .484 343 197 2.066 .533 -1.047 -.907
4 554 238 340 161 214 77 559 242 344 163 219 81 0 0 109 66 53 47 93 65 84 37 291 300 2.779 .36 .37 .421 .524 2.761 32 209 .333 .48 70 1980 7790 35 42 78 85 0 217 147 70 .328 220 74 3.052 .337 -1.61 -1.57
5 811 542 350 162 461 380 773 490 349 165 423 328 0 0 263 244 52 48 98 100 97 97 841 751 1.213 .824 .775 .812 .784 1.74 80 378 .835 .9 100 2140 7800 35 45 93 103 0 494 148 346 .751 446 299 1.332 .706 -.414 -.502
6 662 285 359 171 303 114 629 268 354 171 270 97 0 0 142 86 52 46 100 78 96 53 417 367 2.658 .376 .359 .354 .409 2.079 52 224 .341 .62 80 2280 7800 36 44 108 116 0 260 156 104 .343 244 88 2.918 .327 -1.545 -1.612
7 817 510 344 158 473 352 800 491 344 163 456 333 0 0 179 134 54 49 100 100 98 98 825 789 1.344 .744 .73 .749 .762 1.548 52 301 .724 .84 90 2420 7800 35 44 121 130 0 464 144 321 .678 447 303 1.475 .665 -.561 -.588
8 838 280 337 162 501 118 838 287 339 167 501 125 0 0 173 75 55 46 100 80 98 61 619 626 4.246 .236 .25 .216 .258 2.297 52 313 .211 .62 90 2570 7800 35 44 136 145 0 255 148 107 .215 261 114 4.662 .227 -2.221 -2.138
9 889 548 345 169 544 379 870 557 353 171 525 388 0 0 121 117 63 50 100 100 100 100 923 913 1.435 .697 .739 .68 .687 1.467 52 320 .711 .86 90 2720 7790 34 43 151 160 0 499 154 345 .635 507 353 1.576 .673 -.656 -.571
10 698 246 347 164 351 82 693 257 354 168 346 93 0 0 149 59 56 51 100 65 90 40 433 439 4.28 .234 .269 .213 .308 2.724 32 200 .218 .48 70 2860 7800 36 43 166 173 0 224 149 75 .213 234 85 4.7 .245 -2.233 -2.03
11 3724 702 342 152 3382 550 3704 683 344 160 3362 531 0 0 580 132 55 51 100 100 100 100 3932 3893 6.149 .163 .158 .16 .164 1.358 80 440 .149 .91 110 3010 7800 34 45 179 190 0 639 138 501 .148 622 484 6.752 .144 -2.755 -2.797
12 2117 1718 336 164 1781 1554 2054 1717 341 168 1718 1553 0 0 604 487 57 53 100 100 100 100 3335 3271 1.146 .873 .904 .88 .88 1.374 52 289 .852 .94 90 3160 7800 35 44 195 204 0 1565 149 1415 .795 1564 1414 1.258 .823 -.332 -.281
13 726 977 342 165 384 812 728 937 343 172 386 772 0 0 152 237 54 56 100 100 100 100 1196 1158 .473 2.115 2 2.201 2.097 1.445 52 287 2.125 .88 90 3300 7790 34 43 209 218 0 890 150 740 1.926 853 703 .519 1.821 .945 .865
14 853 592 347 159 506 433 849 581 348 171 502 422 0 0 129 151 54 91 100 98 100 96 939 924 1.169 .856 .841 .822 .827 1.531 120 493 .878 .85 120 3450 7810 35 47 223 235 0 539 145 394 .779 529 384 1.283 .766 -.36 -.385
15 708 1715 334 169 374 1546 691 1772 343 214 357 1603 0 0 248 773 62 184 91 100 75 100 1920 1960 .242 4.134 4.49 5.237 4.315 1.891 12 92 4.004 .91 50 3580 7800 37 42 239 244 0 1562 154 1408 3.765 1614 1460 .266 4.089 1.913 2.032
16 2481 3426 320 153 2161 3273 2359 3047 327 166 2039 2894 0 0 991 1635 53 103 100 100 100 100 5434 4933 .66 1.515 1.419 1.491 1.481 1.299 80 368 1.575 .97 100 3740 7800 35 45 253 263 0 3120 139 2981 1.379 2775 2636 .725 1.293 .464 .37
17 1132 8735 317 145 815 8590 1126 8611 321 170 809 8466 0 0 173 1576 48 165 100 100 100 100 9405 9275 .095 10.54 10.465 10.577 10.521 1.27 120 453 10.888 .94 130 3880 7800 33 46 265 278 0 7955 132 7823 9.599 7842 7710 .104 9.531 3.263 3.253
18 339 157 310 144 29 13 314 149 315 177 4 5 0 0 103 47 51 200 22 0 20 0 42 9 2.231 .448 1.25 .511 .513 3.791 80 286 2.616 .15 100 4020 7800 35 45 281 291 -50 143 131 12 .408 136 5 2.449 1.138 -1.292 .187
19 2330 1069 300 144 2030 925 2334 1080 304 149 2034 936 0 0 370 224 49 45 100 100 100 100 2955 2970 2.195 .456 .46 .447 .455 1.326 80 347 .438 .93 110 4170 7800 34 45 295 306 0 974 131 842 .415 984 852 2.41 .419 -1.269 -1.255
20 1361 947 308 141 1053 806 1395 981 310 146 1087 840 0 0 308 244 49 45 100 99 98 98 1859 1927 1.306 .765 .773 .758 .765 1.458 120 444 .755 .94 130 4320 7800 33 46 309 322 0 862 128 734 .697 893 765 1.434 .704 -.521 -.507

Total number of rows: 43104

Table truncated, full table size 9530 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
Processed data are available on Series record
| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap