NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM144146 Query DataSets for GSM144146
Status Public on Nov 10, 2006
Title LY 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 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 = 13:47:03; Parameter Scanner Model = G2505B; Parameter Scanning software version = A.6.3.1; Parameter Scanning software = ChipScan; Parameter Scan Date = 2004-05-12; 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 = 13:47:03; Parameter Scanner Model = G2505B; Parameter Scanning software version = A.6.3.1; Parameter Scanning software = ChipScan; Parameter Scan Date = 2004-05-12; Performer: Einar Andreas,,Sivertsen
Description Simple annotation: Hematopoiesis, Normal tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2004-06/53392.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
1 170 77 138 54 32 23 168 72 140 56 30 18 0 0 19 23 26 10 55 59 15 48 55 48 1.391 .719 .6 .572 .742 2.614 52 291 .829 .63 80 1480 4250 421 429 144 152 -50 93 65 28 .87 87 22 1.149 .726 -.201 -.461
2 657 166 131 55 526 111 676 176 132 57 545 121 0 0 283 77 11 10 100 90 100 84 637 666 4.739 .211 .222 .196 .198 1.815 32 160 .207 .88 60 1620 4240 421 427 159 165 0 201 67 134 .255 213 146 3.915 .269 -1.969 -1.896
3 426 219 137 56 289 163 191 82 139 58 54 26 0 0 451 260 15 9 82 71 63 55 452 80 1.773 .564 .481 .495 .504 2.352 52 293 .559 .95 80 1780 4250 421 429 174 182 -50 265 68 197 .683 99 31 1.465 .583 -.551 -.779
4 248 102 158 61 90 41 207 81 161 64 49 20 0 0 93 51 28 23 61 50 48 40 131 69 2.195 .456 .408 .422 .444 1.924 52 272 .531 .86 80 1920 4250 421 429 188 196 -50 123 74 50 .551 98 24 1.813 .494 -.859 -1.017
5 6216 5911 177 63 6039 5848 5574 5527 180 68 5397 5464 0 0 3295 4011 22 26 100 100 100 100 11887 10861 1.033 .968 1.012 .825 .93 1.65 32 176 1.058 .94 60 2080 4250 422 428 205 211 0 7155 76 7079 1.172 6690 6614 .853 1.225 .229 .293
6 262 124 191 69 71 55 263 120 195 72 72 51 0 0 30 40 23 21 96 75 78 56 126 123 1.291 .775 .708 .654 .688 1.949 32 170 .917 .74 60 2220 4250 422 428 219 225 0 150 84 67 .938 145 62 1.066 .857 -.093 -.222
7 632 620 178 71 454 549 406 189 186 84 228 118 0 0 537 703 78 144 61 48 53 42 1003 346 .827 1.209 .518 .832 .922 2.141 52 279 1.296 .95 80 2360 4250 421 429 232 240 -50 750 86 665 1.464 229 143 .683 .626 .55 -.675
8 508 106 154 62 354 44 442 96 158 65 288 34 0 0 322 46 22 15 88 67 75 53 398 322 8.045 .124 .118 .139 .113 2.538 52 260 .113 .81 80 2510 4240 420 428 247 255 -50 128 75 53 .15 116 41 6.647 .143 -2.733 -2.807
9 1345 399 145 57 1200 342 1423 378 146 59 1278 321 0 0 492 149 15 12 100 100 100 100 1542 1599 3.509 .285 .251 .297 .274 1.376 32 210 .274 .95 70 2640 4240 420 427 260 267 0 483 69 414 .345 458 389 2.899 .304 -1.535 -1.718
10 289 74 154 59 135 15 250 68 160 65 96 9 0 0 148 31 30 24 63 19 53 11 150 105 9 .111 .094 .161 .124 4.02 52 297 .118 .49 80 2800 4240 420 428 276 284 -50 90 71 18 .134 82 11 7.435 .113 -2.894 -3.139
11 9181 4106 219 66 8962 4040 9083 4561 231 74 8864 4495 0 0 2601 1372 64 28 100 100 100 100 13002 13359 2.218 .451 .507 .437 .438 1.243 32 204 .467 .98 70 2940 4230 419 426 290 297 0 4970 80 4890 .546 5521 5441 1.833 .614 -.874 -.704
12 7609 7143 285 74 7324 7069 7143 4994 299 80 6858 4920 0 0 4109 4124 62 23 100 100 100 100 14393 11778 1.036 .965 .717 .944 .971 1.528 32 170 .977 .96 60 3080 4240 421 427 305 311 0 8646 90 8557 1.168 6045 5955 .856 .868 .224 -.204
13 1163 905 180 63 983 842 1083 483 187 66 903 420 0 0 1005 966 49 16 61 61 59 57 1825 1323 1.167 .857 .465 .507 .735 2.448 52 284 .913 .95 80 3240 4240 420 428 320 328 -50 1095 76 1019 1.037 585 508 .964 .563 .052 -.829
14 217 92 138 59 79 33 203 84 143 64 65 25 0 0 62 37 19 19 80 55 71 34 112 90 2.394 .418 .385 .388 .338 1.904 52 270 .457 .73 80 3380 4240 420 428 334 342 -50 111 71 40 .506 102 30 1.978 .466 -.984 -1.103
15 765 346 129 58 636 288 723 319 132 63 594 261 0 0 220 137 17 19 100 100 100 100 924 855 2.208 .453 .439 .427 .411 1.45 32 155 .489 .9 60 3520 4230 420 426 349 355 0 419 70 349 .548 386 316 1.824 .532 -.867 -.911
16 7590 6586 128 63 7462 6523 7404 7140 132 68 7276 7077 0 0 3494 3695 20 22 100 100 100 100 13985 14353 1.144 .874 .973 .723 .899 1.806 32 170 .918 .97 60 3670 4230 420 426 364 370 0 7972 76 7896 1.058 8643 8566 .945 1.177 .082 .236
17 8048 4756 142 76 7906 4680 7115 4288 300 176 6973 4212 0 0 6007 3857 283 181 96 94 94 90 12586 11185 1.689 .592 .604 .555 .56 1.421 52 275 .586 .96 80 3820 4240 420 428 378 386 -50 5757 92 5665 .717 5190 5098 1.396 .731 -.481 -.452
18 186 89 175 99 11 -10 175 81 325 186 0 -18 0 0 51 30 287 181 0 0 0 0 1 -18 null null null .723 .858 3.271 52 285 .631 .95 80 3970 4240 420 428 393 401 -50 108 120 -12 null 98 -22 null null null null
19 12570 7029 135 72 12435 6957 13744 8242 150 83 13609 8170 0 0 4864 3340 49 36 100 96 100 96 19392 21779 1.787 .559 .6 .435 .558 2.252 32 199 .584 .97 70 4120 4230 419 426 408 415 0 8508 87 8421 .677 9977 9889 1.477 .727 -.562 -.461
20 17614 16482 143 81 17471 16401 17928 15957 175 102 17785 15876 0 0 7823 7401 79 60 100 100 100 100 33872 33661 1.065 .939 .893 .982 .944 1.286 80 446 .938 .99 110 4260 4240 418 429 420 431 0 19951 98 19853 1.136 19315 19217 .88 1.081 .184 .112

Total number of rows: 43104

Table truncated, full table size 9503 Kbytes.




Supplementary data files not provided
| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap