NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM161499 Query DataSets for GSM161499
Status Public on Jan 04, 2010
Title ST173-T9M
Sample type RNA
 
Channel 1
Source name Strat. aRNA 4ug
Organism Homo sapiens
Characteristics Strat. aRNA 4ug
LabeledExtract: 64974.Channel_1
Extracted molecule total RNA
Extraction protocol not provided
Label Cy3
Label protocol not provided
 
Channel 2
Source name ST173-T9M_ 4ug aRNA
Organism Homo sapiens
Characteristics ST173-T9M_ 4ug aRNA
LabeledExtract: 64974.Channel_2
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 = 1400, 6360; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Lucinda,,Thompson
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 = 37.01; Parameter Scan Time = 09:03:35; Parameter PMT Volts = 490; Parameter Scan Date = 2005-10-17; Parameter Pixel Size = 10; Parameter Laser on time = 43232; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 2.35; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.1; Parameter Scanning software = AxImageIO; Performer: Lucinda,,Thompson
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 = 37.01; Parameter Scan Time = 09:03:35; Parameter PMT Volts = 580; Parameter Scan Date = 2005-10-17; Parameter Pixel Size = 10; Parameter Laser on time = 116367; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 2.25; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Lucinda,,Thompson
Description Simple annotation: Pathogen, Salmonella
Image: http://smd.stanford.edu/MicroArray/gifs/2005-11/64974.gif
Compound Based Treatment: Azithromycin
Disease State: Typhoid
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 Feb 09, 2007
Last update date Jan 04, 2010
Contact name Lucinda Thompson
E-mail(s) [email protected]
Phone 650 723 2671
Fax 650 723 1837
Organization name Stanford University
Department Microbiology and Immunology, School of Medicine
Street address Fairchild Bldg., D035, 299 Campus Dr
City Stanford
State/province CA
ZIP/Postal code 94305
Country USA
 
