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Sample GSM144140 Query DataSets for GSM144140
Status Public on Nov 10, 2006
Title EPO 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 stimulated with EPO
Organism Homo sapiens
Characteristics Amplified RNA from early erythroid progenitors stimulated with EPO
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 = 13:28:03; Parameter Scanner Model = G2505B; Parameter Scanning software version = A.6.3.1; Parameter Scanning software = ChipScan; Parameter Scan Date = 2004-05-12; 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 = 13:28:03; Parameter Scanner Model = G2505B; Parameter Scanning software version = A.6.3.1; Parameter Scanning software = ChipScan; Parameter Scan Date = 2004-05-12; Performer: Einar Andreas,,Sivertsen
Description Simple annotation: Hematopoiesis, Normal tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2004-07/53452.gif
Compound Based Treatment: 1
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
1 216 71 131 53 85 18 216 71 131 53 85 18 0 0 30 12 11 6 100 84 100 68 103 103 4.722 .212 .212 .231 .222 1.888 32 176 .21 .69 60 1720 4400 437 443 169 175 0 180 134 46 .537 180 46 1.862 .537 -.897 -.897
2 713 100 131 53 582 47 775 102 131 53 644 49 0 0 309 28 11 6 96 87 96 84 629 693 12.383 .081 .076 .085 .078 1.724 32 215 .075 .91 70 1860 4390 435 442 182 189 0 254 134 119 .205 259 124 4.884 .193 -2.288 -2.374
3 571 204 136 53 435 151 227 77 135 53 91 24 0 0 623 229 10 6 78 76 73 63 586 115 2.881 .347 .264 .309 .301 3.201 52 295 .342 .93 80 2010 4400 436 444 197 205 -50 517 134 383 .88 195 61 1.136 .669 -.184 -.581
4 244 75 140 53 104 22 207 68 141 54 67 15 0 0 107 24 12 8 80 59 73 46 126 82 4.727 .212 .224 .219 .223 2.023 52 274 .201 .85 80 2160 4400 436 444 212 220 -50 190 134 56 .536 172 38 1.864 .568 -.899 -.817
5 7949 2098 142 53 7807 2045 8327 2115 143 54 8185 2062 0 0 3071 845 13 9 100 100 100 100 9852 10247 3.818 .262 .252 .253 .256 1.39 32 206 .259 .96 70 2310 4400 436 443 227 234 0 5319 134 5185 .664 5363 5228 1.506 .639 -.59 -.647
6 173 60 137 52 36 8 177 59 138 53 40 7 0 0 20 9 11 6 84 50 69 26 44 47 4.5 .222 .175 .234 .264 3.029 52 296 .193 .5 80 2450 4400 436 444 241 249 -50 152 132 20 .563 150 18 1.775 .444 -.828 -1.172
7 1115 460 135 53 980 407 1110 448 136 53 975 395 0 0 586 304 10 6 100 100 100 100 1387 1370 2.408 .415 .405 .349 .388 1.755 32 176 .44 .94 60 2600 4400 437 443 257 263 0 1166 134 1032 1.053 1136 1002 .95 1.027 .074 .039
8 777 71 139 53 638 18 781 67 140 53 642 14 0 0 235 13 10 5 100 81 100 65 656 656 35.444 .028 .022 .028 .03 1.699 32 159 .029 .75 60 2750 4400 437 443 272 278 0 180 134 46 .072 170 35 13.979 .055 -3.805 -4.177
9 1456 231 140 53 1316 178 1634 222 140 53 1494 169 0 0 666 109 10 6 100 96 100 96 1494 1663 7.393 .135 .113 .125 .133 1.478 52 271 .138 .96 80 2880 4400 436 444 284 292 0 586 134 451 .343 563 428 2.916 .287 -1.544 -1.802
10 296 62 143 54 153 8 296 61 145 54 153 7 0 0 119 13 16 7 88 44 75 25 161 160 19.125 .052 .046 .067 .06 2.454 52 264 .058 .55 80 3030 4400 436 444 299 307 -50 157 137 20 .133 155 18 7.543 .116 -2.915 -3.108
11 9358 1501 147 54 9211 1447 10009 1639 149 55 9862 1585 0 0 3958 781 19 8 100 100 100 100 10658 11447 6.366 .157 .161 .13 .16 1.652 52 276 .163 .98 80 3170 4390 435 443 313 321 0 3806 137 3669 .398 4156 4019 2.511 .407 -1.328 -1.295
12 12879 2674 155 55 12724 2619 15115 2958 159 56 14960 2903 0 0 6403 1416 27 9 100 100 100 100 15343 17863 4.858 .206 .194 .208 .205 1.489 32 218 .212 .98 70 3310 4390 435 442 327 334 0 6780 139 6640 .522 7500 7360 1.916 .492 -.938 -1.023
13 2824 588 156 55 2668 533 2623 510 165 57 2467 455 0 0 2105 525 72 16 100 96 96 93 3201 2922 5.006 .2 .184 .165 .188 1.725 32 170 .217 .97 60 3460 4390 436 442 343 349 0 1491 139 1351 .507 1293 1154 1.974 .468 -.981 -1.097
14 333 137 153 56 180 81 339 122 154 57 186 66 0 0 56 59 11 7 100 100 100 96 261 252 2.222 .45 .355 .385 .379 1.629 32 170 .508 .83 60 3610 4390 436 442 358 364 0 347 142 205 1.141 309 167 .876 .9 .19 -.153
15 1271 564 166 59 1105 505 1201 609 172 61 1035 550 0 0 278 142 26 11 100 100 100 100 1610 1585 2.188 .457 .531 .449 .432 1.231 32 226 .463 .96 70 3750 4390 435 442 371 378 0 1430 150 1280 1.159 1544 1395 .863 1.347 .213 .43
16 10287 12894 160 62 10127 12832 10665 13999 168 67 10505 13937 0 0 2408 4056 28 18 100 100 100 100 22959 24442 .789 1.267 1.327 1.226 1.287 1.267 32 165 1.327 .98 60 3900 4390 436 442 387 393 0 32692 157 32535 3.213 35494 35337 .311 3.364 1.684 1.75
17 8263 4569 164 60 8099 4509 8687 4878 166 61 8523 4818 0 0 5335 2911 21 12 98 98 98 98 12608 13341 1.796 .557 .565 .526 .571 1.577 80 403 .543 .97 100 4050 4400 435 445 400 410 0 11585 152 11432 1.412 12368 12216 .708 1.433 .497 .519
18 221 69 182 62 39 7 216 66 182 64 34 4 0 0 46 13 41 11 28 26 9 9 46 38 5.571 .179 .118 .21 .271 2.504 52 267 .211 .38 80 4200 4400 436 444 416 424 -50 175 157 18 .455 167 10 2.197 .298 -1.136 -1.745
19 19225 4800 190 62 19035 4738 22008 5598 240 82 21818 5536 0 0 8242 2110 204 108 100 100 100 100 23773 27354 4.018 .249 .254 .255 .246 1.681 32 201 .249 .97 70 4340 4390 435 442 430 437 0 12170 157 12013 .631 14194 14036 1.585 .643 -.664 -.636
20 40270 19859 189 63 40081 19796 42062 21315 212 73 41873 21252 0 0 9402 5769 141 71 100 100 100 100 59877 63125 2.025 .494 .508 .48 .486 1.189 80 406 .505 .98 100 4490 4400 435 445 444 454 0 50352 160 50192 1.252 54043 53884 .799 1.287 .325 .364

Total number of rows: 43104

Table truncated, full table size 9530 Kbytes.




Supplementary data files not provided
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