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Sample GSM81684 Query DataSets for GSM81684
Status Public on Nov 04, 2005
Title BMP4 24hrs
Sample type RNA
 
Channel 1
Source name untreated cells
Organism Homo sapiens
Characteristics untreated cells
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name BMP4 24hrs (AMP3)
Organism Homo sapiens
Characteristics BMP4 24hrs (AMP3)
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: ES cells, cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2001-12/23594.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 Nov 03, 2005
Last update date Sep 22, 2006
Organization Stanford Microarray Database (SMD)
E-mail(s) [email protected]
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 GPL3044
Series (1)
GSE3553 BMP4 initiates human ES cell differentiation

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
1 363 307 163 98 200 209 401 320 172 102 238 222 0 0 210 143 54 32 71 86 67 80 409 460 .957 1.045 .933 .813 .81 1.639 52 281 .79 .82 80 2140 7520 48 56 98 106 0 279 89 190 .95 291 202 1.053 .848 -.074 -.238
2 396 245 162 102 234 143 412 261 185 117 250 159 0 0 235 95 86 58 68 78 62 71 377 409 1.636 .611 .636 .538 .427 2.525 32 189 .516 .78 70 2260 7520 48 55 110 117 0 223 93 130 .556 237 145 1.8 .578 -.848 -.79
3 500 372 165 100 335 272 460 332 185 110 295 232 0 0 308 208 178 52 67 88 35 77 607 527 1.232 .812 .786 .651 .736 2.247 80 475 .378 .72 110 2410 7520 46 57 123 134 0 338 91 247 .738 302 211 1.355 .715 -.438 -.484
4 7369 6347 167 103 7202 6244 6902 5894 207 124 6735 5791 0 0 6372 4333 239 102 75 100 71 96 13446 12526 1.153 .867 .86 1.374 .837 3.141 52 356 .767 .94 90 2570 7520 47 56 140 149 0 5770 94 5676 .788 5358 5265 1.269 .782 -.343 -.355
5 840 751 182 116 658 635 556 671 236 157 374 555 0 0 757 517 200 146 56 78 46 68 1293 929 1.036 .965 1.484 1.089 .904 3.052 32 215 .712 .91 70 2740 7520 48 55 158 165 0 683 105 577 .877 610 505 1.14 1.349 -.189 .432
6 628 510 183 115 445 395 713 478 248 165 530 363 0 0 375 261 223 178 68 75 56 50 840 893 1.127 .888 .685 .861 .788 1.761 32 232 .721 .87 70 2880 7520 48 55 172 179 0 464 105 359 .807 435 330 1.239 .623 -.309 -.684
7 914 946 171 109 743 837 997 1061 222 162 826 952 0 0 580 486 206 191 75 84 62 78 1580 1778 .888 1.127 1.153 1.255 1.103 1.854 32 220 .892 .93 70 3030 7520 48 55 187 194 0 860 99 761 1.024 965 865 .976 1.048 .034 .067
8 4744 5354 151 98 4593 5256 4180 6395 164 110 4029 6297 0 0 4468 3704 66 84 76 100 75 100 9849 10326 .874 1.144 1.563 1.432 1.19 1.852 52 318 .962 .94 90 3170 7520 47 56 200 209 0 4867 89 4778 1.04 5814 5725 .961 1.421 .057 .507
9 1861 1589 151 97 1710 1492 1975 1421 158 98 1824 1324 0 0 1578 1012 44 30 73 100 71 100 3202 3148 1.146 .873 .726 .985 .812 1.866 52 221 .738 .97 80 3300 7520 48 56 214 222 0 1445 88 1356 .793 1292 1204 1.261 .66 -.334 -.6
10 214 167 156 97 58 70 176 154 161 103 20 57 0 0 127 76 46 47 45 53 37 36 128 77 .829 1.207 2.85 .671 .69 3.629 80 343 .508 .47 100 3440 7510 46 56 227 237 -50 152 88 64 1.097 140 52 .911 2.591 .134 1.373
11 4103 4288 164 100 3939 4188 2823 2939 186 139 2659 2839 0 0 3362 3137 148 211 87 100 83 98 8127 5498 .941 1.063 1.068 1.383 1.036 2.311 80 443 1.009 .98 110 3580 7520 46 57 240 251 0 3898 91 3807 .967 2672 2581 1.035 .971 -.049 -.043
12 968 1065 158 100 810 965 1201 1021 181 152 1043 921 0 0 730 647 112 240 62 78 62 65 1775 1964 .839 1.191 .883 1.293 1.04 2.352 32 171 1.01 .95 60 3730 7530 50 56 258 264 0 968 91 877 1.083 928 837 .923 .803 .115 -.317
13 947 857 155 88 792 769 1009 807 169 98 854 719 0 0 695 492 76 76 73 92 69 88 1561 1573 1.03 .971 .842 1.045 .853 1.908 52 293 .743 .92 80 3890 7520 48 56 273 281 0 779 80 699 .883 734 654 1.133 .765 -.18 -.386
14 515 221 183 103 332 118 564 224 196 110 381 121 0 0 150 63 95 41 91 83 91 58 450 502 2.814 .355 .318 .304 .417 1.904 12 63 .231 .68 40 4050 7520 50 54 291 295 0 201 94 107 .323 204 110 3.095 .289 -1.63 -1.792
15 1394 1446 165 95 1229 1351 1555 1398 169 99 1390 1303 0 0 1036 835 49 32 80 98 77 97 2580 2693 .91 1.099 .937 1.265 1.058 1.937 80 341 .942 .94 100 4170 7530 48 58 300 310 0 1315 86 1228 .999 1271 1185 1.001 .852 -.001 -.231
16 1511 1394 166 99 1345 1295 1594 1300 170 102 1428 1201 0 0 1072 787 46 32 82 100 77 98 2640 2629 1.039 .963 .841 1.256 .942 2.368 80 373 .852 .96 100 4320 7530 48 58 315 325 0 1267 90 1177 .875 1182 1092 1.142 .765 -.192 -.387
17 803 755 174 104 629 651 920 763 178 108 746 659 0 0 569 429 50 32 71 96 71 92 1280 1405 .966 1.035 .883 1.013 .922 1.927 52 274 .884 .93 80 4470 7520 48 56 331 339 0 686 95 592 .941 694 599 1.063 .803 -.088 -.316
18 626 468 188 109 438 359 728 435 194 114 540 326 0 0 349 188 53 37 75 96 75 93 797 866 1.22 .82 .604 .679 .631 1.601 32 150 .626 .77 60 4620 7520 49 55 347 353 0 425 99 326 .745 395 296 1.342 .549 -.424 -.866
19 3043 3738 179 113 2864 3625 3292 3649 188 122 3113 3536 0 0 1393 1649 55 66 96 100 93 100 6489 6649 .79 1.266 1.136 1.527 1.239 2.039 80 474 1.236 .97 110 4750 7520 46 57 357 368 0 3398 103 3295 1.151 3317 3215 .869 1.033 .202 .046
20 1644 2039 189 120 1455 1919 1742 2149 230 184 1553 2029 0 0 1109 1283 187 278 81 87 78 81 3374 3582 .758 1.319 1.307 1.391 1.28 1.604 32 205 1.278 .97 70 4890 7530 49 56 373 380 0 1854 109 1745 1.199 1954 1845 .834 1.188 .262 .248

Total number of rows: 43008

Table truncated, full table size 9644 Kbytes.




Supplementary data files not provided
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