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Sample GSM28543 Query DataSets for GSM28543
Status Public on Feb 09, 2005
Title LPS 2hr Rat #3 flip
Sample type RNA
 
Channel 1
Source name LPS 2hr Rat #3
Organism Rattus norvegicus
Extracted molecule total RNA
 
Channel 2
Source name Control Pool 2hr LPS
Organism Rattus norvegicus
Extracted molecule total RNA
 
 
Description LPS 2hr Rat #3 flip
 
Submission date Aug 10, 2004
Last update date May 27, 2005
Contact name Rick David Fannin
E-mail(s) fannin@niehs.nih.gov
Phone 919-541-0992
Fax 919-541-1506
URL http://www.niehs.nih.gov/nct/
Organization name The National Institute of Environmental Health Sciences
Department Office of the Director
Lab National Center for Toxicogenomics/Toxicology-Pathology Working
Street address 111 T.W. Alexander Drive
City Durham
State/province NC
ZIP/Postal code 27709
Country USA
 
Platform ID GPL1344
Series (1)
GSE1658 LPS Blood Time course

Data table header descriptions
ID_REF
SR_top Within each sub-array (pen), column offset (start from 1 at left-most) to the spot of interest
SR_left Bonding box location in Red channel image coordinates - (left) (SR -- Sample in Red channel)
SR_bottom Bonding box location in Red channel image coordinates - (bottom) (SR -- Sample in Red channel)
SR_right Bonding box location in Red channel image coordinates - (right) (SR -- Sample in Red channel)
SR_T. Int. Total Intensity - Sum of all pixel gray-levels within the target area. No data trimming is performed here.
SR_Mean Mean Intensity - Average of all pixel gray-leves within the target area, after trimming top and bottom 5%
SR_S.Dev Std. Dev. Of intensity - Std. Dev. Of signal intensity. Derived along with mean intensity
SR_SNR Signal-to-Noise Ratio. It is roughly the ratio of mean signal intensity to the local background variation.
SR_iQuality The measurement quality. Summarized from Area, Background, Consistency, and Saturation. From 0 (bad) to 1 (good)
SR_bkMean Mean background Intensity
SR_bkDev Std. Dev. Of background intensity
SG_top Bonding box location in Green channel image coordinates - (top) (SG -- Sample in Green channel)
SG_left Bonding box location in Green channel image coordinates - (left) (SG -- Sample in Green channel)
SG_bottom Bonding box location in Green channel image coordinates - (bottom) (SG -- Sample in Green channel)
SG_right Bonding box location in Green channel image coordinates - (right) (SG -- Sample in Green channel)
SG_T. Int. Total Intensity - Sum of all pixel gray-levels within the target area. No data trimming is performed here.
SG_Mean Mean Intensity - Average of all pixel gray-leves within the target area, after trimming top and bottom 5%
SG_S.Dev Std. Dev. Of intensity - Std. Dev. Of signal intensity. Derived along with mean intensity
SG_SNR Signal-to-Noise Ratio. It is roughly the ratio of mean signal intensity to the local background variation.
SG_iQuality The measurement quality. Summarized from Area, Background, Consistency, and Saturation. From 0 (bad) to 1 (good)
SG_bkMean Mean background Intensity
SG_bkDev Std. Dev. Of background intensity
unionArea Union Area - the detected target area. All calculations are based on this region
propArea Proportional area relatively to the mask size.
VALUE log ratio (log2 of PRE_VALUE)
rQuality Ratio measurement quality (including all intensity measurement quality, plus the signal-to-noise-ratio requirement).
confLevel Confidence Level, typically set at 99%
lowerLimit Lower Limit of confidence interval for cal. Ratio
upperLimit Upper Limit of confidence interval for cal. Ratio
M Magnitude parameter for channel compensation
CV Coefficient of variation of the intensity
Flag User flagged. 0 - deleted spot by user, 1 - good spot
HKFlag House Keeping flag
GelBand Number of bands
PRE_VALUE Calibrated ratio, (or normalized ratio)

