|
| Status |
Public on Jul 08, 2006 |
| Title |
NF55-control-HL-1 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
NF55-HL-control
|
| Organism |
Xenopus laevis |
| Characteristics |
Total RNA isolated from hindlimb of indicated treatment group of NF Stage 55 (premetamorphic) tadpoles
|
| Biomaterial provider |
Biswajit,Das
|
| Treatment protocol |
Nontransgenic siblings of F1 progeny Xenopus laevis tadpoles (NF55) containing thyroid receptor dominant negative receptor (expressed with muscle specific promoter) were treated with 50µg doxycycline hyclate for 2weeks in 0.1xMMR solution. This treatment served as control group for transgenic siblings. Total RNA was isolated from dissected hindlimbs.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
standard method using TRIZOL reagent
|
| Label |
Cy3
|
| Label protocol |
Agilent Low RNA Input Fluorescent Linear Amplification Protocol
|
| |
|
| Channel 2 |
| Source name |
Universal mRNA
|
| Organism |
Xenopus laevis |
| Characteristics |
Universal mRNA extracted from whole body of unknown sex Xenopus laevis tadpoles from NF50-66
|
| Biomaterial provider |
Biswajit,Das
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
mRNAs were extracted with QuickPrep Micro mRNA Purification Kit from Amersham
|
| Label |
Cy5
|
| Label protocol |
Agilent Low RNA Input Fluorescent Linear Amplification Protocol
|
| |
|
| |
| Hybridization protocol |
Agilent 60-mer oligo microarray processing protocol (SSC Wash/SureHyb Chamber set-up) V4.1, April 2004. Agilent Publication Number: G4140-90030 V4.1 APRIL 2004. The manual can be found at https://www.chem.agilent.com/scripts/literaturePDF.asp?iWHID=34961, or through a WEB search on the manual title.
|
| Scan protocol |
Scanned using Agilent microarray scanner
|
| Description |
NF55-control-HL-1
|
| Data processing |
Data are extracted with Agilent Feature Extraction Software.The data were further processed with NIA ANOVA tool utilities.See http://lgsun.grc.nia.nih.gov/ANOVA for details.
|
| |
|
| Submission date |
Jul 03, 2006 |
| Last update date |
Mar 09, 2007 |
| Contact name |
Biswajit Das |
| E-mail(s) |
dasbiswa@mail.nih.gov
|
| Organization name |
National Institutes of Health/National Institute of Child Health and Human Development
|
| Department |
Laboratory of Gene Regulation and Development
|
| Lab |
Section on Molecular Morphogenesis
|
| Street address |
18 Library Drive, Building 18T, Room 106
|
| City |
Bethesda |
| State/province |
MD |
| ZIP/Postal code |
20892 |
| Country |
USA |
| |
|
| Platform ID |
GPL3936 |
| Series (1) |
| GSE5249 |
Profiling limb muscle degeneration by inducible dominant negative thyroid hormone receptor transgene over-expression |
|
| Data table header descriptions |
| ID_REF |
Feature number |
| PositionX |
Found X coordinate of feature centroid in pixels |
| PositionY |
Found Y coordinate of feature centroid in pixels |
| VALUE |
-[INV_VALUE] |
| LogRatioError |
error of the log ratio calculated according to the error model chosen |
| PValueLogRatio |
Significance level of the Log Ratio computed for a feature |
| gSurrogateUsed |
The green surrogate value used |
| rSurrogateUsed |
The red surrogate value used |
| gIsFound |
A boolean used to flag found (strong) features.The flag is applied independently in each channel. A feature is considered found if the found spot centroid is within the bounds of the spot deviation limit with respect to corresponding nominal centroid. |
| rIsFound |
A boolean used to flag found (strong) features.The flag is applied independently in each channel. A feature is considered found if the found spot centroid is within the bounds of the spot deviation limit with respect to corresponding nominal centroid. |
| gProcessedSignal |
Dye-normalized signal after surrogate algorithm, green channel, used for computation of log ratio |
| rProcessedSignal |
Dye-normalized signal after surrogate algorithm, red channel, used for computation of log ratio |
| gProcessedSigError |
Standard error of propagated feature signal, green channel |
| rProcessedSigError |
Standard error of propagated feature signal, red channel |
| gNumPixOLHi |
Number of outlier pixels per feature with intensity > upper threshold set via the pixel outlier rejection method. The number is computed independently in each channel. These pixels are omitted from all subsequent calculations. |
| rNumPixOLHi |
Number of outlier pixels per feature with intensity > upper threshold set via the pixel outlier rejection method. The number is computed independently in each channel. These pixels are omitted from all subsequent calculations. |
| gNumPixOLLo |
Number of outlier pixels per feature with intensity < lower threshold set via the pixel outlier rejection method. The number is computed independently in each channel. NOTE: The pixel outlier method is the ONLY step that removes data in Feature Extraction. |
| rNumPixOLLo |
Number of outlier pixels per feature with intensity < lower threshold set via the pixel outlier rejection method. The number is computed independently in each channel. NOTE: The pixel outlier method is the ONLY step that removes data in Feature Extraction. |
| gNumPix |
Total number of pixels used to compute feature statistics; ie.total number of inlier pixels/per spot; same in both channels |
