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Sample GSM93340 Query DataSets for GSM93340
Status Public on Jan 21, 2006
Title SUP-B15 L-asp 2U/ml t=0h
Sample type RNA
 
Channel 1
Source name Stratagene
Organism Homo sapiens
Characteristics Stratagene
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name SUP-B15 L-asp 2U/ml t=0h
Organism Homo sapiens
Characteristics SUP-B15 L-asp 2U/ml t=0h
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: acute lymphoblastic leukemia, cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2001-10/20946.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 Jan 19, 2006
Last update date Sep 22, 2006
Organization Stanford Microarray Database (SMD)
E-mail(s) array@genome.stanford.edu
Phone 650-498-6012
URL http://genome-www5.stanford.edu/
Department Stanford University, School of Medicine
Street address 300 Pasteur Drive
City Stanford
State/province CA
ZIP/Postal code 94305
Country USA
 
Platform ID GPL2705
Series (2)
GSE4072 L-asparaginase exposure in acute lymphoblastic leukemia cell lines time series
GSE4397 In vitro response to l-asparaginase in acute lymphoblastic leukemia

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
1 683 928 219 113 464 815 663 930 222 117 444 817 0 0 268 337 48 31 98 100 98 100 1279 1261 .569 1.756 1.84 1.967 1.741 1.81 52 296 1.67 .9 80 2170 7680 80 88 101 109 0 998 122 876 1.889 1000 878 .529 1.979 .917 .984
2 731 607 223 109 508 498 744 613 229 116 521 504 0 0 236 166 49 33 100 100 98 100 1006 1025 1.02 .98 .967 1.061 .984 1.587 52 274 .895 .9 80 2320 7680 80 88 116 124 0 653 117 535 1.054 659 542 .949 1.04 .076 .057
3 2048 512 229 114 1819 398 2033 511 234 116 1804 397 0 0 772 144 51 29 100 100 100 98 2217 2201 4.57 .219 .22 .224 .235 1.409 52 320 .202 .95 90 2470 7680 79 88 130 139 0 551 123 428 .235 549 427 4.25 .237 -2.088 -2.079
4 6773 5639 228 116 6545 5523 6634 5805 235 120 6406 5689 0 0 4373 3365 60 31 100 100 100 100 12068 12095 1.185 .844 .888 .981 .87 1.786 52 266 .81 .97 80 2610 7670 79 87 145 153 0 6063 125 5939 .907 6242 6117 1.102 .955 -.14 -.067
5 939 500 216 116 723 384 940 502 228 119 724 386 0 0 309 167 60 32 100 100 100 100 1107 1110 1.883 .531 .533 .517 .526 1.623 52 295 .489 .88 80 2760 7680 80 88 160 168 0 538 125 413 .571 540 415 1.751 .573 -.808 -.803
6 709 615 233 119 476 496 691 588 236 122 458 469 0 0 186 136 50 33 100 100 100 100 972 927 .96 1.042 1.024 1.1 .993 1.524 32 220 .962 .89 70 2910 7680 80 87 175 182 0 661 128 533 1.12 632 504 .893 1.101 .164 .139
7 568 373 223 122 345 251 565 369 228 123 342 247 0 0 133 80 51 31 96 100 93 100 596 589 1.375 .728 .722 .784 .71 1.715 32 208 .624 .8 70 3040 7670 79 86 188 195 0 401 131 270 .782 397 266 1.278 .777 -.354 -.365
8 7144 6330 215 114 6929 6216 7522 6562 220 117 7307 6448 0 0 2678 2096 50 28 100 100 100 100 13145 13755 1.115 .897 .882 .912 .848 1.254 52 297 .874 .98 80 3180 7680 80 88 202 210 0 6806 123 6684 .965 7056 6933 1.037 .949 -.052 -.076
