|
| Status |
Public on Sep 02, 2008 |
| Title |
Microbeam Control 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 treatment control cells cultured samely as microbeam irradiated cells
|
| 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 |
