NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM161348 Query DataSets for GSM161348
Status Public on Jan 04, 2010
Title ST66-T28
Sample type RNA
 
Channel 1
Source name Strat. aRNA 4ug
Organism Homo sapiens
Characteristics Strat. aRNA 4ug
LabeledExtract: 64984.Channel_1
Extracted molecule total RNA
Extraction protocol not provided
Label Cy3
Label protocol not provided
 
Channel 2
Source name ST66-T28 4ug aRNA
Organism Homo sapiens
Characteristics ST66-T28 4ug aRNA
LabeledExtract: 64984.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 = 1480, 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 = 38.65; Parameter Scan Time = 13:52:23; Parameter PMT Volts = 490; Parameter Scan Date = 2005-10-17; Parameter Pixel Size = 10; Parameter Laser on time = 43522; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 2.47; 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 = 38.65; Parameter Scan Time = 13:52:23; Parameter PMT Volts = 630; Parameter Scan Date = 2005-10-17; Parameter Pixel Size = 10; Parameter Laser on time = 116657; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 2.62; 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/2005-11/64984.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) lucy.nava@yahoo.com
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
1 404 4723 69 74 335 4649 450 5278 74 85 381 5204 0 0 112 1895 34 82 100 100 98 100 4984 5585 .072 13.878 13.659 13.032 14.362 1.718 52 357 15.504 .9 90 1980 6690 28 37 45 54 0 33698 528 33170 99.016 37658 37130 .01 97.454 6.63 6.607
2 6013 584 72 76 5941 508 6535 626 79 81 6463 550 0 0 3204 184 33 34 100 100 100 100 6449 7013 11.695 .086 .085 .1 .079 1.942 52 243 .072 .92 80 2130 6700 30 38 61 69 0 484 63 421 .071 518 455 14.124 .07 -3.82 -3.827
3 8189 2604 71 76 8118 2528 8162 2473 73 78 8091 2397 0 0 5399 1609 12 15 100 100 100 100 10646 10488 3.211 .311 .296 .335 .305 2.245 52 270 .29 .94 80 2260 6690 29 37 74 82 0 4574 134 4441 .547 4344 4211 1.828 .52 -.87 -.942
4 3551 1886 73 81 3478 1805 3714 2024 75 85 3641 1943 0 0 1524 698 13 25 100 100 100 100 5283 5584 1.927 .519 .534 .525 .499 1.738 52 278 .488 .94 80 2420 6690 29 37 90 98 0 4083 175 3907 1.123 4381 4206 .89 1.155 .168 .208
5 2394 509 76 86 2318 423 2768 564 77 87 2692 478 0 0 1031 230 12 17 100 94 100 90 2741 3170 5.48 .182 .178 .149 .163 2.593 52 269 .171 .89 80 2550 6690 29 37 103 111 0 523 88 434 .187 579 491 5.335 .182 -2.416 -2.455
6 481 590 75 87 406 503 514 641 85 102 439 554 0 0 324 338 106 173 86 78 73 73 909 993 .807 1.239 1.262 1.197 1.263 2.377 52 288 1.214 .74 80 2710 6690 29 37 119 127 0 1427 210 1216 2.996 1550 1340 .334 3.052 1.583 1.61
7 4795 1690 75 86 4720 1604 4809 1332 84 102 4734 1246 0 0 1689 2030 105 169 100 98 100 90 6324 5980 2.943 .34 .263 .256 .254 1.84 52 299 .4 .6 90 2850 6690 28 37 132 141 0 3133 159 2974 .63 2470 2310 1.587 .488 -.666 -1.035
8 1219 883 74 81 1145 802 1375 862 74 84 1301 781 0 0 425 228 9 18 100 100 100 100 1947 2082 1.428 .7 .6 .79 .642 1.848 52 312 .64 .91 90 2980 6700 29 38 145 154 0 1646 151 1495 1.306 1607 1456 .766 1.119 .385 .162
