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Sample GSM144144 Query DataSets for GSM144144
Status Public on Nov 10, 2006
Title 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 LY
Organism Homo sapiens
Characteristics Amplified RNA from early erythroid progenitors stimulated with 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 = 10:22:24; 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 = 10:22:24; 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/2004-07/53456.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) [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
1 387 137 222 60 165 77 388 131 223 62 166 71 0 0 37 29 15 9 100 100 100 96 242 237 2.143 .467 .428 .436 .467 1.539 32 170 .449 .86 60 1810 3790 376 382 178 184 0 189 83 106 .645 181 98 1.55 .591 -.632 -.758
2 642 141 232 64 410 77 669 143 235 65 437 79 0 0 145 27 19 9 100 100 100 96 487 516 5.325 .188 .181 .192 .192 1.4 32 165 .185 .93 60 1950 3790 376 382 192 198 0 195 88 106 .26 198 109 3.851 .25 -1.945 -2
3 477 257 209 63 268 194 263 90 214 65 54 27 0 0 435 314 41 16 51 57 34 42 462 81 1.381 .724 .5 .482 .6 2.007 52 304 .709 .95 80 2100 3790 375 383 206 214 -50 355 87 268 1.001 124 37 .999 .691 .001 -.533
4 403 159 176 60 227 99 364 99 179 61 188 39 0 0 296 265 15 9 96 87 93 84 326 227 2.293 .436 .207 .238 .238 1.905 32 219 .756 .91 70 2250 3790 375 382 221 228 0 220 83 137 .603 137 54 1.658 .287 -.73 -1.802
5 6721 4500 178 60 6543 4440 7993 4718 183 61 7815 4658 0 0 4641 3402 29 10 100 100 98 100 10983 12473 1.474 .679 .596 .547 .676 1.947 52 304 .693 .97 80 2400 3790 375 383 236 244 0 6222 83 6139 .938 6523 6440 1.066 .824 -.092 -.279
6 266 79 177 60 89 19 266 80 178 61 89 20 0 0 39 17 12 10 100 65 93 46 108 109 4.684 .213 .225 .196 .218 1.942 32 226 .226 .61 70 2550 3790 375 382 251 258 0 109 83 26 .295 111 28 3.388 .311 -1.76 -1.686
7 1420 1045 175 62 1245 983 1469 1161 177 63 1294 1099 0 0 399 436 11 11 100 100 100 100 2228 2393 1.267 .79 .849 .725 .79 1.442 32 170 .831 .96 60 2690 3790 376 382 266 272 0 1445 86 1359 1.092 1605 1520 .916 1.174 .127 .232
8 660 137 178 63 482 74 667 133 180 65 489 70 0 0 177 34 14 12 100 100 100 87 556 559 6.514 .154 .143 .148 .153 1.45 32 222 .148 .88 70 2830 3790 375 382 279 286 0 189 87 102 .212 184 97 4.711 .198 -2.236 -2.337
9 1860 499 184 60 1676 439 1812 454 185 63 1628 394 0 0 558 202 15 11 100 100 100 100 2115 2022 3.818 .262 .242 .25 .25 1.248 32 232 .266 .96 70 2970 3790 375 382 293 300 0 690 83 607 .362 628 545 2.761 .335 -1.465 -1.579
10 422 88 193 61 229 27 455 80 204 69 262 19 0 0 107 34 56 38 87 15 81 3 256 281 8.481 .118 .073 .11 .093 2.642 32 172 .107 .45 60 3130 3800 377 383 310 316 0 122 84 37 .163 111 26 6.134 .1 -2.617 -3.318
11 10465 3319 208 64 10257 3255 10653 3292 219 67 10445 3228 0 0 1681 543 41 16 100 100 100 100 13512 13673 3.151 .317 .309 .318 .318 1.08 32 226 .31 .98 70 3260 3790 375 382 322 329 0 4589 88 4501 .439 4552 4463 2.279 .427 -1.188 -1.227
12 12194 5697 222 68 11972 5629 13950 6606 238 73 13728 6538 0 0 4606 2049 50 20 100 100 100 100 17601 20266 2.127 .47 .476 .48 .468 1.353 32 170 .459 .97 60 3410 3790 376 382 338 344 0 7877 94 7783 .65 9134 9040 1.538 .658 -.621 -.603
13 1629 693 256 74 1373 619 1820 740 265 74 1564 666 0 0 548 260 64 19 100 100 100 100 1992 2230 2.218 .451 .426 .437 .447 1.423 32 164 .444 .97 60 3560 3790 376 382 353 359 0 958 102 856 .623 1023 921 1.604 .589 -.682 -.764
14 426 125 270 73 156 52 409 110 267 76 139 37 0 0 112 47 59 17 76 76 53 53 208 176 3 .333 .266 .328 .333 2.421 52 281 .317 .84 80 3700 3790 375 383 366 374 -50 173 101 72 .461 152 51 2.17 .368 -1.118 -1.442
15 1035 420 295 82 740 338 1005 375 283 82 710 293 0 0 255 165 51 16 100 100 100 100 1078 1003 2.189 .457 .413 .451 .423 1.308 32 164 .462 .94 60 3840 3790 376 382 381 387 0 581 113 467 .632 518 405 1.583 .571 -.663 -.809
16 8333 11977 291 86 8042 11891 9790 13459 285 90 9499 13373 0 0 4113 4936 46 23 100 100 100 100 19933 22872 .676 1.479 1.408 1.663 1.429 1.451 32 204 1.409 .98 70 3990 3800 376 383 395 402 0 16560 119 16441 2.044 18609 18490 .489 1.947 1.032 .961
17 5130 2637 304 87 4826 2550 4664 2181 300 106 4360 2094 0 0 3810 1806 115 245 98 98 98 92 7376 6454 1.893 .528 .48 .615 .543 1.93 52 288 .514 .93 80 4130 3790 375 383 409 417 0 3646 120 3526 .731 3016 2895 1.369 .664 -.453 -.591
18 269 81 308 88 -39 -7 277 80 293 90 -31 -8 0 0 107 21 66 25 17 5 3 0 -46 -39 null null null .212 .178 1.934 52 279 .17 .7 80 4290 3790 375 383 425 433 -50 112 122 -10 null 111 -11 null null null null
19 5368 3404 334 98 5034 3306 3209 2472 329 107 2875 2374 0 0 5488 3262 93 44 96 96 93 96 8340 5249 1.523 .657 .826 .727 .794 1.849 32 159 .579 .94 60 4430 3800 377 383 440 446 0 4707 136 4571 .908 3418 3282 1.101 1.142 -.139 .191
20 7965 5619 316 95 7649 5524 3571 2302 324 108 3255 2207 0 0 8668 6292 225 139 98 96 96 93 13173 5462 1.385 .722 .678 .668 .762 2.094 80 396 .725 .96 100 4590 3790 374 384 454 464 0 7769 131 7638 .999 3183 3052 1.001 .937 -.002 -.093

Total number of rows: 43104

Table truncated, full table size 9673 Kbytes.




Supplementary data files not provided
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