| rNumPix |
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) |
| rMeanSignal |
Raw mean signal of feature in red channel (inlier pixels) |
| gMedianSignal |
Raw median signal of feature in green channel (inlier pixels) |
| rMedianSignal |
Raw median signal of feature in red channel (inlier pixels) |
| gPixSDev |
Standard deviation of all inlier pixels per feature; this is computed independently in each channel |
| rPixSDev |
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 |
| rBGNumPix |
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) |
| rBGMeanSignal |
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) |
| rBGMedianSignal |
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 |
| rBGPixSDev |
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 |
| rNumSatPix |
Total number of saturated pixels per feature, computed per channel |
| gIsSaturated |
Boolean flag indicating if a feature is saturated or not |
| rIsSaturated |
Boolean flag indicating if a feature is saturated or not |
| PixCorrelation |
Ratio of estimated feature covariance in RedGreen space to product of feature Standard Deviation in Red Green space. |
| BGPixCorrelation |
Ratio of estimated background covariance in RedGreen space to product of background Standard Deviation in Red Green space. |
| gIsFeatNonUnifOL |
Boolean flag indicating if a feature is NonUniformity Outlier or not Green Channel |
| rIsFeatNonUnifOL |
Boolean flag indicating if a feature is NonUniformity Outlier or not Red Channel |
| gIsBGNonUnifOL |
Boolean flag indicating if background is NonUniformity Outlier or not Green Channel |
| rIsBGNonUnifOL |
Boolean flag indicating if background is NonUniformity Outlier or not Red Channel |
| gIsFeatPopnOL |
Boolean flag indicating if a feature is a Population Outlier or not for Green Channel. Probes with replicate features on a microarray are examined using population statistics |
| rIsFeatPopnOL |
Boolean flag indicating if a feature is a Population Outlier or not for Red Channe. Probes with replicate features on a microarray are examined using population statistics |
| gIsBGPopnOL |
Boolean flag indicating if background is a Population Outlier or not for Green Channel. |
| rIsBGPopnOL |
Boolean flag indicating if background is a Population Outlier or not for Red Channel. |
| IsManualFlag |
Manual Flag |
| gBGSubSignal |
The net g signal following the subtraction of the background from the raw mean g signal |
| rBGSubSignal |
The net r signal following the subtraction of the background from the raw mean r signal |
| gBGSubSigError |
Propagated standard error as computed on net g background subtracted signal |
| rBGSubSigError |
Propagated standard error as computed on net r background subtracted signal |
| BGSubSigCorrelation |
Ratio of estimated background subtracted feature signal covariance in RG space to product of background subtracted feature Standard Deviation in RG space |
| gIsPosAndSignif |
Boolean flag indicating if the mean signal of a feature is greater than the corresponding background (selected by user) and if this difference is significant |
| rIsPosAndSignif |
Boolean flag indicating 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 Mean signal and g background (selected by user) |
| rPValFeatEqBG |
P-value from t-test of significance between r Mean signal and r background (selected by user) |
| gNumBGUsed |
Number of local background regions or features used to calculate the background subtraction on this feature g channel. |
| rNumBGUsed |
Number of local background regions or features used to calculate the background subtraction on this feature r channel. |
| gIsWellAboveBG |
Boolean flag indicating if a feature is WellAbove Background or not |
| rIsWellAboveBG |
Boolean flag indicating if a feature is WellAbove Background or not |
| gBGUsed |
Background value (after global background adjust if turned ON) subtracted from the raw mean signal to generate the BG subtracted signal; this value is computed per channel. If global BG subtraction is used the column is identical for every feature in a given channel |
| rBGUsed |
Background value (after global background adjust if turned ON) subtracted from the raw mean signal to generate the BG subtracted signal; this value is computed per channel. If global BG subtraction is used the column is identical for every feature in a given channel |
| gBGSDUsed |
Standard deviation of background used in g channel |
| rBGSDUsed |
Standard deviation of background used in r channel |
| IsNormalization |
A boolean flag which indicates if a feature is used to measure dye bias |
| gDyeNormSignal |
The dye-normalized signal in the indicated channel |
| rDyeNormSignal |
The dye-normalized signal in the indicated channel |
| gDyeNormError |
The standard error associated with the dye normalized signal |
| rDyeNormError |
The standard error associated with the dye normalized signal |
| DyeNormCorrelation |
Dye-normalized red and green pixel correlation |
| ErrorModel |
Indicates the error model that you chose for Feature Extraction or that the software uses if you have chosen the ""Most Conservative"" option |
| xDev |
|
| INV_VALUE |
log10(REDsignal/GREENsignal) per feature (processed signals used) |
