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Sample GSM144148 Query DataSets for GSM144148
Status Public on Nov 10, 2006
Title Medium 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 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 = 11:35:30; 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 = 11:35:30; 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/2004-07/53414.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 Jul 29, 2008
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
1 544 220 267 69 277 151 526 202 295 74 259 133 0 0 89 79 160 30 93 100 18 96 428 392 1.834 .545 .514 .517 .489 1.379 32 226 .259 .61 70 1700 4500 446 453 166 173 0 235 74 161 .582 216 142 1.718 .548 -.78 -.867
2 1224 452 268 66 956 386 1277 455 291 70 1009 389 0 0 338 126 110 23 100 100 96 100 1342 1398 2.477 .404 .386 .413 .378 1.463 32 214 .361 .92 70 1840 4500 446 453 180 187 0 483 70 412 .431 486 415 2.319 .412 -1.214 -1.28
3 569 218 263 62 306 156 287 75 274 63 24 13 0 0 624 315 87 17 28 42 26 32 462 37 1.962 .51 .542 .543 .568 2.439 52 304 .492 .96 80 1990 4500 446 454 195 203 -50 233 66 167 .544 80 14 1.837 .578 -.877 -.79
4 517 174 272 63 245 111 517 178 273 62 245 115 0 0 90 52 35 7 100 96 96 93 356 360 2.207 .453 .469 .402 .478 1.798 32 170 .453 .92 60 2140 4500 447 453 211 217 0 186 67 119 .484 190 123 2.067 .501 -1.047 -.996
5 12027 7614 282 63 11745 7551 12519 7824 289 66 12237 7761 0 0 4045 2318 40 14 100 100 100 100 19296 19998 1.555 .643 .634 .656 .628 1.272 32 221 .613 .96 70 2280 4500 446 453 224 231 0 8132 67 8064 .687 8356 8289 1.456 .677 -.542 -.562
6 370 105 277 63 93 42 377 107 283 64 100 44 0 0 52 34 43 9 80 75 57 65 135 144 2.214 .452 .44 .385 .472 2.481 52 304 .16 .53 80 2430 4500 446 454 239 247 -50 112 67 45 .482 114 47 2.073 .47 -1.052 -1.09
7 1342 1108 251 61 1091 1047 1234 1169 255 62 983 1108 0 0 888 801 49 9 96 100 87 100 2138 2091 1.042 .96 1.127 1.029 .928 1.941 32 176 .925 .93 60 2580 4500 447 453 255 261 0 1183 65 1118 1.025 1248 1183 .976 1.204 .035 .268
8 822 159 253 61 569 98 783 154 256 62 530 93 0 0 169 31 46 10 100 100 100 96 667 623 5.806 .172 .175 .169 .167 1.539 32 214 .166 .91 70 2720 4500 446 453 268 275 0 170 65 105 .184 164 99 5.437 .187 -2.443 -2.416
9 1272 459 260 61 1012 398 1286 466 260 62 1026 405 0 0 351 182 21 8 100 100 100 100 1410 1431 2.543 .393 .395 .355 .407 1.548 52 286 .394 .96 80 2870 4500 446 454 283 291 0 490 65 425 .42 498 433 2.381 .422 -1.251 -1.246
10 563 115 267 62 296 53 560 110 268 62 293 48 0 0 72 22 19 7 100 100 100 100 349 341 5.585 .179 .164 .172 .176 1.385 32 158 .17 .88 60 3010 4500 447 453 298 304 0 123 66 57 .191 117 51 5.229 .175 -2.387 -2.515
11 5804 2555 281 64 5523 2491 6114 2732 285 65 5833 2668 0 0 1671 763 36 13 100 100 100 100 8014 8501 2.217 .451 .457 .446 .452 1.186 52 328 .441 .98 90 3150 4500 445 454 310 319 0 2729 68 2660 .482 2918 2849 2.076 .488 -1.054 -1.034
12 11336 10510 284 63 11052 10447 13876 12455 290 66 13592 12392 0 0 6522 5874 39 15 100 100 100 100 21499 25984 1.058 .945 .912 1.02 .952 1.44 52 337 .931 .98 90 3300 4500 445 454 325 334 0 11224 67 11157 1.01 13302 13234 .991 .974 .014 -.038
13 1657 1536 276 62 1381 1474 1894 1759 277 63 1618 1697 0 0 850 898 21 10 100 100 100 100 2855 3315 .937 1.067 1.049 1.114 1.076 1.698 52 286 1.065 .97 80 3450 4500 446 454 341 349 0 1640 66 1574 1.14 1879 1812 .877 1.12 .189 .164
14 493 213 285 61 208 152 495 215 288 62 210 154 0 0 59 38 33 9 100 100 100 100 360 364 1.368 .731 .733 .739 .744 1.402 32 226 .634 .89 70 3600 4500 446 453 356 363 0 227 65 162 .78 230 164 1.281 .783 -.358 -.353
15 1093 501 309 62 784 439 1109 519 326 67 800 457 0 0 143 96 59 22 100 100 100 100 1223 1257 1.786 .56 .571 .554 .562 1.16 32 221 .546 .97 70 3740 4490 445 452 370 377 0 535 66 469 .598 554 488 1.672 .61 -.742 -.713
16 9958 12349 303 61 9655 12288 11007 13183 294 62 10704 13122 0 0 3980 5016 69 9 100 100 100 100 21943 23826 .786 1.273 1.226 1.281 1.259 1.355 52 275 1.276 .98 80 3890 4500 446 454 385 393 0 13188 65 13123 1.359 14079 14014 .736 1.309 .443 .389
17 10042 9484 300 63 9742 9421 8424 8453 290 98 8124 8390 0 0 6303 5319 117 250 100 100 100 98 19163 16514 1.034 .967 1.033 .959 .986 1.268 52 256 .956 .96 80 4040 4490 445 453 400 408 0 10129 67 10061 1.033 9028 8960 .968 1.103 .047 .141
18 305 75 286 61 19 14 294 62 279 76 8 1 0 0 71 31 97 92 21 5 0 0 33 9 1.357 .737 .125 .202 .229 6.269 52 264 .059 .23 80 4180 4500 446 454 414 422 -50 80 65 15 .787 66 1 1.271 .133 -.346 -2.905
19 14441 11484 272 68 14169 11416 15002 12582 300 101 14730 12514 0 0 3255 3247 119 126 100 100 100 100 25585 27244 1.241 .806 .85 .773 .817 1.293 32 165 .812 .97 60 4330 4500 447 453 430 436 0 12265 73 12192 .86 13437 13365 1.162 .907 -.217 -.14
20 15173 10484 244 63 14929 10421 17960 12543 258 71 17716 12480 0 0 7523 4953 70 55 100 100 100 100 25350 30196 1.433 .698 .704 .743 .691 1.425 80 467 .68 .99 110 4480 4510 445 456 442 453 0 11197 67 11129 .745 13396 13328 1.341 .752 -.424 -.411

Total number of rows: 43104

Table truncated, full table size 9653 Kbytes.




Supplementary data files not provided
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