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Sample GSM144147 Query DataSets for GSM144147
Status Public on Nov 10, 2006
Title EPO donor 1
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 = 11:53:19; Parameter Scanner Model = G2505B; Parameter Scanning software version = A.6.3.1; Parameter Scanning software = ChipScan; Parameter Scan Date = 2004-04-27; 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 = 11:53:19; Parameter Scanner Model = G2505B; Parameter Scanning software version = A.6.3.1; Parameter Scanning software = ChipScan; Parameter Scan Date = 2004-04-27; Performer: Einar Andreas,,Sivertsen
Description Simple annotation: Hematopoiesis, Normal tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2004-07/53412.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
1 462 150 294 69 168 81 464 148 296 72 170 79 0 0 64 45 42 16 96 93 90 87 249 249 2.074 .482 .465 .432 .462 1.764 32 226 .548 .81 70 1780 3570 353 360 174 181 0 173 80 93 .556 171 91 1.798 .536 -.846 -.9
2 912 235 305 73 607 162 959 231 312 77 654 158 0 0 266 83 45 20 100 100 96 90 769 812 3.747 .267 .242 .254 .259 1.469 32 165 .263 .92 60 1920 3570 354 360 189 195 0 271 84 187 .308 266 182 3.248 .279 -1.7 -1.843
3 724 343 336 76 388 267 512 149 343 77 176 73 0 0 480 351 44 11 75 87 59 75 655 249 1.453 .688 .415 .625 .715 2.118 32 170 .895 .88 60 2070 3580 355 361 204 210 0 396 88 308 .794 172 84 1.26 .478 -.333 -1.064
4 435 146 329 73 106 73 418 122 327 74 89 49 0 0 110 80 25 12 65 63 55 57 179 138 1.452 .689 .551 .61 .655 1.944 52 284 .631 .82 80 2210 3580 354 362 217 225 -50 168 84 84 .794 141 57 1.259 .635 -.332 -.655
5 7605 6202 303 71 7302 6131 7631 6143 308 74 7328 6072 0 0 2883 2874 55 19 100 100 100 100 13433 13400 1.191 .84 .829 .784 .834 1.433 32 211 .865 .97 70 2370 3580 354 361 233 240 0 7154 82 7072 .969 7086 7004 1.033 .956 -.046 -.065
6 306 85 251 65 55 20 301 80 255 68 50 15 0 0 53 22 27 13 57 51 50 36 75 65 2.75 .364 .3 .414 .387 2.441 52 296 .268 .55 80 2500 3570 353 361 246 254 -50 98 75 23 .419 92 17 2.384 .346 -1.253 -1.531
7 1063 1103 239 64 824 1039 759 851 237 66 520 787 0 0 669 917 26 12 93 96 90 96 1863 1307 .793 1.261 1.513 1.033 1.273 2.499 32 170 1.323 .96 60 2660 3570 354 360 263 269 0 1272 74 1198 1.454 982 908 .688 1.746 .54 .804
8 660 152 233 66 427 86 679 148 234 69 446 82 0 0 187 40 29 16 100 100 100 93 513 528 4.965 .201 .184 .205 .207 1.538 32 176 .145 .78 60 2800 3580 355 361 277 283 0 175 76 99 .232 171 95 4.304 .212 -2.106 -2.237
9 1006 526 205 63 801 463 1004 522 209 66 799 459 0 0 228 142 24 14 100 100 100 100 1264 1258 1.73 .578 .574 .571 .579 1.205 32 215 .576 .96 70 2940 3580 354 361 290 297 0 607 73 534 .667 602 529 1.5 .663 -.585 -.594
10 355 92 208 67 147 25 355 88 215 73 147 21 0 0 138 32 33 32 61 34 59 7 172 168 5.88 .17 .143 .261 .157 4.217 52 267 .17 .64 80 3090 3570 353 361 305 313 -50 106 77 29 .196 102 24 5.098 .165 -2.35 -2.601
11 3374 2374 229 68 3145 2306 3660 2596 232 74 3431 2528 0 0 1377 1151 31 30 100 100 100 100 5451 5959 1.364 .733 .737 .67 .729 1.394 52 317 .749 .98 90 3230 3570 352 361 318 327 0 2738 78 2660 .846 2994 2916 1.182 .85 -.242 -.235
12 9117 4079 233 67 8884 4012 7919 3234 238 74 7686 3167 0 0 7721 3626 41 44 100 98 100 86 12896 10853 2.214 .452 .412 .402 .445 1.546 52 256 .456 .98 80 3380 3570 353 361 334 342 0 4705 77 4628 .521 3730 3653 1.92 .475 -.941 -1.073
13 1413 782 258 68 1155 714 1118 725 261 74 860 657 0 0 962 571 40 39 94 96 90 88 1869 1517 1.618 .618 .764 .672 .655 1.672 52 327 .594 .95 90 3510 3580 353 362 346 355 0 902 78 824 .713 836 758 1.402 .881 -.488 -.182
14 453 177 271 68 182 109 442 171 273 71 171 103 0 0 71 63 22 17 100 96 100 84 291 274 1.67 .599 .602 .5 .557 2.014 32 170 .599 .84 60 3670 3570 354 360 364 370 0 204 78 126 .691 197 119 1.448 .695 -.534 -.525
15 912 535 263 67 649 468 923 558 266 73 660 491 0 0 218 156 26 27 100 100 100 100 1117 1151 1.387 .721 .744 .711 .731 1.234 32 171 .735 .95 60 3810 3580 355 361 378 384 0 617 77 540 .832 644 566 1.202 .858 -.266 -.221
16 6247 9886 242 66 6005 9820 6896 11638 248 80 6654 11572 0 0 4092 6632 62 136 100 100 100 98 15825 18226 .612 1.635 1.739 1.709 1.658 1.453 52 265 1.643 .98 80 3960 3580 354 362 392 400 0 11403 76 11327 1.886 13424 13348 .53 2.006 .916 1.004
17 5615 3976 268 75 5347 3901 5465 3972 294 102 5197 3897 0 0 2834 2302 116 198 100 100 100 96 9248 9094 1.371 .73 .75 .681 .719 1.416 52 324 .778 .97 90 4100 3560 351 360 405 414 0 4586 87 4500 .842 4582 4495 1.188 .865 -.249 -.209
18 336 115 291 81 45 34 299 104 301 86 8 23 0 0 85 35 49 25 30 46 21 21 79 31 1.324 .756 2.875 .667 .743 4.561 52 265 .076 .14 80 4260 3570 353 361 422 430 -50 133 93 39 .872 120 27 1.147 3.316 -.198 1.73
19 8455 6139 281 76 8174 6063 8214 5221 289 79 7933 5145 0 0 6430 5123 44 17 100 100 100 100 14237 13078 1.348 .742 .649 .676 .768 1.576 52 244 .763 .98 80 4400 3580 354 362 436 444 0 7081 88 6994 .856 6022 5935 1.169 .748 -.225 -.419
20 6997 6360 263 71 6734 6289 7528 5800 269 77 7265 5729 0 0 4824 4450 48 26 100 100 100 100 13023 12994 1.071 .934 .789 .942 .908 1.305 52 322 .914 .97 90 4540 3580 353 362 449 458 0 7336 82 7254 1.077 6690 6608 .928 .91 .107 -.137

Total number of rows: 43104

Table truncated, full table size 9558 Kbytes.




Supplementary data files not provided
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