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Sample GSM217880 Query DataSets for GSM217880
Status Public on Aug 15, 2007
Title Standard-Expt. 1, Rep. 1
Sample type RNA
 
Channel 1
Source name 400ng Reference
Organism Homo sapiens
Characteristics 400ng Reference
Extracted molecule total RNA
Extraction protocol not provided
Label Cy3
Label protocol not provided
 
Channel 2
Source name 300ng Uninfected HFF, Standard Medium
Organism Homo sapiens
Characteristics 300ng Uninfected HFF, Standard Medium
Extracted molecule total RNA
Extraction protocol not provided
Label Cy5
Label protocol not provided
 
 
Hybridization protocol not provided
Scan protocol Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1130, 7150; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Ashley,,Fouts
Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 30.91; Parameter Scan Time = 13:38:16; Parameter PMT Volts = 720; Parameter Scan Date = 2005-07-25; Parameter Pixel Size = 10; Parameter Laser on time = 38933; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 1.77; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.1; Parameter Scanning software = AxImageIO; Performer: Ashley,,Fouts
Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 30.91; Parameter Scan Time = 13:38:16; Parameter PMT Volts = 820; Parameter Scan Date = 2005-07-25; Parameter Pixel Size = 10; Parameter Laser on time = 112068; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 1.69; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Ashley,,Fouts
Description Simple annotation: Toxoplasma, development
Image: http://smd.stanford.edu/MicroArray/gifs/2005-07/62826.gif
Developmental Stage: Uninfected Standard
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 Aug 14, 2007
Last update date Aug 14, 2007
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 GPL3386
Series (1)
GSE8773 Infection with bradyzoites has a diminished impact on host transcript levels relative to tachyzoite infection.

