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Sample GSM28546 Query DataSets for GSM28546
Status Public on Feb 09, 2005
Title LPS 6hr Rat #4 fluor
Sample type RNA
 
Channel 1
Source name Control Pool 6hr LPS
Organism Rattus norvegicus
Extracted molecule total RNA
 
Channel 2
Source name LPS 6hr Rat #4
Organism Rattus norvegicus
Extracted molecule total RNA
 
 
Description LPS 6hr Rat #4 fluor
 
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 Bonding box location in Red channel image coordinates - (top) (SR -- Sample in Red channel)
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
1 649 81 676 108 77984 96.3 52.2 10.7 1 398 6.3 649 81 676 108 90668 140.7 80.6 12 1 434.3 8.3 158 0.8927 -0.5079933 1 99 0.7232 1.3828 0.9729 0.0871 1 0 1 0.7032
2 643 529 670 556 42839 22.6 46.8 2.4 1 395.6 6.6 643 529 670 556 51088 75.2 40.5 5.8 1 426.6 9.8 101 0.6689 -1.6989983 0.4 99 0.7232 1.3828 0.9729 0.0871 1 0 1 0.308
3 637 985 664 1012 175091 669.7 336.7 73.2 1 397.7 6.3 637 985 664 1012 184051 685.2 320.3 51.3 1 434.9 10.4 163 1 0.0066213 1 99 0.7232 1.3828 0.9729 0.0871 1 0 1 1.0046
4 627 1431 654 1458 343914 1698.4 557 165.5 1 400.1 7.3 627 1431 654 1458 343088 1642.7 527.2 128.5 1 435.7 9 166 1 0.0877343 1 99 0.7232 1.3828 0.9729 0.0871 1 0 1 1.0627
5 648 137 675 164 265602 1088 727.6 120 1 397.5 6.4 648 137 675 164 235478 887.8 543.1 73.3 1 430.2 8.8 177 1 0.3329663 1 99 0.7232 1.3828 0.9729 0.0871 1 0 1 1.2596
6 642 585 669 612 193699 880.7 426.9 99.1 1 392.1 5.7 642 585 669 612 213008 974.6 430.3 79.6 1 424.1 8.9 151 1 -0.1067153 1 99 0.7232 1.3828 0.9729 0.0871 1 0 1 0.9287
7 636 1041 663 1068 159352 573.6 365.2 60.8 1 399.7 6.7 636 1041 663 1068 195201 758.4 483.5 63.3 1 432.4 8.5 163 1 -0.3634573 1 99 0.7232 1.3828 0.9729 0.0871 1 0 1 0.7773
8 626 1487 653 1514 182055 689.7 184.1 68.2 1 401.6 7.1 626 1487 653 1514 224585 895.3 227.1 62.6 1 441.2 11.1 166 1 -0.3369743 1 99 0.7232 1.3828 0.9729 0.0871 1 0 1 0.7917
9 648 193 675 220 460095 2143.7 1214.7 230.4 1 397.6 6.7 648 193 675 220 322301 1342 754.4 113.7 1 429.6 8.4 177 1 0.7151913 1 99 0.7232 1.3828 0.9729 0.0871 1 0 1 1.6417
10 641 641 668 668 203139 956.1 533.4 102.5 1 393.7 6.4 641 641 668 668 212472 983.8 508.6 85 1 422.6 8 151 1 -0.0015883 1 99 0.7232 1.3828 0.9729 0.0871 1 0 1 0.9989
11 635 1096 662 1123 462175 2416 1004 261.8 1 395.6 6.4 635 1096 662 1123 358002 1765.8 626.3 162.1 1 425.9 6.9 163 1 0.4919043 1 99 0.7232 1.3828 0.9729 0.0871 1 0 1 1.4063
12 625 1542 652 1569 228384 986.7 455.5 97.6 1 403.6 7.1 625 1542 652 1569 249317 1066.9 470.9 85.6 1 437.6 8.5 166 1 -0.0730903 1 99 0.7232 1.3828 0.9729 0.0871 1 0 1 0.9506
13 647 249 674 276 206493 788.8 356.8 86.3 1 395.8 6.5 647 249 674 276 186224 639.3 307 54 1 427.8 8.5 177 1 0.3427823 1 99 0.7232 1.3828 0.9729 0.0871 1 0 1 1.2682
14 641 697 668 724 269817 1398.4 739 145 1 394.2 6.8 641 697 668 724 317445 1691.6 874.1 136.8 1 427 9.1 151 1 -0.2349753 1 99 0.7232 1.3828 0.9729 0.0871 1 0 1 0.8497
15 634 1152 661 1179 232157 1012.2 539.5 114 1 393.1 5.9 634 1152 661 1179 240705 1013.9 530.8 85.6 1 427.6 8.3 163 1 0.0370313 1 99 0.7232 1.3828 0.9729 0.0871 1 0 1 1.026
16 625 1598 652 1625 197896 775.5 228.3 76.8 1 403.5 7 625 1598 652 1625 232997 947.8 274 77.3 1 437.7 8.2 166 1 -0.2499943 1 99 0.7232 1.3828 0.9729 0.0871 1 0 1 0.8409
17 647 305 674 332 978528 5132.9 2440.6 561.6 1 395.8 6.5 647 305 674 332 862903 4458.2 2108.8 370.4 1 428.6 8.7 177 1 0.2429383 1 99 0.7232 1.3828 0.9729 0.0871 1 0 1 1.1834
18 640 753 667 780 149711 588.5 295 64.4 1 393.9 6.1 640 753 667 780 168944 674.6 343.1 53.4 1 430.7 9.5 151 1 -0.1574643 1 99 0.7232 1.3828 0.9729 0.0871 1 0 1 0.8966
19 634 1207 661 1234 106340 299 211.9 33.5 1 394 5.9 634 1207 661 1234 117711 340.1 232.9 29.2 1 426 8 153 0.9387 -0.1460843 1 99 0.7232 1.3828 0.9729 0.0871 1 0 1 0.9037
20 624 1653 651 1680 152570 602.2 370.2 57.7 1 403.5 7.5 624 1653 651 1680 184573 780.1 474.6 58.4 1 440.9 9.8 151 0.9096 -0.3338803 1 99 0.7232 1.3828 0.9729 0.0871 1 0 1 0.7934

Total number of rows: 7200

Table truncated, full table size 1252 Kbytes.




Supplementary file Size Download File type/resource
GSM28546.TIF.gz 10.3 Mb (ftp)(http) TIFF

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