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Sample GSM144137 Query DataSets for GSM144137
Status Public on Nov 10, 2006
Title 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 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 = 11:29:49; 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 = 11:29:49; 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/2004-07/53415.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
1 234 65 146 48 88 17 226 65 147 48 80 17 0 0 34 13 12 6 100 78 100 62 105 97 5.176 .193 .213 .172 .228 2.347 32 224 .168 .75 70 1740 4340 430 437 170 177 0 214 158 56 .637 214 56 1.57 .701 -.651 -.513
2 412 98 147 48 265 50 399 97 146 49 252 49 0 0 83 19 12 7 100 100 100 96 315 301 5.3 .189 .194 .183 .205 1.476 32 170 .197 .88 60 1890 4340 431 437 186 192 0 323 158 165 .622 320 162 1.607 .641 -.685 -.641
3 608 146 145 48 463 98 401 118 145 49 256 70 0 0 429 97 10 6 100 90 100 78 561 326 4.724 .212 .273 .187 .2 2.036 32 176 .202 .91 60 2030 4350 432 438 200 206 0 481 158 323 .698 389 231 1.433 .902 -.519 -.149
4 247 59 146 48 101 11 238 57 146 48 92 9 0 0 53 10 11 5 100 62 100 46 112 101 9.182 .109 .098 .122 .138 1.993 32 224 .104 .63 70 2180 4340 430 437 214 221 0 195 158 36 .359 188 30 2.785 .323 -1.477 -1.632
5 9475 2191 145 48 9330 2143 9304 2099 147 48 9159 2051 0 0 3068 697 12 5 100 100 100 100 11473 11210 4.354 .23 .224 .229 .232 1.238 32 212 .219 .96 70 2330 4350 431 438 229 236 0 7224 158 7066 .757 6921 6763 1.32 .738 -.401 -.438
6 169 52 143 47 26 5 166 51 143 47 23 4 0 0 20 7 11 5 78 36 50 13 31 27 5.2 .192 .174 .213 .172 2.695 52 288 .129 .33 80 2470 4350 431 439 243 251 -50 171 155 16 .634 168 13 1.577 .573 -.657 -.802
7 967 292 140 47 827 245 1044 313 139 48 904 266 0 0 458 137 10 5 100 100 100 100 1072 1170 3.376 .296 .294 .299 .295 1.7 32 176 .277 .92 60 2620 4350 432 438 259 265 0 963 155 808 .977 1032 877 1.024 .97 -.034 -.044
8 434 65 140 48 294 17 426 64 141 48 286 16 0 0 102 8 12 5 100 93 100 81 311 302 17.294 .058 .056 .055 .059 1.596 32 159 .05 .69 60 2770 4350 432 438 274 280 0 214 158 56 .191 211 53 5.245 .184 -2.391 -2.439
9 1045 177 142 47 903 130 1035 173 142 48 893 126 0 0 441 57 11 6 100 100 100 100 1033 1019 6.946 .144 .141 .152 .147 1.569 52 281 .131 .93 80 2900 4350 431 439 286 294 0 584 155 429 .475 570 415 2.107 .465 -1.075 -1.104
10 384 59 142 48 242 11 392 58 143 49 250 10 0 0 68 7 11 6 100 68 100 40 253 260 22 .045 .04 .046 .045 1.723 32 164 .045 .65 60 3050 4350 432 438 302 308 0 195 158 36 .15 191 33 6.672 .132 -2.738 -2.923
11 4605 747 143 48 4462 699 4804 739 143 49 4661 691 0 0 1243 174 12 6 100 100 100 100 5161 5352 6.383 .157 .148 .163 .154 1.392 52 332 .149 .97 90 3190 4350 430 439 314 323 0 2463 158 2305 .517 2437 2278 1.936 .489 -.953 -1.033
12 8739 1879 146 48 8593 1831 11151 2273 148 49 11005 2225 0 0 5375 1200 17 6 100 100 100 100 10424 13230 4.693 .213 .202 .213 .218 1.67 52 288 .211 .97 80 3340 4350 431 439 330 338 0 6196 158 6037 .703 7495 7336 1.423 .667 -.509 -.585
13 1536 391 151 49 1385 342 1580 454 154 50 1429 405 0 0 563 194 20 6 100 100 100 100 1727 1834 4.05 .247 .283 .202 .253 1.784 32 220 .262 .95 70 3490 4340 430 437 345 352 0 1289 162 1128 .814 1497 1335 1.228 .935 -.297 -.098
14 336 82 160 49 176 33 330 83 192 49 170 34 0 0 98 22 57 6 84 82 75 78 209 204 5.333 .188 .2 .196 .194 1.623 52 277 .166 .74 80 3640 4350 431 439 360 368 -50 270 162 109 .618 274 112 1.617 .659 -.694 -.601
15 895 191 221 51 674 140 822 180 211 52 601 129 0 0 337 81 48 8 100 100 100 100 814 730 4.814 .208 .215 .193 .198 1.449 52 246 .229 .89 80 3780 4340 430 438 374 382 0 630 168 462 .685 594 425 1.46 .708 -.546 -.499
16 5604 4509 229 52 5375 4457 6074 5013 231 54 5845 4961 0 0 2078 1904 25 9 100 100 100 100 9832 10806 1.206 .829 .849 .774 .798 1.528 52 246 .839 .96 80 3920 4340 430 438 388 396 0 14867 171 14696 2.734 16529 16358 .366 2.799 1.451 1.485
17 6976 2573 223 52 6753 2521 6019 2166 233 56 5796 2114 0 0 5103 2069 101 44 96 93 95 92 9274 7910 2.679 .373 .365 .338 .358 1.543 80 372 .37 .95 100 4070 4350 430 440 402 412 0 8484 171 8312 1.231 7142 6970 .812 1.203 .3 .266
18 240 54 233 54 7 0 226 53 245 56 -7 -1 0 0 47 7 41 11 15 9 5 1 7 -8 null null null .222 .231 3.208 52 258 .089 .43 80 4220 4350 431 439 418 426 -50 178 178 0 null 175 -3 null null null null
19 9994 4000 289 61 9705 3939 11514 4701 287 72 11225 4640 0 0 5269 2226 87 37 100 100 100 100 13644 15865 2.464 .406 .413 .383 .412 1.743 52 254 .401 .97 80 4370 4350 431 439 433 441 0 13189 201 12988 1.338 15501 15299 .747 1.363 .42 .447
20 11884 5386 296 61 11588 5325 13262 6202 299 66 12966 6141 0 0 4696 2334 64 29 100 100 98 100 16913 19107 2.176 .46 .474 .453 .461 1.555 80 426 .468 .98 110 4520 4350 429 440 446 457 0 17759 201 17558 1.515 20450 20249 .66 1.562 .6 .643

Total number of rows: 43104

Table truncated, full table size 9524 Kbytes.




Supplementary data files not provided
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