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Sample GSM515768 Query DataSets for GSM515768
Status Public on Jul 11, 2010
Title shcz064 | 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 AML 62; Sample source=BM; CBF group=t(8;21)
Organism Homo sapiens
Characteristics source: AML 62; Sample source=BM; CBF group=t(8;21)
age: 71.9890486 years
overall survival time: 140 days
overall survival status: dead
genotype: t(8;21)
gender: male
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/2002-08/32140.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 Aug 02, 2010
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 (3)
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
1 572 1426 144 117 428 1309 594 1335 147 120 450 1218 0 0 176 578 37 38 100 100 97 100 1737 1668 .327 3.058 2.707 3.075 3.253 1.552 80 410 3.43 .85 100 1600 8260 61 71 39 49 0 1602 131 1471 3.436 1500 1369 .291 3.041 1.781 1.605
2 4270 1648 147 117 4123 1531 3669 1529 153 129 3522 1412 0 0 1775 534 51 81 100 100 100 100 5654 4934 2.693 .371 .401 .382 .394 1.227 52 312 .35 .97 90 1750 8260 61 70 54 63 0 1852 131 1720 .417 1718 1587 2.397 .45 -1.261 -1.151
3 1916 1816 143 119 1773 1697 1585 1610 148 123 1442 1491 0 0 965 809 42 40 100 100 100 100 3470 2933 1.045 .957 1.034 .995 .983 1.3 52 302 .969 .96 90 1890 8260 61 70 68 77 0 2040 134 1907 1.075 1809 1675 .93 1.162 .105 .216
4 722 639 143 120 579 519 692 633 146 123 549 513 0 0 220 189 38 40 100 100 100 100 1098 1062 1.116 .896 .934 .895 .857 1.424 52 313 .852 .9 90 2040 8260 61 70 83 92 0 718 135 583 1.007 711 576 .993 1.05 .01 .07
5 484 275 144 116 340 159 430 264 148 120 286 148 0 0 238 98 34 38 97 88 92 81 499 434 2.138 .468 .517 .486 .465 1.963 80 364 .4 .81 100 2190 8260 61 71 98 108 0 309 130 179 .525 297 166 1.903 .581 -.928 -.782
6 476 389 146 124 330 265 462 375 152 130 316 251 0 0 112 86 37 42 100 100 100 100 595 567 1.245 .803 .794 .819 .757 1.431 32 206 .789 .87 70 2330 8250 61 68 113 120 0 437 139 298 .902 421 282 1.108 .892 -.148 -.164
7 516 986 148 117 368 869 475 887 153 123 327 770 0 0 243 545 39 37 98 100 98 100 1237 1097 .423 2.361 2.355 2.441 2.44 1.624 52 332 2.37 .93 90 2490 8250 60 69 128 137 0 1108 131 976 2.653 997 865 .377 2.646 1.408 1.404
8 491 214 145 113 346 101 493 200 150 119 348 87 0 0 107 65 36 40 100 80 100 55 447 435 3.426 .292 .25 .266 .332 2.084 52 256 .209 .51 80 2630 8250 61 69 143 151 0 240 127 113 .328 225 98 3.049 .281 -1.608 -1.832
9 328 330 142 123 186 207 316 330 148 126 174 207 0 0 98 87 36 39 96 100 93 93 393 381 .899 1.113 1.19 1.174 1.165 1.837 32 198 1.008 .73 70 2770 8250 61 68 157 164 0 371 138 233 1.25 371 233 .8 1.337 .322 .419
10 482 185 144 120 338 65 468 177 146 124 324 57 0 0 154 64 34 40 100 62 98 32 403 381 5.2 .192 .176 .197 .227 2.698 80 377 .144 .43 100 2930 8250 60 70 172 182 0 208 135 73 .216 199 64 4.628 .198 -2.21 -2.339
11 642 470 144 120 498 350 669 454 145 125 525 334 0 0 171 173 36 40 100 98 100 96 848 859 1.423 .703 .636 .632 .681 1.666 52 291 .707 .87 90 3060 8240 59 68 185 194 0 528 135 393 .79 510 375 1.266 .715 -.341 -.484
12 941 938 143 116 798 822 911 908 147 122 768 792 0 0 352 365 41 40 100 100 100 100 1620 1560 .971 1.03 1.031 1.033 1.019 1.31 52 303 1.028 .95 90 3220 8240 59 68 201 210 0 1054 130 924 1.157 1020 890 .864 1.159 .211 .213
13 523 556 141 115 382 441 510 574 144 120 369 459 0 0 220 193 36 36 100 100 96 98 823 828 .866 1.154 1.244 1.166 1.216 1.579 52 264 1.021 .89 80 3360 8240 60 68 216 224 0 625 129 496 1.297 645 516 .771 1.398 .375 .483
14 272 397 136 127 136 270 264 408 139 128 128 281 0 0 78 150 31 43 96 96 75 84 406 409 .504 1.985 2.195 1.799 1.833 2.05 32 164 2.326 .72 60 3510 8240 61 67 232 238 0 446 143 303 2.231 458 316 .448 2.467 1.157 1.303
15 988 6371 141 114 847 6257 364 5409 142 121 223 5295 0 0 3443 3545 34 41 95 100 88 100 7104 5518 .135 7.387 23.744 22.06 23.872 2.72 80 371 4.222 .32 100 3650 8240 59 69 244 254 0 7158 128 7030 8.3 6078 5949 .12 26.679 3.053 4.738
16 1762 2936 141 115 1621 2821 1660 2905 143 122 1519 2790 0 0 751 1276 35 42 97 100 97 100 4442 4309 .575 1.74 1.837 1.837 1.749 1.509 80 350 1.728 .96 100 3800 8240 59 69 259 269 0 3299 129 3170 1.955 3264 3135 .511 2.064 .967 1.045
17 724 5687 143 118 581 5569 649 4728 146 123 506 4610 0 0 334 3460 36 41 100 100 96 100 6150 5116 .104 9.585 9.111 9.752 9.556 1.521 80 355 10.306 .94 100 3950 8230 58 68 274 284 0 6390 133 6257 10.77 5312 5180 .093 10.237 3.429 3.356
18 304 275 148 120 156 155 295 269 152 123 147 149 0 0 85 102 37 44 93 87 84 62 311 296 1.006 .994 1.014 .886 .935 2.338 32 178 1.098 .64 70 4090 8230 59 66 289 296 0 309 135 174 1.116 302 167 .896 1.139 .159 .188
19 403 433 145 119 258 314 358 342 151 122 213 223 0 0 193 285 38 43 91 87 81 77 572 436 .822 1.217 1.047 1.12 1.321 2.253 80 370 1.453 .78 100 4230 8230 58 68 302 312 0 487 134 353 1.367 384 251 .731 1.176 .452 .234
20 529 498 146 117 383 381 486 469 149 122 340 352 0 0 210 161 38 39 100 100 98 98 764 692 1.005 .995 1.035 1.018 1.088 1.785 52 254 .893 .76 80 4390 8230 59 67 319 327 0 560 131 428 1.118 527 396 .895 1.163 .161 .218

Total number of rows: 43008

Table truncated, full table size 9287 Kbytes.




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

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