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Sample GSM226688 Query DataSets for GSM226688
Status Public on Sep 02, 2008
Title Microbeam sham 6 h B
Sample type RNA
 
Source name Normal human fibroblast cells
Organism Homo sapiens
Characteristics AG01522D primary normal human diploid fibroblasts were obtained and routinely passaged as previously described (N. Hamada et al. LET-dependent survival of irradiated normal human fibroblasts and their descendents, Radiat. Res. 166 (2006) 24-30).
Extracted molecule total RNA
Extraction protocol RNeasy Mini Kit (QIAGEN)
Label Cy3
Label protocol Agilent Low RNA Input Linear Amplification Kit
 
Hybridization protocol according to standard Agilent protocol
Scan protocol Scanned on an Agilent G2565BA scanner. Images were quantified using Agilent Feature Extraction Software (version 9.1).
Description no irradiated cells with sham microbeam irradiation, harvested at 6 h postirradiatin
Data processing Signals were calculated by the Agilent Feature Extraction software and automatically underwent Lowess normalization.
 
Submission date Sep 03, 2007
Last update date Aug 14, 2011
Contact name Kaori Imadome
Organization name National institute of radiological sciences
Department Research Center of Charged Particle Therapy
Lab RadGenomics Project
Street address Anagawa 4-9-1
City Chiba
State/province Chiba
ZIP/Postal code 2658333
Country Japan
 
Platform ID GPL4133
Series (1)
GSE8993 Normal human fibroblast cell line bystander effects by Carbon ion irradiation

Data table header descriptions
ID_REF Agilent feature number
VALUE Processed Cy3 Signal
gProcessedSigError Standard error of propagated feature signal, per channel
gSurrogateUsed The green surrogate value used
gIsFound A boolean used to flag found (strong) features. The flag is applied independently in each channel
gNumPixOLHi Number of outlier pixels per feature with intensity > upper threshold set via the pixel outlier rejection method
gNumPixOLLo Number of outlier pixels per feature with intensity < lower threshold set via the pixel outlier rejection method
gNumPix Total number of pixels used to compute feature statistics; ie. total number of inlier pixels/per spot; same in both channels
gMeanSignal Raw mean signal of feature in green channel (inlier pixels)
gMedianSignal Median local background signal (local to corresponding feature) computed per channel (inlier pixels)
gPixSDev Standard deviation of all inlier pixels per feature; this is computed independently in each channel
gBGNumPix Total number of pixels used to compute local BG statistics per spot; ie. total number of BG inlier pixels; same in both channels
gBGMeanSignal Mean local background signal (local to corresponding feature) computed per channel (inlier pixels)
gBGMedianSignal Median local background signal (local to corresponding feature) computed per channel (inlier pixels)
gBGPixSDev Standard deviation of all inlier pixels per local BG of each feature, computed independently in each channel
gNumSatPix Total number of saturated pixels per feature, computed per channel
gIsSaturated Boolean flag indicating if a feature is saturated or not. A feature is saturated IF 50% of the pixels in a feature are above the saturation threshold
gIsLowPMTScaledUp Reports if the feature signal value is from the scaled-up low signal image or from the high signal image
gIsFeatNonUnifOL Boolean flag indicating if a feature is a NonUniformity Outlier or not. A feature is non-uniform if the pixel noise of feature exceeds a threshold established for a uniform feature
gIsBGNonUnifOL The same concept as above but in case of background
gIsFeatPopnOL Boolean flag indicating if a feature is a Population Outlier or not. Probes with replicate features on a microarray are examined using population statistics
gIsBGPopnOL The same concept as above but in case of background
IsManualFlag Boolean is manual flag
gBGSubSignal Background-subtracted signal
gBGSubSigError Propagated standard error as computed on net g(r) background subtracted signal
gIsPosAndSignif Boolean flag, established via a 2-sided t-test, indicates if the mean signal of a feature is greater than the corresponding background (selected by user) and if this difference is significant
gPValFeatEqBG P-value from t-test of significance between g(r) Mean signal and g(r) background (selected by user)
gNumBGUsed Background used to subtract from the MeanSignal; variable also used in t-test
gIsWellAboveBG Boolean flag indicating if a feature is WellAbove Background or not
gBGUsed Background used to subtract fromthe MeanSignal; variable also used in t-test
gBGSDUsed Standard deviation of background used in g(r) channel; variable also used in t-test and surrogate algorithms
ErrorModel Indicates the error model that you chose for feature extraction or that the software uses if you have chosen the most conservative option
IsUsedBGAdjust Boolean used to flag features used for computation of global BG offset

