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Sample GSM144139 Query DataSets for GSM144139
Status Public on Nov 10, 2006
Title EPO+LY 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 mplified RNA from early erythroid progenitors stimulated with EPO and LY
Organism Homo sapiens
Characteristics mplified RNA from early erythroid progenitors stimulated with EPO and 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 = 11:48:04; 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 = 11:48:04; 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/2004-07/53417.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) 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
1 231 70 139 50 92 20 219 69 138 53 80 19 0 0 30 9 12 8 100 90 100 59 112 99 4.6 .217 .238 .21 .211 1.563 32 230 .192 .72 70 1710 4390 435 442 167 174 0 202 144 58 .626 199 55 1.597 .684 -.675 -.547
2 349 104 130 52 219 52 337 104 129 53 207 52 0 0 55 17 10 8 100 100 100 100 271 259 4.212 .237 .251 .231 .241 1.281 32 159 .238 .9 60 1860 4390 436 442 183 189 0 300 150 150 .684 300 150 1.462 .724 -.548 -.467
3 471 139 125 51 346 88 227 71 125 52 102 20 0 0 461 129 10 7 84 63 75 57 434 122 3.932 .254 .196 .214 .213 2.975 52 297 .256 .93 80 2000 4390 435 443 196 204 -50 400 147 254 .733 205 58 1.365 .565 -.449 -.824
4 203 59 124 51 79 8 191 59 125 52 67 8 0 0 50 9 11 7 100 53 100 9 87 75 9.875 .101 .119 .103 .108 2.138 32 171 .099 .49 60 2160 4400 437 443 213 219 0 170 147 23 .292 170 23 3.428 .344 -1.777 -1.54
5 9286 2933 133 52 9153 2881 9254 2743 136 53 9121 2691 0 0 4271 1190 17 8 100 100 100 100 12034 11812 3.177 .315 .295 .335 .309 1.445 32 220 .287 .95 70 2300 4400 436 443 226 233 0 8450 150 8300 .907 7902 7753 1.103 .85 -.141 -.235
6 187 58 136 50 51 8 185 58 136 52 49 8 0 0 22 8 10 8 100 46 93 15 59 57 6.375 .157 .163 .184 .177 2.36 32 176 .101 .24 60 2450 4400 437 443 242 248 0 167 144 23 .452 167 23 2.213 .47 -1.146 -1.088
7 1005 328 136 53 869 275 1008 325 135 54 872 272 0 0 517 199 10 8 100 100 100 96 1144 1144 3.16 .316 .312 .261 .298 2.115 32 228 .319 .92 70 2600 4400 436 443 256 263 0 945 153 792 .912 936 784 1.097 .899 -.133 -.154
8 388 75 131 51 257 24 377 73 131 52 246 22 0 0 78 14 10 6 100 93 100 81 281 268 10.708 .093 .089 .088 .088 1.719 32 166 .087 .75 60 2740 4400 437 443 271 277 0 216 147 69 .269 210 63 3.717 .258 -1.894 -1.957
9 1537 223 131 51 1406 172 1613 234 132 53 1482 183 0 0 571 90 11 8 100 98 100 92 1578 1665 8.174 .122 .123 .104 .117 1.656 52 344 .126 .94 90 2880 4390 434 443 283 292 0 642 147 496 .352 674 527 2.837 .356 -1.505 -1.491
10 391 65 132 51 259 14 398 64 134 53 266 13 0 0 84 9 16 8 100 62 100 40 273 279 18.5 .054 .049 .047 .047 2.06 32 164 .046 .54 60 3020 4390 436 442 299 305 0 187 147 40 .156 184 37 6.422 .141 -2.683 -2.828
11 9827 1593 129 51 9698 1542 10100 1702 131 54 9971 1651 0 0 2378 539 18 9 100 100 100 100 11240 11622 6.289 .159 .166 .149 .162 1.329 52 324 .162 .97 90 3170 4390 434 443 312 321 0 4589 147 4442 .458 4903 4756 2.183 .477 -1.126 -1.068
12 8880 2778 122 52 8758 2726 10773 3447 124 54 10651 3395 0 0 5462 1654 19 11 100 100 100 100 11484 14046 3.213 .311 .319 .308 .308 1.611 52 329 .303 .98 90 3310 4390 434 443 326 335 0 8003 150 7853 .897 9930 9781 1.115 .918 -.157 -.123
13 1560 723 121 51 1439 672 1661 724 133 58 1540 673 0 0 519 209 97 45 100 100 100 100 2111 2213 2.141 .467 .437 .486 .461 1.354 32 221 .459 .94 70 3450 4390 435 442 341 348 0 2083 147 1936 1.345 2086 1939 .743 1.259 .428 .332
14 306 100 119 49 187 51 301 100 120 51 182 51 0 0 62 26 9 8 100 100 100 93 238 233 3.667 .273 .28 .259 .272 1.563 32 170 .259 .83 60 3600 4390 436 442 357 363 0 288 141 147 .786 288 147 1.273 .807 -.348 -.309
15 672 161 121 50 551 111 658 150 121 52 537 100 0 0 219 65 9 10 100 100 100 98 662 637 4.964 .201 .186 .19 .193 1.394 52 266 .206 .92 80 3750 4390 435 443 371 379 0 464 144 320 .58 432 288 1.723 .536 -.785 -.898
16 6325 4373 122 50 6203 4323 6962 5064 123 54 6840 5014 0 0 3360 2532 10 14 100 100 100 100 10526 11854 1.435 .697 .733 .653 .684 1.547 52 315 .725 .97 90 3890 4380 433 442 384 393 0 12598 144 12454 2.008 14589 14445 .498 2.112 1.006 1.078
17 10083 4417 122 49 9961 4368 9119 3740 122 51 8997 3691 0 0 7901 3931 9 9 100 100 98 100 14329 12688 2.28 .439 .41 .429 .416 1.504 80 396 .459 .94 100 4050 4390 434 444 400 410 0 12725 141 12584 1.263 10775 10633 .792 1.182 .337 .241
18 129 53 122 49 7 4 125 52 133 52 3 3 0 0 18 8 89 13 0 17 0 0 11 6 1.75 .571 1 .644 .693 3.094 52 246 .27 .39 80 4200 4390 435 443 416 424 -50 153 141 12 1.646 150 9 .607 2.881 .719 1.527
19 17191 2366 123 51 17068 2315 20109 3067 143 55 19986 3016 0 0 11083 1706 103 16 100 100 100 100 19383 23002 7.373 .136 .151 .118 .134 1.49 52 287 .144 .97 90 4340 4380 433 442 429 438 0 6816 147 6669 .391 8836 8689 2.559 .435 -1.356 -1.202
20 34791 21046 124 51 34667 20995 43823 25320 136 59 43699 25269 0 0 20847 13310 74 78 99 99 99 97 55662 68968 1.651 .606 .578 .58 .597 1.753 120 475 .613 .99 120 4490 4400 434 446 443 455 0 60632 147 60485 1.745 72945 72798 .573 1.666 .803 .736

Total number of rows: 43104

Table truncated, full table size 9600 Kbytes.




Supplementary data files not provided
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