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Sample GSM144141 Query DataSets for GSM144141
Status Public on Nov 10, 2006
Title EPO+LY 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 and LY
Organism Homo sapiens
Characteristics Amplified RNA from early erythroid progenitors stimulated with EPO and LY
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 = 13:37:48; 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 = 13:37:48; 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/2004-07/53453.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) [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 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
1 185 60 144 48 41 12 187 60 143 48 43 12 0 0 21 8 12 6 90 71 78 46 53 55 3.417 .293 .279 .316 .337 2.105 32 164 .195 .52 60 1660 4380 435 441 163 169 0 218 175 44 1.065 218 44 .939 1.016 .091 .022
2 603 72 144 49 459 23 583 69 147 50 439 20 0 0 156 15 12 6 100 87 100 81 482 459 19.957 .05 .046 .045 .049 1.622 32 165 .051 .81 60 1810 4380 435 441 178 184 0 262 178 84 .182 251 73 5.484 .166 -2.455 -2.592
3 593 130 150 50 443 80 268 68 150 51 118 18 0 0 562 121 15 8 96 65 93 53 523 136 5.538 .181 .153 .121 .155 2.569 32 230 .21 .94 70 1960 4370 433 440 192 199 0 473 182 291 .657 247 66 1.522 .555 -.606 -.849
4 267 58 140 48 127 10 270 55 141 49 130 7 0 0 68 10 11 5 100 56 100 40 137 137 12.7 .079 .054 .081 .08 2.023 32 230 .09 .7 70 2110 4380 434 441 207 214 0 211 175 36 .287 200 25 3.49 .196 -1.803 -2.351
5 5285 1819 139 49 5146 1770 5670 1859 140 49 5531 1810 0 0 2492 743 12 5 100 100 100 100 6916 7341 2.907 .344 .327 .366 .339 1.394 32 220 .317 .97 70 2260 4390 435 442 222 229 0 6620 178 6442 1.252 6766 6587 .799 1.191 .324 .252
6 160 52 140 49 20 3 162 50 141 49 22 1 0 0 16 7 15 6 71 30 25 13 23 23 6.667 .15 .045 .33 .318 3.507 52 290 .095 .23 80 2400 4380 434 442 236 244 -50 189 178 11 .546 182 4 1.832 .165 -.873 -2.596
7 743 301 147 49 596 252 652 292 147 49 505 243 0 0 406 182 12 6 100 100 100 96 848 748 2.365 .423 .481 .362 .414 1.787 32 176 .423 .96 60 2550 4390 436 442 252 258 0 1095 178 917 1.539 1063 884 .65 1.751 .622 .808
8 521 63 149 49 372 14 549 62 150 50 400 13 0 0 150 12 11 5 100 81 100 53 386 413 26.571 .038 .033 .039 .033 1.884 32 211 .038 .7 70 2700 4380 434 441 266 273 0 229 178 51 .137 226 47 7.301 .118 -2.868 -3.08
9 877 102 149 49 728 53 909 99 151 50 760 50 0 0 365 35 20 6 100 90 100 84 781 810 13.736 .073 .066 .068 .078 1.734 52 265 .074 .92 80 2830 4380 434 442 279 287 0 371 178 193 .265 360 182 3.774 .239 -1.916 -2.062
10 329 55 149 49 180 6 341 53 149 50 192 4 0 0 59 10 12 6 100 28 100 15 186 196 30 .033 .021 .033 .032 2.347 32 164 .036 .42 60 2970 4380 435 441 294 300 0 200 178 22 .121 193 15 8.243 .076 -3.043 -3.721
11 6334 900 148 50 6186 850 6645 945 149 50 6497 895 0 0 2229 365 12 6 100 100 100 100 7036 7392 7.278 .137 .138 .131 .137 1.395 52 289 .138 .97 80 3120 4380 434 442 308 316 0 3275 182 3093 .5 3439 3257 2 .501 -1 -.996
12 10750 2491 149 50 10601 2441 11404 2606 150 51 11255 2556 0 0 3805 901 15 7 100 100 100 100 13042 13811 4.343 .23 .227 .235 .229 1.312 32 224 .226 .97 70 3260 4380 434 441 322 329 0 9066 182 8884 .838 9484 9302 1.193 .826 -.255 -.275
13 1437 320 147 50 1290 270 1376 270 148 51 1229 220 0 0 1080 255 13 7 96 90 92 82 1560 1449 4.778 .209 .179 .186 .197 1.7 52 284 .217 .97 80 3420 4370 433 441 338 346 0 1165 182 983 .762 983 801 1.313 .651 -.393 -.618
14 214 63 144 49 70 14 217 62 148 52 73 13 0 0 33 15 34 20 78 21 59 6 84 86 5 .2 .178 .235 .232 2.214 32 210 .172 .53 70 3550 4370 433 440 351 358 0 229 178 51 .728 226 47 1.374 .648 -.458 -.626
15 701 109 144 52 557 57 734 102 147 54 590 50 0 0 164 36 23 17 100 84 100 78 614 640 9.772 .102 .085 .091 .099 1.857 32 160 .115 .81 60 3700 4370 434 440 367 373 0 397 189 207 .372 371 182 2.685 .308 -1.425 -1.697
16 8123 4872 152 51 7971 4821 7863 4935 152 53 7711 4884 0 0 2300 1420 14 9 100 100 100 100 12792 12595 1.653 .605 .633 .606 .594 1.285 32 226 .601 .97 70 3840 4370 433 440 380 387 0 17731 186 17545 2.201 17960 17775 .454 2.305 1.138 1.205
17 6838 1658 169 50 6669 1608 6309 1484 172 51 6140 1434 0 0 3060 781 25 6 100 100 98 98 8277 7574 4.147 .241 .234 .247 .245 1.357 52 335 .225 .95 90 4000 4390 434 443 395 404 0 6034 182 5852 .878 5401 5219 1.14 .85 -.189 -.235
18 203 52 186 50 17 2 195 52 188 51 9 2 0 0 28 7 17 7 34 17 21 5 19 11 8.5 .118 .222 .299 .269 3.255 52 270 .087 .27 80 4150 4380 434 442 411 419 -50 189 182 7 .428 189 7 2.336 .809 -1.224 -.306
19 16848 3153 193 52 16655 3101 17362 3208 198 54 17169 3156 0 0 4596 802 42 10 100 100 100 100 19756 20325 5.371 .186 .184 .191 .175 1.325 32 200 .191 .97 70 4290 4380 434 441 425 432 0 11475 189 11286 .678 11675 11486 1.476 .669 -.561 -.58
20 25879 11098 176 51 25703 11047 26841 11311 180 52 26665 11260 0 0 6910 3254 31 9 100 100 100 100 36750 37925 2.327 .43 .422 .428 .433 1.178 80 390 .43 .99 100 4440 4390 434 444 439 449 0 40390 186 40204 1.564 41165 40979 .639 1.537 .645 .62

Total number of rows: 43104

Table truncated, full table size 9405 Kbytes.




Supplementary data files not provided
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