Data table
ID_REF VALUE gProcessedSigError gSurrogateUsed gIsFound gNumPixOLHi gNumPixOLLo gNumPix gMeanSignal gMedianSignal gPixSDev gBGNumPix gBGMeanSignal gBGMedianSignal gBGPixSDev gNumSatPix gIsSaturated gIsLowPMTScaledUp gIsFeatNonUnifOL gIsBGNonUnifOL gIsFeatPopnOL gIsBGPopnOL IsManualFlag gBGSubSignal gBGSubSigError gIsPosAndSignif gPValFeatEqBG gNumBGUsed gIsWellAboveBG gBGUsed gBGSDUsed ErrorModel IsUsedBGAdjust
1 2.50E+05 2.50E+04 0 1 0 0 63 2.08E+05 206296 1.55E+04 660 3.82E+01 38 9.13E+00 0 0 1 0 0 0 0 0 207587 20758.7 1 0 1 1 43.572 9.12645 1 0
2 3.04E+01 3.03E+01 30.4321 1 3 1 62 3.65E+01 35.5 7.94E+00 515 4.03E+01 40 8.32E+00 0 0 0 0 0 1 0 0 -7.13691 25 0 0.459213 1 0 43.653 8.3229 1 0
3 3.06E+01 3.05E+01 30.6086 0 0 0 65 4.38E+01 43 8.88E+00 522 4.08E+01 40.5 7.73E+00 0 0 0 0 0 0 0 0 0.0859287 25 0 0.992883 1 0 43.7295 7.72764 1 0
4 3.08E+01 3.06E+01 30.7576 0 1 0 67 4.33E+01 44 8.73E+00 520 4.07E+01 40 8.10E+00 0 0 0 0 0 0 0 0 -0.434171 25 0 0.96405 1 0 43.7775 8.09614 1 0
5 3.09E+01 3.07E+01 30.8902 0 0 0 64 4.37E+01 43.5 1.03E+01 520 4.12E+01 41 8.22E+00 0 0 0 0 0 0 0 0 -0.0870423 25 0 0.99279 1 0 43.8214 8.22458 1 0
6 3.10E+01 3.09E+01 31.0041 0 2 0 62 4.43E+01 44 7.82E+00 524 4.07E+01 41 7.96E+00 0 0 0 0 0 0 0 0 0.428536 25 0 0.964517 1 0 43.894 7.95856 1 0
7 3.11E+01 3.10E+01 31.0976 0 1 0 63 4.29E+01 42 8.74E+00 521 4.06E+01 40 7.78E+00 0 0 0 0 0 0 0 0 -1.0975 25 0 0.909294 1 0 43.9864 7.77735 1 0
8 3.12E+01 3.10E+01 31.1754 0 1 0 68 4.33E+01 42.5 9.37E+00 499 4.08E+01 40 7.77E+00 0 0 0 0 0 0 0 0 -0.807569 25 0 0.933189 1 0 44.0576 7.77114 1 0
9 3.12E+01 3.11E+01 31.2345 0 1 0 64 4.54E+01 44 9.51E+00 523 4.08E+01 41 7.24E+00 0 0 0 0 0 0 0 0 1.33455 25.0004 0 0.889817 1 0 44.1029 7.24439 1 0
10 3.13E+01 3.11E+01 31.2777 0 1 0 61 4.52E+01 44 8.27E+00 531 4.05E+01 40 7.98E+00 0 0 0 0 0 0 0 0 1.03414 25.0002 0 0.91451 1 0 44.1462 7.98421 1 0
11 3.13E+01 3.12E+01 31.3049 0 2 1 61 4.31E+01 43 6.81E+00 525 3.99E+01 39 7.70E+00 0 0 0 0 0 0 0 0 -1.01942 25 0 0.915722 1 0 44.167 7.69817 1 0
12 6.51E+02 7.21E+01 0 1 0 0 64 5.66E+02 560.5 8.75E+01 519 3.99E+01 40 7.39E+00 0 0 0 0 0 0 0 0 521.744 57.8547 1 1.70E-94 1 1 44.2246 7.38543 1 0
13 1.22E+02 3.35E+01 0 1 2 0 62 1.42E+02 139 2.29E+01 535 4.06E+01 40 7.42E+00 0 0 0 0 0 0 0 0 97.5964 26.8375 1 2.14E-18 1 0 44.2907 7.41651 1 0
14 1.36E+03 1.39E+02 0 1 0 0 64 1.13E+03 1104.5 1.98E+02 522 4.04E+01 40 7.46E+00 0 0 0 0 0 0 0 0 1089.18 111.75 1 2.94E-137 1 1 44.3216 7.45978 1 0
15 4.03E+01 3.14E+01 0 0 1 0 63 7.67E+01 76 1.60E+01 522 4.02E+01 39.5 7.83E+00 0 0 0 0 0 0 0 0 32.3601 25.2086 1 0.000991721 1 0 44.386 7.83407 1 0
16 2.64E+04 2.64E+03 0 1 0 0 66 2.13E+04 20638.7 3.20E+03 514 4.16E+01 41 8.02E+00 0 0 1 0 0 0 0 0 21207.4 2120.89 1 1.36448e-313 1 1 44.4457 8.02226 1 0
17 3.12E+01 3.11E+01 31.1804 1 2 0 64 5.52E+01 54.5 1.09E+01 521 4.04E+01 40 7.27E+00 0 0 0 0 0 0 0 0 10.6813 25.0228 0 0.268578 1 0 44.4906 7.2664 1 0
18 3.66E+02 4.80E+01 0 1 2 0 62 3.40E+02 340 4.61E+01 521 4.05E+01 41 7.37E+00 0 0 0 0 0 0 0 0 295.76 38.7265 1 2.25E-63 1 1 44.5465 7.36601 1 0
19 1.18E+05 1.18E+04 0 1 0 0 69 9.51E+04 91470.5 1.45E+04 519 4.02E+01 40 7.81E+00 0 0 1 0 0 0 0 0 95082.1 9508.24 1 0 1 1 44.6098 7.81397 1 0
20 3.10E+01 3.08E+01 30.965 1 0 0 69 5.25E+01 52 1.10E+01 518 3.97E+01 39 7.71E+00 0 0 0 0 0 0 0 0 7.83151 25.0123 0 0.416785 1 0 44.6757 7.70878 1 0

Total number of rows: 45015

Table truncated, full table size 6588 Kbytes.




Supplementary file Size Download File type/resource
GSM226688.txt.gz 6.5 Mb (ftp)(http) TXT
Processed data included within Sample table

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