Platform ID GPL4858
Series (1)
GSE7000 Vietnam Typhoid Study

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
1 476 589 74 51 402 538 528 632 76 52 454 581 0 0 166 142 13 8 100 100 98 100 940 1035 .747 1.338 1.28 1.51 1.251 1.979 52 293 1.265 .92 80 1860 6800 40 48 42 50 0 1336 116 1220 3.035 1433 1317 .33 2.902 1.602 1.537
2 10445 503 80 52 10365 451 11254 546 85 53 11174 494 0 0 2938 127 24 11 100 100 100 100 10816 11668 22.982 .044 .044 .043 .044 1.417 32 199 .042 .93 70 2010 6800 40 47 57 64 0 242 25 217 .021 263 238 47.783 .021 -5.578 -5.555
3 7579 951 76 52 7503 899 7915 965 79 52 7839 913 0 0 4800 617 20 8 100 100 100 100 8402 8752 8.346 .12 .116 .102 .108 1.893 52 304 .118 .96 80 2150 6790 39 47 71 79 0 740 40 700 .093 751 710 10.725 .091 -3.423 -3.464
4 3510 1045 76 52 3434 993 3871 1122 77 52 3795 1070 0 0 926 235 13 8 100 100 100 100 4427 4865 3.458 .289 .282 .295 .284 1.325 32 211 .27 .95 70 2300 6800 40 47 86 93 0 1139 57 1082 .315 1223 1166 3.172 .307 -1.666 -1.702
5 1368 233 74 52 1294 181 1596 247 76 52 1522 195 0 0 644 82 12 9 100 100 98 96 1475 1717 7.149 .14 .128 .155 .131 2.678 52 286 .126 .92 80 2430 6800 40 48 99 107 0 195 44 152 .117 207 163 8.539 .107 -3.094 -3.221
6 408 595 76 51 332 544 372 617 76 52 296 566 0 0 212 152 9 9 100 100 100 100 876 862 .61 1.639 1.912 1.78 1.832 1.544 32 231 1.516 .82 70 2590 6800 40 47 115 122 0 1460 125 1335 4.021 1514 1389 .249 4.692 2.008 2.23
7 2707 434 78 52 2629 382 2999 487 79 53 2921 435 0 0 758 165 9 8 100 100 100 100 3011 3356 6.882 .145 .149 .125 .145 1.682 52 273 .149 .94 80 2740 6790 39 47 130 138 0 345 41 303 .115 387 346 8.663 .118 -3.115 -3.079
8 799 378 83 57 716 321 893 411 85 58 810 354 0 0 251 97 12 10 100 100 100 100 1037 1164 2.231 .448 .437 .467 .443 1.625 52 243 .425 .94 80 2870 6800 40 48 143 151 0 530 80 450 .628 576 496 1.592 .612 -.671 -.708
9 1538 445 80 57 1458 388 1700 479 82 57 1620 422 0 0 422 139 13 10 100 100 100 100 1846 2042 3.758 .266 .26 .253 .266 1.453 52 265 .258 .93 80 3010 6800 40 48 157 165 0 483 62 421 .289 520 458 3.461 .283 -1.791 -1.822
10 3018 747 80 56 2938 691 3116 791 81 55 3036 735 0 0 525 188 10 8 100 100 100 100 3629 3771 4.252 .235 .242 .225 .237 1.355 52 312 .234 .95 90 3160 6790 38 47 171 180 0 734 55 679 .231 778 723 4.325 .238 -2.113 -2.071
11 9905 311 83 57 9822 254 11006 345 87 59 10923 288 0 0 3252 109 22 14 100 98 100 94 10076 11211 38.669 .026 .026 .024 .027 1.689 52 334 .026 .94 90 3300 6790 38 47 185 194 0 115 21 94 .01 128 107 104.244 .01 -6.704 -6.676
12 8702 16227 79 54 8623 16173 7500 16383 82 58 7421 16329 0 0 7937 13908 22 16 98 100 93 100 24796 23750 .533 1.876 2.2 2.431 1.773 3.012 80 362 1.858 .95 100 3460 6800 39 49 201 211 0 38717 129 38588 4.475 39089 38960 .223 5.25 2.162 2.392
13 4720 3412 74 52 4646 3360 5518 3766 76 54 5444 3714 0 0 2959 2006 11 18 100 100 100 100 8006 9158 1.383 .723 .682 .777 .655 2.522 80 355 .684 .91 100 3600 6800 39 49 215 225 0 6074 93 5981 1.287 6704 6612 .777 1.214 .365 .28
14 772 403 73 52 699 351 827 423 74 57 754 371 0 0 179 85 11 22 100 100 100 100 1050 1125 1.991 .502 .492 .506 .492 1.321 52 335 .482 .94 90 3750 6790 38 47 230 239 0 595 77 518 .742 625 548 1.348 .727 -.431 -.461
15 374 13638 74 54 300 13584 476 15428 77 58 402 15374 0 0 192 8116 18 17 90 100 84 100 13884 15776 .022 45.28 38.244 47.911 40.947 2.063 52 293 48.524 .9 90 3910 6800 39 48 246 255 0 140695 557 140138 467.127 159162 158604 .002 394.539 8.868 8.624
16 7643 7288 74 53 7569 7235 8355 7218 79 55 8281 7165 0 0 4939 5098 34 21 100 100 100 100 14804 15446 1.046 .956 .865 .914 .942 1.831 120 479 .981 .92 120 4060 6790 37 49 260 272 0 13878 101 13777 1.82 13745 13644 .549 1.648 .864 .72
17 6312 3609 74 52 6238 3557 7974 4439 78 55 7900 4387 0 0 3529 1932 38 25 100 98 98 97 9795 12287 1.754 .57 .555 .557 .529 2.015 80 314 .543 .95 100 4200 6790 38 48 275 285 0 5744 83 5661 .907 7065 6982 1.102 .884 -.14 -.178
18 2748 389 74 53 2674 336 2856 410 78 54 2782 357 0 0 618 127 21 11 100 100 100 98 3010 3139 7.958 .126 .128 .112 .129 1.604 52 288 .126 .95 90 4340 6790 38 47 289 298 0 291 40 251 .094 307 267 10.633 .096 -3.411 -3.38
19 13412 5537 75 52 13337 5485 14877 5939 81 55 14802 5887 0 0 4771 1785 31 14 100 100 100 100 18822 20689 2.432 .411 .398 .424 .402 1.694 80 423 .387 .94 110 4490 6790 37 48 303 314 0 7105 67 7038 .528 7621 7554 1.895 .51 -.922 -.97
20 13551 4199 75 53 13476 4146 16488 4960 80 56 16413 4907 0 0 6048 1848 28 16 100 100 100 100 17622 21320 3.25 .308 .299 .301 .305 1.977 80 342 .292 .95 100 4640 6800 39 49 319 329 0 4834 61 4773 .354 5710 5649 2.823 .344 -1.497 -1.539

Total number of rows: 41472

Table truncated, full table size 9288 Kbytes.




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