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Sample GSM144145 Query DataSets for GSM144145
Status Public on Nov 10, 2006
Title Medium donor 3
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 = 11:20:40; Parameter Scanner Model = G2505B; Parameter Scanning software version = A.6.3.1; Parameter Scanning software = ChipScan; Parameter Scan Date = 2004-05-05; 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 = 11:20:40; Parameter Scanner Model = G2505B; Parameter Scanning software version = A.6.3.1; Parameter Scanning software = ChipScan; Parameter Scan Date = 2004-05-05; Performer: Einar Andreas,,Sivertsen
Description Simple annotation: Hematopoiesis, Normal tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2004-07/53457.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
1 241 95 121 55 120 40 248 92 122 55 127 37 0 0 48 19 9 8 100 93 100 90 160 164 3 .333 .291 .316 .303 1.76 32 230 .331 .84 70 1840 3720 368 375 180 187 0 141 82 60 .496 137 55 2.015 .434 -1.01 -1.205
2 388 199 120 54 268 145 396 213 121 55 276 159 0 0 88 60 9 8 100 100 100 100 413 435 1.848 .541 .576 .518 .494 1.443 32 206 .554 .9 70 1990 3720 368 375 195 202 0 296 80 216 .806 317 237 1.241 .858 -.312 -.221
3 335 139 121 54 214 85 160 75 122 55 39 21 0 0 314 134 10 9 75 65 67 53 299 60 2.518 .397 .538 .36 .36 3.256 52 304 .392 .91 80 2130 3720 368 376 209 217 -50 207 80 127 .592 112 31 1.691 .802 -.758 -.319
4 227 73 113 53 114 20 233 72 113 54 120 19 0 0 42 16 10 9 100 75 100 53 134 139 5.7 .175 .158 .16 .181 2.046 32 171 .166 .61 60 2290 3730 370 376 226 232 0 109 79 30 .261 107 28 3.828 .236 -1.936 -2.084
5 8160 3298 111 52 8049 3246 8344 3552 113 54 8233 3500 0 0 3494 1692 14 12 100 100 100 100 11295 11733 2.48 .403 .425 .349 .414 1.705 32 222 .431 .97 70 2430 3720 368 375 239 246 0 4911 77 4834 .601 5290 5212 1.665 .633 -.736 -.66
6 183 68 117 53 66 15 178 69 118 54 61 16 0 0 29 10 11 8 100 71 93 46 81 77 4.4 .227 .262 .213 .238 2.176 32 232 .195 .51 70 2570 3730 369 376 253 260 0 101 79 22 .338 103 24 2.955 .391 -1.563 -1.356
7 1042 515 123 53 919 462 1062 513 122 54 939 460 0 0 453 259 9 8 100 100 100 100 1381 1399 1.989 .503 .49 .454 .466 1.571 32 232 .498 .94 70 2730 3730 369 376 269 276 0 767 79 688 .749 764 685 1.336 .73 -.418 -.455
8 437 96 123 52 314 44 428 98 123 52 305 46 0 0 89 18 9 6 100 100 100 93 358 351 7.136 .14 .151 .131 .14 1.602 32 165 .135 .86 60 2870 3720 369 375 284 290 0 143 77 66 .209 146 69 4.792 .225 -2.261 -2.155
9 1187 257 127 51 1060 206 1344 282 127 52 1217 231 0 0 532 100 15 7 100 100 100 98 1266 1448 5.146 .194 .19 .192 .185 1.498 52 289 .186 .97 80 3010 3730 369 377 297 305 0 383 76 307 .289 420 344 3.455 .283 -1.789 -1.823
10 316 70 123 52 193 18 327 70 124 53 204 18 0 0 62 10 10 8 100 84 100 53 211 222 10.722 .093 .088 .09 .09 1.929 32 165 .09 .71 60 3160 3730 370 376 313 319 0 104 77 27 .139 104 27 7.2 .131 -2.848 -2.928
11 7925 2802 124 53 7801 2749 8984 3262 127 54 8860 3209 0 0 3151 1313 13 8 100 100 100 100 10550 12069 2.838 .352 .362 .311 .357 1.437 52 340 .366 .99 90 3300 3720 367 376 325 334 0 4173 79 4094 .525 4858 4779 1.906 .539 -.93 -.891
12 5377 2766 128 53 5249 2713 6165 3413 129 54 6037 3360 0 0 3839 1990 12 7 100 100 100 100 7962 9397 1.935 .517 .557 .534 .51 1.79 52 340 .509 .97 90 3450 3730 368 377 340 349 0 4119 79 4040 .77 5083 5004 1.299 .829 -.378 -.271
13 1329 766 129 53 1200 713 1330 815 131 56 1201 762 0 0 455 343 30 22 100 100 100 100 1913 1963 1.683 .594 .634 .555 .589 1.395 32 218 .612 .96 70 3590 3720 368 375 355 362 0 1141 79 1062 .885 1214 1135 1.13 .945 -.177 -.082
14 286 99 127 53 159 46 287 93 127 53 160 40 0 0 33 28 10 7 100 100 100 96 205 200 3.457 .289 .25 .252 .258 1.585 32 164 .313 .83 60 3740 3720 369 375 371 377 0 147 79 69 .431 138 60 2.321 .372 -1.215 -1.425
15 537 218 125 52 412 166 578 227 127 53 453 175 0 0 203 91 16 8 100 98 94 92 578 628 2.482 .403 .386 .394 .405 1.475 52 277 .404 .96 80 3880 3720 368 376 384 392 0 325 77 247 .6 338 261 1.667 .575 -.737 -.798
16 4633 4449 121 54 4512 4395 5377 5342 123 55 5256 5288 0 0 2407 2407 12 9 100 100 100 100 8907 10544 1.027 .974 1.006 .881 .952 1.607 52 277 .98 .98 80 4030 3720 368 376 399 407 0 6625 80 6545 1.451 7955 7875 .689 1.498 .537 .583
17 12515 10263 119 54 12396 10209 8707 7111 131 90 8588 7057 0 0 9656 8342 95 311 100 100 100 96 22605 15645 1.214 .824 .822 .769 .792 1.594 52 303 .835 .97 90 4180 3710 366 375 413 422 0 15284 80 15203 1.226 10590 10509 .815 1.224 .294 .291
18 124 56 116 53 8 3 118 54 117 56 2 1 0 0 21 8 20 13 15 11 5 0 11 3 2.667 .375 .5 .732 .75 3.719 52 246 .424 .27 80 4320 3720 368 376 428 436 -50 83 79 4 .558 80 1 1.791 .745 -.841 -.425
19 8275 3199 111 56 8164 3143 4241 1876 113 58 4130 1820 0 0 7980 3091 14 11 100 98 100 97 11307 5950 2.598 .385 .441 .366 .369 1.701 80 371 .379 .98 100 4470 3730 368 378 442 452 0 4764 83 4681 .573 2794 2710 1.744 .656 -.803 -.608
20 10445 7964 110 59 10335 7905 8059 6073 113 62 7949 6014 0 0 8520 6873 18 14 100 100 100 100 18240 13963 1.307 .765 .757 .712 .741 1.343 80 362 .783 .98 100 4630 3730 368 378 458 468 0 11860 88 11772 1.139 9044 8956 .878 1.127 .188 .172

Total number of rows: 43104

Table truncated, full table size 9568 Kbytes.




Supplementary data files not provided
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