|
Status |
Public on Dec 31, 2008 |
Title |
HEK293-PITX2_vs_Ctrl_Std-rep1 |
Sample type |
RNA |
|
|
Channel 1 |
Source name |
HEK293 transfected with pEGFP-NFLAG-PITX2c
|
Organism |
Homo sapiens |
Characteristics |
Cell line: HEK293 Transfected with pEGFP-NFLAG-PITX2c
|
Treatment protocol |
Transient transfection of Pitx2
|
Growth protocol |
Hek293 cells grown in DMEM media
|
Extracted molecule |
total RNA |
Extraction protocol |
Total RNA isolated using TRI Reagent (Ambion)
|
Label |
Cy5
|
Label protocol |
Agilent QuickAmp labeling protocol with Cy5-CTP from Perkin Elmer
|
|
|
Channel 2 |
Source name |
HEK293 transfected with pEGFP-N1
|
Organism |
Homo sapiens |
Characteristics |
Cell line: HEK293 Transfected with pEGFP-N1
|
Treatment protocol |
Transient transfection of Pitx2
|
Growth protocol |
Hek293 cells grown in DMEM media
|
Extracted molecule |
total RNA |
Extraction protocol |
Total RNA isolated using TRI Reagent (Ambion)
|
Label |
Cy3
|
Label protocol |
Agilent QuickAmp labeling protocol with Cy3-CTP from Perkin Elmer
|
|
|
|
Hybridization protocol |
825 ng of each Cy3- and Cy5-labeled cRNA in Agilent Hi RPM hybridization solution; 17 hours at 65 degree Celcius
|
Scan protocol |
Scanned on an Agilent DNA Microarray scanner Quantification using Agilent Feature Extraction v. 9.5.
|
Description |
PITX2 overexpressed HEK293 cells vs control (mock transfected HEK293 cells). Standard (control on channel 2), biological replicate 1 of 4.
|
Data processing |
Lowess normalized, background subtracted log2 of sample signal / control signal. Agilent Feature Extraction software was used.
|
|
|
Submission date |
Oct 15, 2008 |
Last update date |
Oct 16, 2008 |
Contact name |
James Denvir |
E-mail(s) |
denvir@marshall.edu
|
Organization name |
Marshall University School of Medicine
|
Department |
Biochemistry and Microbiology
|
Lab |
Genomics and Bioinformatics Core Facility
|
Street address |
One John Marshall Drive
|
City |
Huntington |
State/province |
WV |
ZIP/Postal code |
25755 |
Country |
USA |
|
|
Platform ID |
GPL4133 |
Series (1) |
GSE13216 |
Expression profile of PITX2 overexpressed HEK293 cells |
|
Data table header descriptions |
ID_REF |
|
VALUE |
log base 2 of sample/control |
PositionX |
Standard column from Feature Extraction output |
PositionY |
Standard column from Feature Extraction output |
LogRatio |
Standard column from Feature Extraction output |
LogRatioError |
Standard column from Feature Extraction output |
PValueLogRatio |
Standard column from Feature Extraction output |
gSurrogateUsed |
Standard column from Feature Extraction output |
rSurrogateUsed |
Standard column from Feature Extraction output |
gIsFound |
Standard column from Feature Extraction output |
rIsFound |
Standard column from Feature Extraction output |
gProcessedSignal |
Standard column from Feature Extraction output |
rProcessedSignal |
Standard column from Feature Extraction output |
gProcessedSigError |
Standard column from Feature Extraction output |
rProcessedSigError |
Standard column from Feature Extraction output |
gNumPixOLHi |
Standard column from Feature Extraction output |
rNumPixOLHi |
Standard column from Feature Extraction output |
gNumPixOLLo |
Standard column from Feature Extraction output |
rNumPixOLLo |
Standard column from Feature Extraction output |
gNumPix |
Standard column from Feature Extraction output |
rNumPix |
Standard column from Feature Extraction output |
gMeanSignal |
Standard column from Feature Extraction output |
rMeanSignal |
Standard column from Feature Extraction output |
gMedianSignal |
Standard column from Feature Extraction output |
rMedianSignal |
Standard column from Feature Extraction output |
gPixSDev |
Standard column from Feature Extraction output |
rPixSDev |
Standard column from Feature Extraction output |
gPixNormIQR |
Standard column from Feature Extraction output |
rPixNormIQR |
Standard column from Feature Extraction output |
gBGNumPix |
Standard column from Feature Extraction output |
rBGNumPix |
Standard column from Feature Extraction output |
gBGMeanSignal |
Standard column from Feature Extraction output |
rBGMeanSignal |
Standard column from Feature Extraction output |
gBGMedianSignal |
Standard column from Feature Extraction output |
rBGMedianSignal |
Standard column from Feature Extraction output |
