|
Status |
Public on Oct 31, 2006 |
Title |
SRF No Treatment, replicate 1, array b Jurkat cells |
Sample type |
other |
|
|
Channel 1 |
Source name |
SRF ChIP DNA from Jurkat, no treatment
|
Organism |
Homo sapiens |
Characteristics |
ChIP enriched sample Antibody: SRF Santa Cruz sc-335 From Jurkat cells
|
Extracted molecule |
other |
Extraction protocol |
ChIP enriched DNA
|
Label |
Alexa Fluor 647
|
|
|
Channel 2 |
Source name |
Mock IP DNA Jurkat cells
|
Organism |
Homo sapiens |
Characteristics |
Mock IP, no antibody, Sheared genomic DNA
|
Extracted molecule |
other |
Extraction protocol |
sheared genomic DNA
|
Label |
Alexa fluor 555
|
|
|
|
Description |
followed agilent hybridization and wash conditions for Array CGH
|
Data processing |
Feature Extraction 8.5 Agilent
|
|
|
Submission date |
Oct 09, 2006 |
Last update date |
Oct 11, 2006 |
Contact name |
Sara Cooper |
Organization name |
Stanford University
|
Department |
Genetics
|
Street address |
300 Pasteur Drive
|
City |
Stanford |
State/province |
CA |
ZIP/Postal code |
94305 |
Country |
USA |
|
|
Platform ID |
GPL4090 |
Series (1) |
GSE5998 |
Identification of SRF binding sites in Three Human Cell types |
|
Data table header descriptions |
ID_REF |
|
VALUE |
log 2 ratio |
LogRatioError |
error of log ratio |
PValueLogRatio |
p-value |
gProcessedSignal |
green processed signal |
rProcessedSignal |
red processed signal |
gProcessedSigError |
green processed signal error |
rProcessedSigError |
red processed signal error |
gNumPixOLHi |
pixel outlier g high |
rNumPixOLHi |
pixel outlier r high |
gNumPixOLLo |
pixel outlier g low |
rNumPixOLLo |
pixel outlier r low |
gNumPix |
green number of pixels |
rNumPix |
red number of pixels |
gMeanSignal |
green mean signal (raw) |
rMeanSignal |
red mean signal (raw) |
gMedianSignal |
green median signal |
rMedianSignal |
red median signal |
gPixSDev |
green pixel standard deviation |
rPixSDev |
red pixel standard deviation |
gBGNumPix |
green background number pixelsq |
rBGNumPix |
red background number pixels |
gBGMeanSignal |
green background signal (mean) |
rBGMeanSignal |
red background signal (mean) |
gBGMedianSignal |
green background signal (median) |
rBGMedianSignal |
red background signal (median) |
gBGPixSDev |
green background pixel SD |
rBGPixSDev |
red background pixel SD |
gNumSatPix |
green saturated pixels |
rNumSatPix |
red saturated pixels |
gIsSaturated |
green spot is saturated (flag) |
rIsSaturated |
red spot is saturated (Flag) |
PixCorrelation |
pixel correlation |
BGPixCorrelation |
background pixel correlation |
gIsFeatNonUnifOL |
green nonuniformity outlier |
rIsFeatNonUnifOL |
red nonuniformity outlier |
gIsBGNonUnifOL |
green background nonuniformity outlier |
rIsBGNonUnifOL |
red background nonuniformity outlier |
gIsFeatPopnOL |
green feature population outlier |
rIsFeatPopnOL |
red feature population outlier |
gIsBGPopnOL |
green background population outlier |
rIsBGPopnOL |
red background population outlier |
IsManualFlag |
manual flag |
gBGSubSignal |
background subtracted signal |
rBGSubSignal |
red background subtraction signal |
gBGSubSigError |
background subtracted signal error |
rBGSubSigError |
red background subtracted signal error |
BGSubSigCorrelation |
background subtracted signal correlation |
gIsPosAndSignif |
flag is significant and positive |
rIsPosAndSignif |
red flag is significant and positive |
gPValFeatEqBG |
green pval |
rPValFeatEqBG |
red pval |
gNumBGUsed |
green number background used |
rNumBGUsed |
red number background used |
gIsWellAboveBG |
green is well above background flag |
rIsWellAboveBG |
red is well above background flag |
gBGUsed |
green background used |
rBGUsed |
red background used |
gBGSDUsed |
green background SD used |
rBGSDUsed |
red background SD used |
IsNormalization |
normalized |
gDyeNormSignal |
green dye normalized signal |
rDyeNormSignal |
red dye normalized signal |
gDyeNormError |
green dye normalized error |
rDyeNormError |
red dye normalized error |
DyeNormCorrelation |
dye normalized correlation |
ErrorModel |
error model |
gIsInNegCtrlRange |
green is in negative control range |
rIsInNegCtrlRange |
red is in negative control range |