9 2727 2216 222 117 2505 2099 2856 2303 227 121 2634 2186 0 0 890 742 50 31 100 100 100 100 4604 4820 1.193 .838 .83 .835 .841 1.313 52 285 .827 .97 80 3340 7680 80 88 218 226 0 2383 126 2257 .901 2476 2351 1.11 .892 -.15 -.164
10 820 456 233 122 587 334 832 453 234 123 599 331 0 0 202 143 50 29 100 100 100 100 921 930 1.757 .569 .553 .554 .581 1.402 32 213 .544 .9 70 3480 7670 79 86 232 239 0 490 131 359 .612 487 356 1.634 .594 -.709 -.751
11 2616 2229 245 128 2371 2101 2340 2164 253 132 2095 2036 0 0 1109 913 75 35 100 100 100 100 4472 4131 1.129 .886 .972 .895 .875 1.334 52 326 .87 .96 90 3630 7680 79 88 246 255 0 2397 138 2259 .953 2327 2189 1.05 1.045 -.07 .063
12 2691 2755 237 127 2454 2628 2636 2680 252 130 2399 2553 0 0 1382 1185 78 35 96 100 96 100 5082 4952 .934 1.071 1.064 1.162 1.076 1.416 52 325 1 .97 90 3770 7670 78 87 260 269 0 2962 137 2826 1.152 2882 2745 .868 1.144 .204 .194
13 2061 1778 230 119 1831 1659 2013 1745 236 125 1783 1626 0 0 654 477 59 36 100 100 100 100 3490 3409 1.104 .906 .912 .929 .903 1.252 52 274 .87 .97 80 3930 7680 80 88 277 285 0 1912 128 1784 .974 1876 1748 1.026 .981 -.038 -.028
14 757 338 237 121 520 217 749 327 245 127 512 206 0 0 234 113 65 38 100 98 100 90 737 718 2.396 .417 .402 .408 .445 1.612 52 253 .386 .86 80 4070 7680 80 88 291 299 0 363 130 233 .449 352 222 2.229 .433 -1.156 -1.209
15 11467 7688 235 127 11232 7561 11399 8214 239 137 11164 8087 0 0 5393 3382 52 54 100 100 100 100 18793 19251 1.486 .673 .724 .691 .699 1.332 52 314 .643 .98 90 4200 7680 79 88 303 312 0 8267 137 8130 .724 8832 8696 1.382 .779 -.466 -.36
16 2544 2019 226 130 2318 1889 2412 1914 231 134 2186 1784 0 0 830 585 54 38 100 100 100 100 4207 3970 1.227 .815 .816 .831 .799 1.214 52 284 .788 .98 80 4360 7680 80 88 320 328 0 2171 140 2031 .876 2058 1918 1.141 .878 -.191 -.188
17 558 496 226 125 332 371 533 490 233 129 307 365 0 0 148 119 59 35 100 100 93 100 703 672 .895 1.117 1.189 1.189 1.163 1.609 32 212 .992 .84 70 4500 7680 80 87 334 341 0 533 134 399 1.202 527 392 .832 1.278 .265 .354
18 583 472 236 123 347 349 560 458 238 129 324 335 0 0 194 135 60 41 100 100 96 100 696 659 .994 1.006 1.034 1.076 .969 1.509 32 219 .866 .84 70 4650 7670 79 86 349 356 0 508 132 375 1.081 492 360 .925 1.112 .113 .153
19 2256 1817 234 123 2022 1694 2155 1730 238 132 1921 1607 0 0 1018 579 63 45 100 100 98 100 3716 3528 1.194 .838 .837 .972 .848 1.797 52 320 .769 .95 90 4800 7680 79 88 363 372 0 1954 132 1822 .901 1860 1728 1.11 .9 -.151 -.153
20 722 633 227 130 495 503 761 633 231 133 534 503 0 0 245 180 55 35 96 100 93 100 998 1037 .984 1.016 .942 1.048 .963 1.531 32 205 .885 .88 70 4930 7680 80 87 377 384 0 681 140 541 1.093 681 541 .915 1.013 .128 .018

Total number of rows: 43008

Table truncated, full table size 9632 Kbytes.




Supplementary data files not provided
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