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Sample GSM100320 Query DataSets for GSM100320
Status Public on Mar 15, 2006
Title 129SvJ_2- P.1 output
Sample type RNA
 
Channel 1
Source name 10X library
Organism Salmonella enterica subsp. enterica serovar Typhimurium
Characteristics 10X library
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name P.1 output (spleen pool)
Organism Salmonella enterica subsp. enterica serovar Typhimurium
Characteristics P.1 output (spleen pool)
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Comparative genomics, mouse
Image: http://smd.stanford.edu/MicroArray/gifs/2005-03/60300.gif
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 Mar 13, 2006
Last update date Sep 22, 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 GPL3545
Series (1)
GSE4461 Genome-wide screen for salmonella genes required for long-term systemic infection of the mouse.

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
1 676 588 135 77 541 511 664 586 135 81 529 509 0 0 87 123 20 28 100 100 100 100 1052 1038 1.059 .945 .962 .927 .936 1.281 120 769 .952 .95 120 1740 7060 36 48 36 48 0 806 106 700 1.295 803 698 .772 1.319 .372 .399
2 376 205 132 70 244 135 384 201 133 72 252 131 0 0 66 54 20 24 98 96 97 94 379 383 1.807 .553 .52 .531 .521 1.917 156 942 .543 .84 140 1980 7070 36 50 59 73 0 281 96 185 .758 275 180 1.319 .712 -.399 -.489
3 452 256 127 65 325 191 451 253 128 68 324 188 0 0 60 68 18 22 100 100 100 100 516 512 1.702 .588 .58 .559 .582 1.421 120 837 .602 .88 130 2210 7050 34 47 82 95 0 351 89 262 .805 347 258 1.242 .795 -.312 -.331
4 403 234 127 70 276 164 398 227 128 73 271 157 0 0 45 57 19 34 100 100 100 96 440 428 1.683 .594 .579 .563 .568 1.449 120 751 .639 .83 120 2450 7060 36 48 107 119 0 321 96 225 .814 311 215 1.228 .794 -.296 -.333
5 503 282 133 68 370 214 498 280 133 71 365 212 0 0 58 68 20 24 100 100 100 100 584 577 1.729 .578 .581 .553 .589 1.378 120 838 .59 .91 130 2690 7060 35 48 130 143 0 386 93 293 .793 384 291 1.262 .796 -.335 -.329
6 595 268 129 66 466 202 602 262 130 69 473 196 0 0 116 67 20 22 99 100 98 99 668 669 2.307 .433 .414 .435 .416 1.632 156 970 .416 .89 140 2930 7070 36 50 154 168 0 367 90 277 .594 359 269 1.683 .568 -.751 -.816
7 338 170 124 65 214 105 348 170 125 67 224 105 0 0 61 42 20 21 99 98 97 94 319 329 2.038 .491 .469 .486 .498 1.895 120 727 .474 .82 120 3170 7070 37 49 179 191 0 233 89 144 .672 233 144 1.487 .642 -.572 -.638
8 481 273 124 69 357 204 478 279 126 71 354 210 0 0 49 60 20 24 100 99 100 99 561 564 1.75 .571 .593 .547 .593 1.424 120 838 .585 .9 130 3410 7060 35 48 202 215 0 374 95 280 .783 382 288 1.277 .813 -.353 -.299
9 581 379 120 68 461 311 564 366 122 72 444 298 0 0 100 108 23 26 100 100 100 100 772 742 1.482 .675 .671 .65 .667 1.384 120 821 .705 .92 130 3640 7070 36 49 225 238 0 519 93 426 .925 502 408 1.082 .92 -.113 -.12
10 449 275 119 68 330 207 446 278 121 72 327 210 0 0 56 61 23 32 100 100 100 98 537 537 1.594 .627 .642 .606 .641 1.399 120 843 .635 .9 130 3890 7080 37 50 250 263 0 377 93 284 .86 381 288 1.163 .88 -.218 -.184
11 375 193 123 69 252 124 374 188 125 71 251 119 0 0 52 49 21 24 100 100 100 96 376 370 2.032 .492 .474 .466 .451 1.589 120 789 .501 .83 130 4140 7080 37 50 275 288 0 265 95 170 .674 258 163 1.483 .65 -.568 -.622
12 697 345 122 70 575 275 713 343 124 75 591 273 0 0 164 95 22 28 99 98 98 96 850 864 2.091 .478 .462 .469 .475 1.778 156 892 .471 .93 140 4370 7080 37 51 298 312 0 473 96 377 .655 470 374 1.526 .633 -.609 -.659
13 689 700 120 70 569 630 716 700 121 75 596 630 0 0 172 205 22 31 98 99 97 98 1199 1226 .903 1.107 1.057 1.113 1.055 1.946 156 906 1.118 .94 140 4610 7080 37 51 322 336 0 959 96 863 1.517 959 863 .659 1.449 .602 .535
14 715 694 122 73 593 621 717 685 123 80 595 612 0 0 172 183 20 48 98 99 96 98 1214 1207 .955 1.047 1.029 1.118 1.012 2.029 156 909 1.052 .93 140 4850 7080 37 51 346 360 0 951 100 851 1.435 939 839 .697 1.41 .521 .495
15 532 425 125 76 407 349 528 410 125 80 403 334 0 0 89 139 18 29 100 100 100 100 756 737 1.166 .857 .829 .82 .839 1.347 120 837 .916 .93 130 5080 7060 35 48 369 382 0 582 104 478 1.175 562 458 .851 1.136 .233 .184
16 856 707 131 88 725 619 842 696 131 94 711 608 0 0 155 167 19 39 100 100 100 100 1344 1319 1.171 .854 .855 .845 .834 1.253 120 860 .892 .95 130 1720 7290 58 71 33 46 0 969 121 848 1.17 954 833 .855 1.172 .227 .229
17 641 415 130 73 511 342 620 401 132 76 490 328 0 0 99 102 19 27 100 100 100 100 853 818 1.494 .669 .669 .651 .66 1.317 120 805 .684 .93 130 1970 7290 58 71 58 71 0 569 100 469 .917 550 450 1.09 .917 -.125 -.124
18 698 633 128 68 570 565 671 615 130 71 543 547 0 0 135 149 19 25 100 100 100 100 1135 1090 1.009 .991 1.007 .984 .989 1.207 120 836 1.033 .95 130 2210 7290 58 71 82 95 0 868 93 774 1.359 843 750 .736 1.381 .442 .465
19 617 472 125 71 492 401 628 479 126 77 503 408 0 0 148 146 20 36 99 97 98 96 893 911 1.227 .815 .811 .788 .802 1.917 156 887 .831 .94 140 2460 7290 58 72 107 121 0 647 97 550 1.117 656 559 .895 1.112 .16 .153
20 525 341 125 68 400 273 516 328 128 72 391 260 0 0 85 88 19 26 100 100 100 100 673 651 1.465 .683 .665 .663 .665 1.299 120 786 .735 .92 130 2690 7290 58 71 130 143 0 467 93 374 .935 450 356 1.069 .911 -.096 -.134

Total number of rows: 6528

Table truncated, full table size 1409 Kbytes.




Supplementary data files not provided
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