9 3946 723 73 80 3873 643 4077 737 74 83 4004 657 0 0 893 221 9 15 100 100 100 100 4516 4661 6.023 .166 .164 .155 .179 1.597 52 320 .165 .92 90 3140 6690 28 37 161 170 0 771 85 686 .177 786 701 5.648 .175 -2.498 -2.515
10 4584 1330 72 79 4512 1251 4806 1250 74 82 4734 1171 0 0 857 643 11 19 100 100 100 100 5763 5905 3.607 .277 .247 .255 .253 1.5 52 301 .277 .87 90 3270 6690 28 37 174 183 0 2131 127 2005 .444 2003 1876 2.251 .396 -1.17 -1.335
11 16821 568 76 85 16745 483 18368 603 86 99 18292 518 0 0 4704 204 36 49 100 96 100 94 17228 18810 34.669 .029 .028 .026 .03 1.659 52 294 .028 .78 80 3420 6690 29 37 190 198 0 356 53 303 .018 378 325 55.318 .018 -5.79 -5.816
12 15083 17628 69 82 15014 17546 16699 20079 78 92 16630 19997 0 0 7330 8984 34 39 100 100 100 100 32560 36627 .856 1.169 1.202 1.034 1.161 2.383 52 342 1.194 .95 90 3580 6690 28 37 205 214 0 37124 173 36952 2.461 42286 42114 .406 2.532 1.299 1.34
13 5552 3220 69 84 5483 3136 5803 3528 73 90 5734 3444 0 0 1257 981 18 30 100 100 100 100 8619 9178 1.748 .572 .601 .536 .6 1.456 52 322 .626 .9 90 3720 6690 28 37 219 228 0 7502 196 7307 1.333 8220 8024 .75 1.399 .414 .485
14 987 853 69 81 918 772 1009 736 73 88 940 655 0 0 154 448 18 30 100 100 100 100 1690 1595 1.189 .841 .697 .774 .756 1.388 52 344 .948 .83 90 3870 6690 28 37 234 243 0 1734 165 1569 1.71 1496 1332 .585 1.417 .774 .502
15 769 13170 67 81 702 13089 820 15196 69 86 753 15115 0 0 440 5748 12 33 98 100 96 100 13791 15868 .054 18.645 20.073 23.011 21.579 4.172 52 300 23.148 .73 90 4020 6690 28 37 249 258 0 146081 898 145183 206.813 168554 167655 .005 222.65 7.692 7.799
16 5569 4697 66 75 5503 4622 6848 5811 68 81 6782 5736 0 0 3187 2517 10 35 100 100 100 98 10125 12518 1.191 .84 .846 .983 .831 4.123 80 387 .811 .93 100 4170 6690 28 38 264 274 0 12609 201 12408 2.255 15600 15399 .444 2.271 1.173 1.183
17 8457 3578 67 74 8390 3504 11178 4652 70 77 11111 4578 0 0 5471 2171 18 21 100 98 100 98 11894 15689 2.394 .418 .412 .476 .41 3.886 80 374 .39 .94 100 4310 6690 28 38 278 288 0 6979 144 6834 .815 9073 8929 1.228 .804 -.296 -.315
18 5441 869 71 80 5370 789 5399 717 79 93 5328 637 0 0 765 499 29 52 100 100 100 100 6159 5965 6.806 .147 .12 .134 .123 1.447 52 250 .146 .8 80 4460 6690 29 37 294 302 0 987 91 896 .167 814 723 5.993 .136 -2.583 -2.881
19 18978 9679 88 111 18890 9568 21088 9804 91 115 21000 9693 0 0 6309 2476 31 51 100 100 100 100 28458 30693 1.974 .507 .462 .546 .462 1.965 80 365 .458 .89 100 4600 6690 28 38 307 317 0 15101 173 14928 .79 15296 15123 1.265 .72 -.34 -.474
20 19556 11803 75 89 19481 11714 23722 13716 85 101 23647 13627 0 0 9607 5092 44 50 100 100 100 100 31195 37274 1.663 .601 .576 .683 .575 2.59 80 370 .561 .93 100 4750 6700 29 39 322 332 0 19028 143 18884 .969 22112 21968 1.032 .929 -.045 -.106

Total number of rows: 41472

Table truncated, full table size 9406 Kbytes.




Supplementary data files not provided

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap
External link. Please review our privacy policy.