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Sample GSM93329 Query DataSets for GSM93329
Status Public on Jan 21, 2006
Title RS in 2U/ml L-asp t=12h
Sample type RNA
 
Channel 1
Source name Stratagene
Organism Homo sapiens
Characteristics Stratagene
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name RS in 2U/ml L-asp t=12h
Organism Homo sapiens
Characteristics RS in 2U/ml L-asp t=12h
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: acute lymphoblastic leukemia, cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2001-11/22431.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 GPL3254
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
1 803 1183 121 110 682 1073 833 1294 134 129 712 1184 0 0 383 368 70 121 90 100 84 98 1755 1896 .636 1.573 1.663 2.04 1.696 2.224 52 336 1.457 .92 90 1840 8230 142 151 77 86 0 1443 134 1309 1.919 1578 1444 .521 2.028 .94 1.02
2 973 799 123 113 850 686 980 874 135 128 857 761 0 0 321 260 65 115 100 98 100 93 1536 1618 1.239 .807 .888 .799 .755 1.273 80 346 .796 .96 100 2000 8240 143 153 93 103 0 974 138 837 .984 1066 928 1.016 1.083 -.023 .115
3 1898 982 130 133 1768 849 2017 874 136 139 1887 741 0 0 929 494 36 42 98 99 94 99 2617 2628 2.082 .48 .393 .502 .465 1.842 120 446 .457 .88 120 2150 8240 142 154 107 119 0 1198 162 1035 .586 1066 904 1.708 .479 -.772 -1.062
4 6562 6124 125 134 6437 5990 6752 5747 129 139 6627 5613 0 0 3335 2882 30 41 100 100 100 100 12427 12240 1.075 .931 .847 .962 .944 1.304 80 363 .909 .97 110 2290 8240 142 153 121 132 0 7468 163 7305 1.135 7009 6845 .881 1.033 .182 .047
5 1421 805 122 119 1299 686 1515 863 123 121 1393 744 0 0 453 217 28 30 100 100 100 100 1985 2137 1.894 .528 .534 .547 .542 1.357 52 264 .481 .94 90 2430 8240 143 152 136 145 0 982 145 837 .644 1052 907 1.553 .651 -.635 -.619
6 596 610 126 126 470 484 602 575 132 131 476 449 0 0 257 246 42 39 97 100 91 100 954 925 .971 1.03 .943 1.108 .991 1.853 80 412 .99 .84 100 2580 8240 143 153 151 161 0 744 154 590 1.256 701 548 .796 1.15 .329 .202
7 624 680 124 138 500 542 659 740 130 145 535 602 0 0 245 255 35 40 98 98 94 92 1042 1137 .923 1.084 1.125 1.039 1.07 1.692 52 232 1.073 .89 80 2740 8230 143 151 168 176 0 829 168 661 1.322 902 734 .756 1.372 .403 .457
8 6538 9065 123 133 6415 8932 7195 9792 131 140 7072 9659 0 0 2767 3511 39 43 100 100 100 100 15347 16731 .718 1.392 1.366 1.429 1.407 1.253 80 418 1.377 .98 110 2870 8240 142 153 179 190 0 11055 162 10893 1.698 11941 11779 .589 1.666 .764 .736
9 2263 2256 117 113 2146 2143 2469 2222 121 120 2352 2109 0 0 1103 981 32 35 100 100 100 100 4289 4461 1.001 .999 .897 1.095 1.04 1.456 52 319 .941 .96 90 3020 8230 142 151 195 204 0 2751 138 2613 1.218 2710 2572 .821 1.094 .284 .129
10 652 421 122 113 530 308 482 377 158 137 360 264 0 0 321 169 110 93 100 100 91 66 838 624 1.721 .581 .733 .592 .582 1.921 12 104 .627 .88 50 3150 8230 144 149 210 215 0 513 138 376 .709 460 322 1.411 .894 -.497 -.161
11 2683 2880 118 107 2565 2773 2527 2679 132 115 2409 2572 0 0 1600 1449 67 56 98 100 98 99 5338 4981 .925 1.081 1.068 1.213 1.125 1.526 120 501 1.019 .96 120 3310 8240 142 154 223 235 0 3512 130 3382 1.318 3267 3137 .758 1.302 .399 .381
12 1714 2112 117 108 1597 2004 1990 2453 125 112 1873 2345 0 0 968 1133 45 40 96 100 96 100 3601 4218 .797 1.255 1.252 1.356 1.245 1.489 52 282 1.218 .97 90 3460 8230 142 151 239 248 0 2576 132 2444 1.53 2991 2860 .653 1.527 .614 .611
13 2000 1435 116 103 1884 1332 2351 1582 123 108 2235 1479 0 0 973 643 39 30 94 98 92 96 3216 3714 1.414 .707 .662 .787 .72 1.62 52 307 .685 .96 90 3610 8230 142 151 254 263 0 1750 126 1624 .862 1929 1804 1.16 .807 -.214 -.309
14 656 444 114 102 542 342 667 481 118 104 553 379 0 0 233 152 28 27 100 93 96 90 884 932 1.585 .631 .685 .62 .672 1.578 32 199 .542 .84 70 3760 8240 144 151 270 277 0 541 124 417 .77 587 462 1.3 .836 -.378 -.259
15 9469 10490 113 105 9356 10385 10870 10731 118 112 10757 10626 0 0 4935 4787 28 45 100 100 100 100 19741 21383 .901 1.11 .988 1.253 1.144 1.579 80 424 1.073 .97 110 3900 8240 142 153 282 293 0 12793 128 12665 1.354 13087 12959 .739 1.205 .437 .269
16 2095 1877 112 100 1983 1777 2442 1974 116 104 2330 1874 0 0 1052 753 27 25 97 100 97 100 3760 4204 1.116 .896 .804 1.113 .934 2.033 80 345 .844 .96 100 4050 8240 143 153 298 308 0 2289 122 2167 1.093 2407 2285 .915 .981 .128 -.028
17 548 582 113 95 435 487 567 623 132 98 454 528 0 0 230 252 264 25 76 98 38 96 922 982 .893 1.12 1.163 1.151 1.167 1.577 52 245 .522 .54 80 4190 8230 143 151 313 321 0 710 116 594 1.365 760 644 .732 1.418 .449 .504
18 555 580 113 100 442 480 589 612 137 102 476 512 0 0 204 168 274 26 82 100 28 100 922 988 .921 1.086 1.076 1.141 1.112 1.639 52 227 1.008 .91 80 4340 8230 143 151 328 336 0 707 122 585 1.324 746 624 .755 1.312 .405 .391
19 2020 1206 115 100 1905 1106 1773 1123 118 103 1658 1023 0 0 1195 590 26 24 99 100 98 100 3011 2681 1.722 .581 .617 .653 .59 1.727 120 416 .532 .95 120 4480 8240 142 154 340 352 0 1471 122 1349 .708 1370 1248 1.412 .752 -.498 -.41
20 893 640 118 103 775 537 942 688 122 107 824 585 0 0 318 188 53 27 96 100 96 100 1312 1409 1.443 .693 .71 .722 .693 1.616 80 316 .654 .93 110 4620 8240 142 153 354 365 0 780 126 655 .845 839 713 1.183 .866 -.243 -.208

Total number of rows: 43008

Table truncated, full table size 9652 Kbytes.




Supplementary data files not provided
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