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Sample GSM144138 Query DataSets for GSM144138
Status Public on Nov 10, 2006
Title EPO 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 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 = 11:38:51; 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 = 11:38:51; 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/2004-07/53416.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
1 263 65 155 50 108 15 260 64 158 52 105 14 0 0 35 10 27 9 100 56 93 34 123 119 7.2 .139 .133 .124 .135 2.07 32 230 .125 .63 70 1730 4310 427 434 169 176 0 379 291 87 .809 373 82 1.236 .776 -.306 -.365
2 430 87 154 51 276 36 437 87 154 51 283 36 0 0 83 17 10 7 100 93 100 87 312 319 7.667 .13 .127 .114 .123 1.894 32 166 .133 .83 60 1880 4310 428 434 185 191 0 507 297 210 .76 507 210 1.317 .741 -.397 -.433
3 444 91 156 51 288 40 261 74 157 52 105 23 0 0 330 49 12 7 94 67 86 57 328 128 7.2 .139 .219 .154 .149 2.149 52 276 .134 .91 80 2030 4310 427 435 199 207 0 530 297 233 .809 431 134 1.236 1.276 -.306 .351
4 221 56 157 51 64 5 213 56 157 52 56 5 0 0 46 7 13 6 88 40 78 15 69 61 12.8 .078 .089 .108 .115 2.3 52 269 .057 .24 80 2180 4310 427 435 214 222 0 326 297 29 .455 326 29 2.198 .52 -1.136 -.944
5 10059 1546 159 50 9900 1496 10593 1465 161 51 10434 1415 0 0 4913 702 21 8 100 100 100 100 11396 11849 6.618 .151 .136 .161 .153 1.407 32 200 .14 .96 70 2320 4320 428 435 228 235 0 9003 291 8712 .88 8531 8240 1.136 .79 -.184 -.341
6 184 55 149 49 35 6 187 53 151 51 38 4 0 0 22 7 15 7 73 36 57 9 41 42 5.833 .171 .105 .159 .159 3.468 52 287 .114 .33 80 2460 4310 427 435 242 250 -50 320 285 35 .998 309 23 1.002 .613 -.002 -.706
7 893 174 142 48 751 126 700 142 142 50 558 94 0 0 558 101 12 8 100 96 100 87 877 652 5.96 .168 .168 .153 .174 1.96 32 170 .164 .94 60 2610 4310 428 434 258 264 0 1013 280 734 .977 827 547 1.024 .981 -.034 -.028
8 416 61 156 49 260 12 420 61 155 50 264 12 0 0 77 10 11 7 100 71 100 34 272 276 21.667 .046 .045 .049 .054 1.771 32 159 .041 .54 60 2760 4320 429 435 273 279 0 355 285 70 .269 355 70 3.721 .265 -1.896 -1.918
9 1662 161 156 51 1506 110 1719 166 157 51 1563 115 0 0 524 54 13 7 100 96 100 96 1616 1678 13.691 .073 .074 .067 .071 1.434 52 269 .077 .96 80 2900 4310 427 435 286 294 0 938 297 641 .425 967 670 2.351 .428 -1.233 -1.223
10 299 57 157 52 142 5 297 56 180 55 140 4 0 0 99 9 233 33 25 0 0 0 147 144 28.4 .035 .029 .066 .058 2.219 52 256 .048 .51 80 3050 4310 427 435 301 309 -50 332 303 29 .205 326 23 4.877 .166 -2.286 -2.587
11 11647 1003 157 51 11490 952 11188 986 176 54 11031 935 0 0 3277 385 215 30 100 100 100 100 12442 11966 12.069 .083 .085 .077 .083 1.345 52 301 .085 .97 90 3190 4310 426 435 314 323 0 5841 297 5544 .482 5742 5445 2.073 .494 -1.051 -1.019
12 9117 1114 154 51 8963 1063 9972 1207 156 52 9818 1156 0 0 5610 657 16 7 100 100 100 100 10026 10974 8.432 .119 .118 .128 .118 1.472 52 270 .116 .98 80 3330 4320 428 436 329 337 0 6487 297 6190 .691 7029 6732 1.448 .686 -.534 -.544
13 1564 368 150 50 1414 318 1605 373 152 51 1455 323 0 0 737 169 12 6 100 100 100 100 1732 1778 4.447 .225 .222 .235 .217 1.379 32 224 .219 .96 70 3470 4310 427 434 343 350 0 2143 291 1852 1.31 2172 1881 .764 1.293 .389 .37
14 246 58 151 49 95 9 223 58 151 50 72 9 0 0 59 9 11 6 100 65 98 32 104 81 10.556 .095 .125 .106 .109 2.016 52 286 .077 .51 80 3630 4310 427 435 359 367 0 338 285 52 .552 338 52 1.813 .728 -.858 -.458
15 641 118 154 49 487 69 591 115 156 50 437 66 0 0 291 62 17 6 100 100 100 100 556 503 7.058 .142 .151 .129 .133 1.337 32 207 .119 .9 70 3770 4310 427 434 373 380 0 687 285 402 .825 670 384 1.212 .88 -.277 -.185
16 7524 2428 155 50 7369 2378 8343 2635 157 51 8188 2585 0 0 3184 1025 16 6 100 100 100 100 9747 10773 3.099 .323 .316 .335 .322 1.369 52 317 .317 .98 90 3910 4310 426 435 386 395 0 14139 291 13848 1.879 15345 15054 .532 1.838 .91 .879
17 8909 2428 155 50 8754 2378 8757 2157 159 53 8602 2107 0 0 6532 2121 44 35 97 96 96 93 11132 10709 3.681 .272 .245 .27 .246 1.628 80 421 .249 .89 110 4060 4320 426 437 400 411 0 14139 291 13848 1.582 12561 12270 .632 1.426 .662 .512
18 164 52 153 50 11 2 160 51 157 51 7 1 0 0 18 7 21 8 19 13 9 1 13 8 5.5 .182 .143 .447 .5 4.39 52 246 .105 .16 80 4210 4310 427 435 417 425 -50 303 291 12 1.059 297 6 .944 .832 .082 -.265
19 18806 3037 155 51 18651 2986 19989 3234 159 52 19834 3183 0 0 11380 1938 21 8 100 100 100 100 21637 23017 6.246 .16 .16 .144 .149 1.603 52 301 .157 .95 90 4350 4310 426 435 430 439 0 17686 297 17389 .932 18833 18536 1.073 .935 -.101 -.098
20 52827 14493 159 51 52668 14442 58637 15137 161 52 58478 15086 0 0 14436 4394 16 8 100 100 100 100 67110 73564 3.647 .274 .258 .275 .269 1.242 80 449 .271 .98 110 4500 4320 426 437 444 455 0 84399 297 84102 1.597 88149 87852 .626 1.502 .675 .587

Total number of rows: 43104

Table truncated, full table size 9542 Kbytes.




Supplementary data files not provided
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