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 2635 2245 2247 2314 388 -69 2606 2149 2255 2306 359 -165 0 0 274 358 220 208 80 21 38 9 319 194 null null null .78 .732 4.209 52 286 .745 .22 80 1360 7630 44 52 19 27 -50 2285 2355 -70 null 2187 -168 null -.468 null null
2 7178 11088 2278 2313 4900 8775 6800 11073 2303 2369 4522 8760 0 0 2164 3228 259 356 100 100 100 100 13675 13282 .558 1.791 1.937 1.853 1.793 1.257 80 355 1.752 .97 100 1520 7630 43 53 34 44 0 11285 2354 8931 1.823 11270 8916 .549 1.972 .866 .979
3 7523 7987 2212 2257 5311 5730 6025 6612 2233 2278 3813 4355 0 0 4037 4070 266 344 97 97 97 97 11041 8168 .927 1.079 1.142 1.199 1.104 1.724 80 378 1.053 .97 100 1670 7610 41 51 49 59 0 8125 2296 5829 1.098 6726 4430 .911 1.162 .134 .216
4 5464 3787 2125 2080 3339 1707 5443 3651 2135 2094 3318 1571 0 0 1674 963 226 257 100 98 100 92 5046 4889 1.956 .511 .473 .506 .526 1.334 52 243 .527 .93 80 1810 7620 43 51 64 72 0 3853 2116 1737 .52 3715 1598 1.923 .482 -.943 -1.054
5 3191 4259 2057 2006 1134 2253 3135 4318 2090 2001 1078 2312 0 0 473 1003 224 206 98 100 94 100 3387 3390 .503 1.987 2.145 1.913 1.981 1.479 52 254 2.123 .88 80 1950 7630 44 52 78 86 0 4329 2039 2290 2.02 4389 2350 .495 2.18 1.014 1.124
6 3124 2552 2007 1925 1117 627 2864 2477 2014 1929 857 552 0 0 880 490 192 208 93 85 83 70 1744 1409 1.781 .561 .644 .596 .721 3.553 80 377 .513 .7 100 2100 7620 42 52 92 102 0 2596 1958 638 .571 2519 561 1.752 .655 -.809 -.61
7 5973 7697 1994 1921 3979 5776 5653 7013 2009 1937 3659 5092 0 0 2686 4084 222 234 100 100 98 98 9755 8751 .689 1.452 1.392 1.405 1.399 1.336 80 411 1.49 .98 110 2250 7610 40 51 106 117 0 7833 1955 5878 1.477 7137 5182 .677 1.416 .563 .502
8 6971 4085 1985 1896 4986 2189 3711 2870 1996 1917 1726 974 0 0 5614 2512 203 226 95 90 90 82 7175 2700 2.278 .439 .564 .504 .455 1.885 120 458 .437 .97 120 2390 7630 42 54 120 132 0 4161 1931 2230 .447 2923 992 2.236 .575 -1.161 -.799
9 2310 1938 1986 1902 324 36 2335 1974 1987 1916 349 72 0 0 260 271 197 204 71 28 40 9 360 421 9 .111 .206 .565 .629 3.08 52 243 .463 .22 80 2530 7620 43 51 136 144 -50 1978 1941 37 .113 2014 73 8.819 .211 -3.141 -2.248
10 4017 3363 1963 1908 2054 1455 4060 3212 2054 2097 2097 1304 0 0 627 604 1542 1996 81 15 6 0 3509 3401 1.412 .708 .622 .695 .665 1.471 80 372 .963 .95 100 2680 7620 42 52 150 160 0 3443 1953 1490 .725 3288 1335 1.379 .637 -.464 -.652
11 7838 12043 1932 1880 5906 10163 8876 13829 2036 2056 6944 11949 0 0 3924 6510 1539 1992 82 91 62 70 16069 18893 .581 1.721 1.721 1.784 1.694 1.243 80 374 1.65 .96 110 2820 7630 42 53 163 174 0 12359 1929 10430 1.766 14192 12263 .566 1.766 .82 .82
12 11410 15070 1924 1838 9486 13232 12313 16121 1931 1841 10389 14283 0 0 4855 6422 209 200 100 100 100 100 22718 24672 .717 1.395 1.375 1.433 1.428 1.254 80 410 1.387 .98 110 2970 7620 41 52 178 189 0 15537 1895 13642 1.438 16621 14726 .695 1.417 .524 .503
13 4343 5627 1933 1827 2410 3800 4434 5791 1933 1839 2501 3964 0 0 993 1303 190 205 100 100 100 100 6210 6465 .634 1.577 1.585 1.639 1.589 1.284 80 368 1.544 .96 110 3120 7630 42 53 193 204 0 5809 1886 3923 1.628 5978 4092 .614 1.636 .703 .71
14 3188 2508 1912 1823 1276 685 3118 2370 1915 1835 1206 547 0 0 519 479 170 213 100 85 100 66 1961 1753 1.863 .537 .454 .461 .488 2.136 80 341 1.267 .8 100 3260 7620 42 52 208 218 0 2589 1882 707 .554 2446 565 1.805 .468 -.852 -1.095
15 2009 1692 1917 1816 92 -124 1997 1679 1925 1828 80 -137 0 0 267 245 186 206 34 9 17 3 -32 -57 null null null 1.035 .784 4.365 52 242 .741 .21 80 3400 7620 43 51 223 231 -50 1743 1870 -128 null 1729 -141 null -1.764 null null
16 6447 7039 1926 1783 4521 5256 6468 7250 1938 1789 4542 5467 0 0 2608 2778 213 212 100 100 98 100 9777 10009 .86 1.163 1.204 1.219 1.199 1.3 80 390 1.133 .97 100 3560 7620 42 52 238 248 0 7221 1829 5392 1.193 7438 5609 .838 1.235 .254 .304
17 8649 6954 1879 1759 6770 5195 10140 7641 1893 1773 8261 5882 0 0 3884 2660 194 201 100 100 100 100 11965 14143 1.303 .767 .712 .814 .769 1.273 80 304 .74 .99 100 3710 7630 43 53 253 263 0 7101 1796 5305 .784 7803 6007 1.276 .727 -.352 -.46
18 2553 2964 1860 1740 693 1224 2521 2897 1858 1747 661 1157 0 0 332 471 186 187 95 100 88 98 1917 1818 .566 1.766 1.75 1.866 1.721 1.688 80 397 1.785 .77 110 3840 7620 41 52 265 276 0 3016 1770 1245 1.797 2948 1177 .556 1.781 .846 .833
19 21256 24636 1895 1814 19361 22822 23319 25775 1895 1830 21424 23961 0 0 9613 10808 212 297 100 100 100 100 42183 45385 .848 1.179 1.118 1.234 1.144 1.282 80 425 1.172 .98 110 4000 7610 40 51 281 292 0 25002 1841 23161 1.196 26158 24317 .836 1.135 .259 .183
20 14271 17359 1943 1893 12328 15466 14409 17080 1951 1930 12466 15187 0 0 3864 5069 215 325 100 100 100 100 27794 27653 .797 1.255 1.218 1.283 1.234 1.227 52 310 1.269 .98 90 4140 7620 42 51 296 305 0 17588 1918 15670 1.271 17305 15387 .787 1.234 .346 .304

Total number of rows: 41472

Table truncated, full table size 9806 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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