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Sample GSM144143 Query DataSets for GSM144143
Status Public on Nov 10, 2006
Title Medium donor 2
Sample type RNA
 
Channel 1
Source name Amplified Universal Human Reference RNA (Stratagene)
Organism Homo sapiens
Characteristics Amplified Universal Human Reference RNA (Stratagene)
Extracted molecule total RNA
Extraction protocol not provided
Label Cy3
Label protocol not provided
 
Channel 2
Source name Amplified RNA from early erythroid progenitors cultured in medium
Organism Homo sapiens
Characteristics Amplified RNA from early erythroid progenitors cultured in medium
Extracted molecule total RNA
Extraction protocol not provided
Label Cy5
Label protocol not provided
 
 
Hybridization protocol not provided
Scan protocol not provided
Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 0, 0; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Einar Andreas,,Sivertsen
Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Agilent Technologies Scanner; Parameter Pixel Size = 10; Parameter Scan Time = 10:31:24; Parameter Scanner Model = G2505B; Parameter Scanning software version = A.6.3.1; Parameter Scanning software = ChipScan; Parameter Scan Date = 2004-04-30; Performer: Einar Andreas,,Sivertsen
Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Agilent Technologies Scanner; Parameter Pixel Size = 10; Parameter Scan Time = 10:31:24; Parameter Scanner Model = G2505B; Parameter Scanning software version = A.6.3.1; Parameter Scanning software = ChipScan; Parameter Scan Date = 2004-04-30; Performer: Einar Andreas,,Sivertsen
Description Simple annotation: Hematopoiesis, Normal tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2004-07/53455.gif
Compound Based Treatment: 0
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 09, 2006
Last update date Nov 09, 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 GPL3528
Series (1)
GSE6260 Erythroid progenitors stimulated with EPO

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
1 542 136 426 73 116 63 538 135 430 75 112 62 0 0 40 30 28 11 100 100 96 90 179 174 1.841 .543 .554 .499 .505 1.689 32 227 .489 .78 70 1810 3860 382 389 177 184 0 160 86 74 .64 159 73 1.562 .652 -.644 -.616
2 1460 705 421 73 1039 632 1379 692 444 93 958 619 0 0 413 251 74 89 100 100 100 98 1671 1577 1.644 .608 .646 .614 .598 1.4 52 280 .715 .9 90 1960 3890 384 393 191 200 0 831 86 745 .717 816 729 1.395 .761 -.48 -.393
3 600 168 409 69 191 99 429 77 417 75 20 8 0 0 370 208 47 42 34 28 30 23 290 28 1.929 .518 .4 .416 .456 2.686 52 274 .538 .95 80 2090 3870 383 391 205 213 -50 198 81 117 .611 91 9 1.637 .471 -.711 -1.085
4 537 98 388 67 149 31 532 94 391 68 144 27 0 0 67 26 26 8 100 87 93 65 180 171 4.806 .208 .188 .171 .187 1.869 32 171 .216 .76 60 2250 3880 385 391 222 228 0 115 79 37 .245 111 32 4.078 .221 -2.028 -2.178
5 9129 5924 392 67 8737 5857 9209 6084 404 68 8817 6017 0 0 4113 2433 64 11 100 100 100 100 14594 14834 1.492 .67 .682 .72 .704 1.342 32 232 .631 .97 70 2390 3880 384 391 235 242 0 6981 79 6902 .79 7170 7091 1.266 .804 -.34 -.314
6 536 122 388 67 148 55 535 112 392 70 147 45 0 0 54 36 27 11 100 93 96 87 203 192 2.691 .372 .306 .313 .357 1.93 32 170 .411 .9 60 2540 3870 384 390 251 257 0 144 79 65 .438 132 53 2.283 .361 -1.191 -1.471
7 1429 1140 382 68 1047 1072 1361 946 382 69 979 878 0 0 739 778 19 9 96 96 96 96 2119 1857 .977 1.024 .897 .994 .996 1.641 32 176 1.029 .97 60 2690 3880 385 391 266 272 0 1343 80 1263 1.207 1115 1035 .829 1.057 .271 .08
8 1037 172 398 70 639 102 1020 171 402 77 622 101 0 0 200 55 28 33 100 93 100 75 741 723 6.265 .16 .162 .144 .165 1.676 32 187 .165 .77 70 2830 3870 383 390 279 286 0 203 82 120 .188 202 119 5.316 .191 -2.41 -2.386
9 2703 968 377 66 2326 902 2095 749 380 70 1718 683 0 0 2593 1052 39 24 87 81 85 76 3228 2401 2.579 .388 .398 .318 .387 2.333 80 398 .396 .97 100 2950 3860 381 391 290 300 0 1141 78 1063 .457 883 805 2.188 .469 -1.13 -1.094
10 535 97 368 67 167 30 519 93 364 67 151 26 0 0 134 28 36 11 80 69 67 53 197 177 5.567 .18 .172 .191 .184 1.998 52 256 .145 .51 80 3110 3870 383 391 307 315 -50 114 79 35 .212 110 31 4.724 .203 -2.24 -2.301
11 8782 3514 390 67 8392 3447 8722 3148 390 71 8332 3081 0 0 5948 2519 44 19 98 100 98 100 11839 11413 2.435 .411 .37 .374 .405 1.918 52 340 .404 .96 90 3250 3860 381 390 320 329 0 4141 79 4062 .484 3710 3631 2.066 .436 -1.047 -1.198
12 14343 8519 368 68 13975 8451 15703 9288 371 72 15335 9220 0 0 4241 2933 41 19 100 100 100 100 22426 24555 1.654 .605 .601 .587 .613 1.275 32 170 .61 .98 60 3410 3870 384 390 338 344 0 10040 80 9959 .713 10946 10866 1.403 .709 -.489 -.497
13 2200 1717 344 65 1856 1652 2369 1844 342 67 2025 1779 0 0 766 601 38 13 100 100 100 100 3508 3804 1.123 .89 .879 .927 .861 1.358 32 170 .86 .98 60 3550 3870 384 390 352 358 0 2023 77 1947 1.049 2173 2097 .953 1.035 .069 .05
14 515 186 331 69 184 117 521 171 332 70 190 102 0 0 156 115 36 13 76 78 67 67 301 292 1.573 .636 .537 .581 .615 2.524 52 296 .624 .89 80 3700 3870 383 391 366 374 -50 219 81 138 .749 202 120 1.334 .633 -.416 -.66
15 1454 826 332 71 1122 755 1509 828 335 76 1177 757 0 0 217 140 34 19 100 100 100 100 1877 1934 1.486 .673 .643 .677 .659 1.266 32 213 .663 .96 70 3840 3870 383 390 380 387 0 973 84 890 .793 976 892 1.261 .758 -.335 -.4
16 6584 17344 363 67 6221 17277 8436 22944 375 96 8073 22877 0 0 3957 10853 228 481 100 100 92 96 23498 30950 .36 2.777 2.834 2.874 2.783 1.741 52 279 2.803 .98 80 3990 3870 383 391 395 403 0 20440 79 20361 3.273 27039 26960 .306 3.34 1.711 1.74
17 11163 18604 394 67 10769 18537 9598 16702 660 561 9204 16635 0 0 6565 10442 1375 2414 93 93 90 90 29306 25839 .581 1.721 1.807 1.775 1.763 1.253 32 213 1.692 .97 70 4130 3860 382 389 409 416 0 21925 79 21846 2.029 19683 19604 .493 2.13 1.02 1.091
18 329 102 370 66 -41 36 356 88 394 110 -14 22 0 0 79 40 280 357 0 0 0 0 -5 8 null null null .554 .432 3.44 52 267 2.149 .58 80 4280 3870 383 391 424 432 -50 120 78 42 null 104 26 null null null null
19 11032 10617 357 63 10675 10554 11703 10807 356 70 11346 10744 0 0 8822 8946 31 28 100 100 100 100 21229 22090 1.011 .989 .947 .959 1.002 1.573 52 312 1.011 .98 90 4420 3870 382 391 437 446 0 12512 74 12438 1.165 12736 12662 .858 1.116 .22 .158
20 11807 11435 352 63 11455 11372 6260 5387 353 66 5908 5324 0 0 11050 11511 24 18 100 100 100 100 22827 11232 1.007 .993 .901 .984 .993 1.445 80 390 1.02 .98 100 4580 3880 383 393 453 463 0 13476 74 13402 1.17 6349 6274 .855 1.062 .226 .087

Total number of rows: 43104

Table truncated, full table size 9664 Kbytes.




Supplementary data files not provided
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