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Sample GSM516029 Query DataSets for GSM516029
Status Public on Jul 11, 2010
Title shfe084 | 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 01KM2324; Sample source=BM; CBF group=t(8;21)
Organism Homo sapiens
Characteristics source: 01KM2324; Sample source=BM; CBF group=t(8;21)
age: 50.58726899 years
overall survival time: 31 days
overall survival status: dead
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/2005-07/62895.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
1 558 1184 316 476 242 708 564 1166 318 479 248 690 0 0 76 265 41 87 100 100 98 97 950 938 .342 2.926 2.782 2.836 3.01 1.484 80 374 3.551 .85 100 2370 5840 51 61 48 58 0 1358 546 812 3.356 1338 792 .298 3.192 1.747 1.674
2 7741 490 330 482 7411 8 8387 486 345 489 8057 4 0 0 2302 98 77 91 100 22 100 2 7419 8061 926.375 .001 0 .01 .012 3.186 80 347 -.004 -.12 110 2510 5840 50 61 61 72 0 562 553 9 .001 558 5 807.457 .001 -9.657 -10.778
3 2624 1582 345 530 2279 1052 2318 1376 362 533 1973 846 0 0 1242 586 82 102 100 100 100 100 3331 2819 2.166 .462 .429 .457 .446 1.386 52 244 .448 .93 80 2660 5830 51 59 78 86 0 1815 608 1207 .53 1579 971 1.888 .492 -.917 -1.023
4 1584 404 362 544 1222 -140 1443 385 372 553 1081 -159 0 0 420 81 69 99 100 0 100 0 1082 922 null null null .007 .014 3.757 52 312 -.107 -.48 90 2800 5830 50 59 91 100 0 463 624 -161 null 442 -182 null null null null
5 1087 477 362 514 725 -37 1045 478 393 527 683 -36 0 0 218 105 98 95 100 6 100 6 688 647 null null null .101 .082 3.078 32 198 -.037 -.1 70 2950 5830 51 58 107 114 0 547 590 -42 null 548 -41 null null null null
6 541 239 336 498 205 -259 535 212 342 505 199 -286 0 0 62 112 56 96 100 1 90 0 -54 -87 null null null .629 .651 1.447 52 266 -1.823 -.63 80 3090 5830 51 59 121 129 0 274 571 -297 null 243 -328 null null null null
7 1388 349 324 496 1064 -147 1370 335 332 498 1046 -161 0 0 306 99 47 93 100 3 100 0 917 885 null null null .023 .039 7.297 52 255 -.146 -.55 80 3240 5840 52 60 136 144 0 400 569 -169 null 384 -185 null null null null
8 1264 456 352 494 912 -38 1291 461 368 495 939 -33 0 0 173 89 83 88 100 9 100 0 874 906 null null null .035 .053 4.686 32 192 -.021 -.06 70 3380 5830 51 58 150 157 0 523 567 -44 null 529 -38 null null null null
9 1389 566 336 517 1053 49 1379 553 352 515 1043 36 0 0 184 114 78 93 100 30 100 13 1102 1079 21.49 .047 .035 .055 .076 4.029 80 309 .061 .27 100 3520 5830 50 60 163 173 0 649 593 56 .053 634 41 18.731 .04 -4.227 -4.658
10 1739 3377 327 513 1412 2864 1826 3760 331 518 1499 3247 0 0 440 1179 52 97 100 98 100 97 4276 4746 .493 2.028 2.166 1.794 2.105 1.703 120 344 2.209 .96 120 3670 5830 49 61 177 189 0 3874 589 3286 2.327 4314 3725 .43 2.485 1.219 1.313
11 3924 934 314 497 3610 437 4023 920 319 500 3709 423 0 0 904 137 55 102 100 100 100 96 4047 4132 8.261 .121 .114 .12 .124 1.482 120 347 .123 .88 120 3820 5830 49 61 192 204 0 1072 570 501 .139 1055 485 7.2 .131 -2.848 -2.934
12 25870 10670 299 475 25571 10195 28660 11822 306 477 28361 11347 0 0 7554 3393 52 106 100 100 100 100 35766 39708 2.508 .399 .4 .381 .401 1.267 120 421 .403 .98 130 3960 5830 48 61 205 218 0 12241 545 11696 .457 13563 13018 2.186 .459 -1.128 -1.123
13 2531 6032 295 437 2236 5595 2671 6342 300 441 2376 5905 0 0 527 1410 50 97 100 100 100 100 7831 8281 .4 2.502 2.485 2.461 2.464 1.297 120 391 2.572 .97 120 4110 5830 49 61 221 233 0 6920 501 6419 2.871 7276 6775 .348 2.851 1.521 1.512
14 515 1907 298 431 217 1476 516 1912 301 438 218 1481 0 0 52 240 41 93 100 100 97 100 1693 1699 .147 6.802 6.794 6.947 6.788 1.316 80 348 6.956 .88 110 4250 5820 48 59 235 246 0 2188 494 1693 7.804 2194 1699 .128 7.794 2.964 2.962
15 774 51718 299 442 475 51276 785 55346 303 452 486 54904 0 0 104 11529 41 92 100 100 100 100 51751 55390 .009 107.949 112.971 106.999 112.645 1.345 120 439 114.071 .95 130 4400 5830 48 61 249 262 0 59335 507 58828 123.848 63497 62990 .008 129.609 6.952 7.018
16 10083 15473 309 465 9774 15008 11237 16715 318 472 10928 16250 0 0 2872 3895 82 98 100 100 100 100 24782 27178 .651 1.536 1.487 1.576 1.508 1.348 120 342 1.527 .98 120 4550 5830 49 61 265 277 0 17752 533 17218 1.762 19177 18643 .568 1.706 .817 .771
17 5835 5019 335 504 5500 4515 6335 5399 350 512 6000 4895 0 0 1318 1337 99 106 100 100 100 100 10015 10895 1.218 .821 .816 .786 .824 1.289 120 349 .827 .97 120 4690 5830 49 61 279 291 0 5758 578 5180 .942 6194 5616 1.062 .936 -.086 -.095
18 1146 390 348 499 798 -109 1142 381 371 507 794 -118 0 0 86 80 110 101 100 0 100 0 689 676 null null null .027 .028 2.364 52 199 -.176 -.58 80 4830 5820 50 58 295 303 0 447 572 -125 null 437 -135 null null null null
19 10655 2948 332 506 10323 2442 11357 3090 344 507 11025 2584 0 0 2310 718 87 96 100 100 100 100 12765 13609 4.227 .237 .234 .229 .235 1.262 120 390 .239 .97 120 4980 5830 49 61 308 320 0 3382 581 2802 .271 3545 2965 3.685 .269 -1.882 -1.895
20 9681 6670 313 490 9368 6180 10209 7140 322 519 9896 6650 0 0 1859 1470 53 236 100 100 100 100 15548 16546 1.516 .66 .672 .652 .677 1.207 120 421 .664 .98 130 5130 5830 48 61 322 335 0 7652 562 7090 .757 8192 7629 1.321 .771 -.402 -.375

Total number of rows: 41472

Table truncated, full table size 9367 Kbytes.




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

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