gBGPixSDev |
Standard column from Feature Extraction output |
rBGPixSDev |
Standard column from Feature Extraction output |
gBGPixNormIQR |
Standard column from Feature Extraction output |
rBGPixNormIQR |
Standard column from Feature Extraction output |
gNumSatPix |
Standard column from Feature Extraction output |
rNumSatPix |
Standard column from Feature Extraction output |
gIsSaturated |
Standard column from Feature Extraction output |
rIsSaturated |
Standard column from Feature Extraction output |
PixCorrelation |
Standard column from Feature Extraction output |
BGPixCorrelation |
Standard column from Feature Extraction output |
gIsFeatNonUnifOL |
Standard column from Feature Extraction output |
rIsFeatNonUnifOL |
Standard column from Feature Extraction output |
gIsBGNonUnifOL |
Standard column from Feature Extraction output |
rIsBGNonUnifOL |
Standard column from Feature Extraction output |
gIsFeatPopnOL |
Standard column from Feature Extraction output |
rIsFeatPopnOL |
Standard column from Feature Extraction output |
gIsBGPopnOL |
Standard column from Feature Extraction output |
rIsBGPopnOL |
Standard column from Feature Extraction output |
IsManualFlag |
Standard column from Feature Extraction output |
gBGSubSignal |
Standard column from Feature Extraction output |
rBGSubSignal |
Standard column from Feature Extraction output |
gBGSubSigError |
Standard column from Feature Extraction output |
rBGSubSigError |
Standard column from Feature Extraction output |
BGSubSigCorrelation |
Standard column from Feature Extraction output |
gIsPosAndSignif |
Standard column from Feature Extraction output |
rIsPosAndSignif |
Standard column from Feature Extraction output |
gPValFeatEqBG |
Standard column from Feature Extraction output |
rPValFeatEqBG |
Standard column from Feature Extraction output |
gNumBGUsed |
Standard column from Feature Extraction output |
rNumBGUsed |
Standard column from Feature Extraction output |
gIsWellAboveBG |
Standard column from Feature Extraction output |
rIsWellAboveBG |
Standard column from Feature Extraction output |
gBGUsed |
Standard column from Feature Extraction output |
rBGUsed |
Standard column from Feature Extraction output |
gBGSDUsed |
Standard column from Feature Extraction output |
rBGSDUsed |
Standard column from Feature Extraction output |
IsNormalization |
Standard column from Feature Extraction output |
gDyeNormSignal |
Standard column from Feature Extraction output |
rDyeNormSignal |
Standard column from Feature Extraction output |
gDyeNormError |
Standard column from Feature Extraction output |
rDyeNormError |
Standard column from Feature Extraction output |
DyeNormCorrelation |
Standard column from Feature Extraction output |
ErrorModel |
Standard column from Feature Extraction output |
xDev |
Standard column from Feature Extraction output |
gSpatialDetrendIsInFilteredSet |
Standard column from Feature Extraction output |
rSpatialDetrendIsInFilteredSet |
Standard column from Feature Extraction output |
gSpatialDetrendSurfaceValue |
Standard column from Feature Extraction output |
rSpatialDetrendSurfaceValue |
Standard column from Feature Extraction output |
SpotExtentX |
Standard column from Feature Extraction output |
SpotExtentY |
Standard column from Feature Extraction output |
gNetSignal |
Standard column from Feature Extraction output |
rNetSignal |
Standard column from Feature Extraction output |
gMultDetrendSignal |
Standard column from Feature Extraction output |
rMultDetrendSignal |
Standard column from Feature Extraction output |
gProcessedBackground |
Standard column from Feature Extraction output |
rProcessedBackground |
Standard column from Feature Extraction output |
gProcessedBkngError |
Standard column from Feature Extraction output |
rProcessedBkngError |
Standard column from Feature Extraction output |
IsUsedBGAdjust |
Standard column from Feature Extraction output |
gInterpolatedNegCtrlSub |
Standard column from Feature Extraction output |
rInterpolatedNegCtrlSub |
Standard column from Feature Extraction output |
gIsInNegCtrlRange |
Standard column from Feature Extraction output |
rIsInNegCtrlRange |
Standard column from Feature Extraction output |
gIsUsedInMD |
Standard column from Feature Extraction output |
rIsUsedInMD |
Standard column from Feature Extraction output |