Data table
ID_REF SR_top SR_left SR_bottom SR_right SR_T. Int. SR_Mean SR_S.Dev SR_SNR SR_iQuality SR_bkMean SR_bkDev SG_top SG_left SG_bottom SG_right SG_T. Int. SG_Mean SG_S.Dev SG_SNR SG_iQuality SG_bkMean SG_bkDev unionArea propArea VALUE rQuality confLevel lowerLimit upperLimit M CV Flag HKFlag GelBand PRE_VALUE
1 637 173 664 200 96982 110.3 72.7 8.7 1 443 9 637 173 664 200 86282 95.7 58.5 11 1 397.9 6.1 174 0.9667 0.5172253 1 99 0.873 1.1455 0.8052 0.0372 1 0 1 1.4312
2 635 621 662 648 41469 68.1 69.9 4.7 0.362 447.3 11.4 635 621 662 648 33067 20.5 11.7 2.3 1 397.4 6.3 79 0.5725 2.0414883 0.2 99 0.873 1.1455 0.8052 0.0372 1 0 1 4.1167
3 639 1075 666 1102 171652 668.8 299.7 46 1 435.3 11.5 639 1075 666 1102 195171 858.7 400.4 91.4 1 399 6.8 155 1 -0.0479653 1 99 0.873 1.1455 0.8052 0.0372 1 0 1 0.9673
4 637 1525 664 1552 340982 1618.4 621.9 120.3 1 431 8.7 637 1525 664 1552 405750 2035.6 784.3 215.6 1 397.7 6.3 165 1 -0.0182933 1 99 0.873 1.1455 0.8052 0.0372 1 0 1 0.9874
5 637 229 664 256 244282 910.6 558.2 71.8 1 441.4 8.9 637 229 664 256 271975 1107.5 703.8 127.8 1 396.1 6 180 1 0.0302653 1 99 0.873 1.1455 0.8052 0.0372 1 0 1 1.0212
6 635 677 662 704 197395 993.2 342.7 77.1 1 443.5 9.3 635 677 662 704 213898 1157.9 414.8 126.4 1 398.1 6.6 138 1 0.0912603 1 99 0.873 1.1455 0.8052 0.0372 1 0 1 1.0653
7 639 1131 666 1158 216378 968.9 254.4 79.2 1 432.4 8.4 639 1131 666 1158 235327 1131.3 327.2 126.7 1 395.3 6.1 155 1 0.0892273 1 99 0.873 1.1455 0.8052 0.0372 1 0 1 1.0638
8 637 1581 664 1608 208350 833.1 174.3 66.3 1 430.6 7.3 637 1581 664 1608 233757 1021.6 229.4 111.4 1 395.3 5.9 165 1 0.0183493 1 99 0.873 1.1455 0.8052 0.0372 1 0 1 1.0128
9 637 285 664 312 295059 1193.2 705.5 92.1 1 441.3 9.4 637 285 664 312 334357 1448.7 860.7 172.2 1 393.6 5.6 180 1 0.0326653 1 99 0.873 1.1455 0.8052 0.0372 1 0 1 1.0229
10 635 733 662 760 225583 1188.5 435.9 90.7 1 443.1 9.6 635 733 662 760 250823 1415.4 516.6 154.7 1 398.2 6.6 138 1 0.0604623 1 99 0.873 1.1455 0.8052 0.0372 1 0 1 1.0428
11 639 1187 666 1214 271819 1321.8 431.5 105.3 1 436 8.9 639 1187 666 1214 418382 2290.5 821.4 250.2 1 399.1 6.4 155 1 -0.4805593 1 99 0.873 1.1455 0.8052 0.0372 1 0 1 0.7167
12 637 1637 664 1664 232718 985.5 382.1 73.5 1 431.7 8.6 637 1637 664 1664 261992 1195.7 476.2 124.5 1 398.4 6.6 165 1 0.0336523 1 99 0.873 1.1455 0.8052 0.0372 1 0 1 1.0236
13 637 341 664 368 150839 394.3 228.9 32.7 1 438.9 8.1 637 341 664 368 174838 575 341.3 69 1 394.5 5.5 180 1 -0.2315833 1 99 0.873 1.1455 0.8052 0.0372 1 0 1 0.8517
14 635 789 662 816 322386 1895.8 777 138.6 1 443.5 10.4 635 789 662 816 365790 2267.4 958.5 262.5 1 396.1 5.9 138 1 0.0543623 1 99 0.873 1.1455 0.8052 0.0372 1 0 1 1.0384
15 639 1243 666 1270 185912 770.2 304.5 62 1 437.5 8.7 639 1243 666 1270 207210 950.1 383.3 111.6 1 397.2 5.5 155 1 0.0097773 1 99 0.873 1.1455 0.8052 0.0372 1 0 1 1.0068
16 637 1693 664 1720 208300 847.6 210.6 70.3 1 423.2 6.3 637 1693 664 1720 236654 1047.6 273.3 110.1 1 396.8 6.4 165 1 0.0070523 1 99 0.873 1.1455 0.8052 0.0372 1 0 1 1.0049
17 637 396 664 423 610523 3031.5 1429.3 257.6 1 397.4 7.6 637 396 664 423 833428 4296.8 2110 586.6 1 384.1 3.8 180 1 -0.1906683 1 99 0.873 1.1455 0.8052 0.0372 1 0 1 0.8762
18 635 844 662 871 173390 804.1 266.3 59.3 1 441.9 10.3 635 844 662 871 183495 920.6 302.7 101.6 1 398.5 6.5 138 1 0.1174293 1 99 0.873 1.1455 0.8052 0.0372 1 0 1 1.0848
19 639 1298 666 1325 96662 285.9 176.3 24 1 433.4 8 639 1298 666 1325 95178 314.6 197.6 34.6 1 399.5 6.4 134 0.8645 0.1746623 1 99 0.873 1.1455 0.8052 0.0372 1 0 1 1.1287
20 637 1748 664 1775 152763 517 348.8 39.3 1 433 8.2 637 1748 664 1775 200992 834.4 595.1 86.2 1 398.1 6.7 159 0.9636 -0.3780073 1 99 0.873 1.1455 0.8052 0.0372 1 0 1 0.7695

Total number of rows: 7200

Table truncated, full table size 1236 Kbytes.




Supplementary file Size Download File type/resource
GSM28543.TIF.gz 11.8 Mb (ftp)(http) TIFF

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