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Sample GSM515716 Query DataSets for GSM515716
Status Public on Jul 11, 2010
Title shfs185 | normal 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 99KM279
Organism Homo sapiens
Characteristics source: 99KM279
age: 47.53456537 years
overall survival time: 557 days
overall survival status: dead
genotype: normal karyotype
gender: female
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/2005-08/63384.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 (3)
GSE16432 Musashi-2 regulates normal hematopoiesis and promotes aggressive myeloid leukemia
GSE22778 Musashi 2 regulates normal hematopoiesis and accelerates leukemogenesis
GSE32246 TET2 mutations in acute myeloid leukemia: Results from a comprehensive genetic and clinical analysis 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
1 882 326 178 262 704 64 964 319 180 265 786 57 0 0 192 50 22 43 100 61 100 26 768 843 11 .091 .073 .08 .081 2.474 52 276 .066 .38 80 2190 6100 23 31 19 27 0 413 332 81 .115 404 72 8.689 .092 -3.119 -3.445
2 4699 491 186 265 4513 226 5292 517 189 267 5106 252 0 0 1660 97 30 42 100 96 100 90 4739 5358 19.969 .05 .049 .049 .05 1.448 52 313 .047 .86 90 2330 6090 21 30 32 41 0 622 335 286 .063 654 319 15.774 .062 -3.979 -4
3 4146 2832 184 269 3962 2563 4966 3097 200 270 4782 2828 0 0 2156 1242 118 48 100 100 100 100 6525 7610 1.546 .647 .591 .718 .65 1.625 52 282 .612 .96 80 2480 6090 22 30 48 56 0 3585 341 3245 .819 3921 3580 1.221 .749 -.288 -.418
4 1775 630 183 273 1592 357 1973 653 187 273 1790 380 0 0 616 145 43 48 100 96 100 96 1949 2170 4.459 .224 .212 .221 .222 1.574 52 279 .219 .93 80 2630 6100 23 31 63 71 0 798 346 452 .284 827 481 3.523 .269 -1.817 -1.896
5 1137 268 185 263 952 5 1087 259 188 263 902 -4 0 0 338 54 31 43 100 18 100 9 957 898 190.4 .005 null .033 .037 2.5 32 208 .009 .08 70 2770 6090 22 29 77 84 0 339 333 6 .007 328 -5 150.401 null -7.233 null
6 968 211 192 266 776 -55 1023 192 203 268 831 -74 0 0 183 57 47 43 100 9 100 6 721 757 null null null .239 .291 1.426 32 232 -.106 -.52 70 2910 6090 22 29 91 98 0 267 337 -70 null 243 -94 null null null null
7 2242 496 178 270 2064 226 2190 462 186 272 2012 192 0 0 1008 126 37 44 100 98 100 88 2290 2204 9.133 .109 .095 .108 .099 1.806 52 272 .096 .82 80 3070 6100 23 31 107 115 0 628 342 286 .139 585 243 7.214 .121 -2.851 -3.049
8 1074 436 178 270 896 166 1169 431 181 272 991 161 0 0 260 65 24 41 100 98 100 92 1062 1152 5.398 .185 .162 .179 .167 1.82 52 243 .162 .75 80 3210 6090 22 30 121 129 0 552 342 210 .235 546 204 4.264 .206 -2.092 -2.282
9 1072 714 180 270 892 444 1127 728 183 271 947 458 0 0 206 137 25 44 100 98 100 98 1336 1405 2.009 .498 .484 .487 .491 1.363 80 323 .491 .93 100 3350 6100 22 32 134 144 0 904 342 562 .63 922 580 1.587 .612 -.666 -.708
10 2154 2093 181 272 1973 1821 2394 2186 189 274 2213 1914 0 0 639 736 78 44 100 100 100 98 3794 4127 1.083 .923 .865 .876 .958 1.378 80 323 .959 .96 100 3490 6100 22 32 148 158 0 2650 344 2305 1.168 2767 2423 .856 1.095 .225 .131
11 3500 748 180 271 3320 477 3560 754 193 273 3380 483 0 0 671 122 84 46 100 100 100 100 3797 3863 6.96 .144 .143 .141 .149 1.306 52 326 .142 .94 90 3640 6090 21 30 163 172 0 947 343 604 .182 955 611 5.498 .181 -2.459 -2.467
12 10486 11501 173 253 10313 11248 13192 14371 182 259 13019 14118 0 0 5348 6111 44 51 100 100 100 100 21561 27137 .917 1.091 1.084 1.08 1.105 1.675 80 399 1.108 .98 100 3800 6100 22 32 179 189 0 14560 320 14239 1.381 18193 17873 .724 1.373 .465 .457
13 2213 4067 171 245 2042 3822 2256 4123 173 248 2085 3878 0 0 394 700 26 43 100 100 100 100 5864 5963 .534 1.872 1.86 1.873 1.919 1.173 52 288 1.869 .96 90 3940 6090 21 30 193 202 0 5149 310 4838 2.369 5220 4909 .422 2.355 1.245 1.235
14 886 932 170 249 716 683 919 957 177 257 749 708 0 0 116 138 35 69 100 100 100 100 1399 1457 1.048 .954 .945 .945 .984 1.208 52 301 .959 .95 90 4070 6090 21 30 206 215 0 1180 315 865 1.208 1212 896 .828 1.197 .272 .259
15 664 24693 173 253 491 24440 740 29066 179 264 567 28813 0 0 201 9455 48 63 92 100 91 100 24931 29380 .02 49.776 50.817 51.604 50.318 1.693 80 420 51.475 .95 110 4230 6090 20 31 221 232 0 31260 320 30940 63.014 36796 36476 .016 64.331 5.978 6.007
16 8974 15448 174 257 8800 15191 11045 18474 176 260 10871 18217 0 0 3920 5893 25 48 100 100 100 100 23991 29088 .579 1.726 1.676 1.91 1.689 1.97 80 366 1.705 .97 100 4380 6090 21 31 237 247 0 19556 325 19231 2.185 23387 23062 .458 2.121 1.128 1.085
17 3209 7483 171 257 3038 7226 3666 8635 173 258 3495 8378 0 0 1132 2437 22 45 100 100 100 100 10264 11873 .42 2.379 2.397 2.572 2.433 1.643 80 316 2.4 .96 100 4520 6090 21 31 251 261 0 9473 325 9148 3.011 10931 10606 .332 3.035 1.59 1.602
18 746 241 169 255 577 -14 742 243 171 257 573 -12 0 0 134 37 21 42 100 7 100 0 563 561 null null null .027 .035 3.392 80 339 -.022 -.14 100 4660 6090 21 31 265 275 0 305 323 -18 null 308 -15 null null null null
19 7915 4900 170 257 7745 4643 8824 5564 173 259 8654 5307 0 0 2419 1670 25 42 100 100 100 100 12388 13961 1.668 .599 .613 .551 .614 1.495 80 376 .607 .97 110 4810 6100 21 32 279 290 0 6203 325 5878 .759 7044 6718 1.318 .776 -.398 -.365
20 7013 6734 172 261 6841 6473 7262 7037 176 267 7090 6776 0 0 1159 1118 35 57 100 100 100 100 13314 13866 1.057 .946 .956 .947 .961 1.161 80 414 .947 .97 110 4950 6090 20 31 293 304 0 8525 330 8195 1.198 8909 8578 .835 1.21 .26 .275

Total number of rows: 41472

Table truncated, full table size 9398 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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