|
| Status |
Public on Dec 21, 2006 |
| Title |
ZHBTc4(Tc+), 0hr, #1(16011321000070) |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
ZHBTc4(Tc+), 0hr, #1
|
| Organism |
Mus musculus |
| Characteristics |
embryonic stem cell 129/Ola male gene knock in
|
| Biomaterial provider |
Dr. Hitoshi Niwa, Laboratory for Pluripotent Cell Studies,RIKEN Center for Developmental Biology,2-2-3 Minatojima-minamimachi,Chu-o-ku, Kobe 6500047,Japan. E-mail: niwa@cdb.riken.jp
|
| Growth protocol |
The cells were derived from CGR8 ES cells and carry the transgenes for tetracycline-regulatable Oct-3/4 expression as described previously (Niwa et al., nature genetics 2000). 500000 cells were seeded on gelatinized 90 mm dish in ES medium with or without 1 uM tetracycline.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
see Niwa et al. nature genetics, 24(2000) 372-376.
|
| Label |
Cy3
|
| |
|
| Channel 2 |
| Source name |
ZHBTc4(Tc+), 120hr, #1
|
| Organism |
Mus musculus |
| Characteristics |
embryonic stem cell 129/Ola male gene knock in
|
| Biomaterial provider |
Dr. Hitoshi Niwa, Laboratory for Pluripotent Cell Studies,RIKEN Center for Developmental Biology,2-2-3 Minatojima-minamimachi,Chu-o-ku, Kobe 6500047,Japan. E-mail: niwa@cdb.riken.jp
|
| Treatment protocol |
Tet inducible system
|
| Growth protocol |
The cells were derived from CGR8 ES cells and carry the transgenes for tetracycline-regulatable Oct-3/4 expression as described previously (Niwa et al., nature genetics 2000). 500000 cells were seeded on gelatinized 90 mm dish in ES medium with or without 1 uM tetracycline.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
see Niwa et al. nature genetics, 24(2000) 372-376.
|
| Label |
Cy5
|
| |
|
| |
| Description |
ZHBTc4(Tc+), 120hr
|
| 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 |
Sep 28, 2006 |
| Last update date |
Dec 21, 2006 |
| Contact name |
Minoru S.H. Ko |
| E-mail(s) |
kom@mail.nih.gov
|
| Phone |
410-558-8359
|
| Organization name |
NIH
|
| Department |
National Institute on Aging
|
| Lab |
Lab of Genetics
|
| Street address |
251 Bayview Blvd, Suite 100, 10C
|
| City |
Baltimore |
| State/province |
MD |
| ZIP/Postal code |
21224 |
| Country |
USA |
| |
|
| Platform ID |
GPL870 |
| Series (1) |
| GSE5936 |
Dissecting Oct3/4-regulated gene networks in embryonic stem cells by 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 |
log(REDsignal/GREENsignal) per feature |
| 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 |
| IsUsedBGAdjust |
A boolean used to flag features used for computation of global BG offset |
| 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 |
