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Sample GSM139293 Query DataSets for GSM139293
Status Public on Oct 31, 2006
Title SRF No Treatment, replicate 1, array a Jurkat cells
Sample type other
 
Channel 1
Source name SRF ChIP DNA from Jurkat
Organism Homo sapiens
Characteristics anti-SRF antibody sc-335, 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 No treatment, 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 GPL4089
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

Data table
ID_REF VALUE LogRatioError PValueLogRatio gProcessedSignal rProcessedSignal gProcessedSigError rProcessedSigError gNumPixOLHi rNumPixOLHi gNumPixOLLo rNumPixOLLo gNumPix rNumPix gMeanSignal rMeanSignal gMedianSignal rMedianSignal gPixSDev rPixSDev gBGNumPix rBGNumPix gBGMeanSignal rBGMeanSignal gBGMedianSignal rBGMedianSignal gBGPixSDev rBGPixSDev gNumSatPix rNumSatPix gIsSaturated rIsSaturated PixCorrelation BGPixCorrelation gIsFeatNonUnifOL rIsFeatNonUnifOL gIsBGNonUnifOL rIsBGNonUnifOL gIsFeatPopnOL rIsFeatPopnOL gIsBGPopnOL rIsBGPopnOL IsManualFlag gBGSubSignal rBGSubSignal gBGSubSigError rBGSubSigError BGSubSigCorrelation gIsPosAndSignif rIsPosAndSignif gPValFeatEqBG rPValFeatEqBG gNumBGUsed rNumBGUsed gIsWellAboveBG rIsWellAboveBG gBGUsed rBGUsed gBGSDUsed rBGSDUsed IsNormalization gDyeNormSignal rDyeNormSignal gDyeNormError rDyeNormError DyeNormCorrelation ErrorModel gIsInNegCtrlRange rIsInNegCtrlRange
1 -3.14E-01 8.20E-02 1.28E-04 1.62E+03 7.87E+02 5.18E+01 2.81E+01 1 0 0 0 29 29 2.00E+02 1.27E+02 197 128 2.16E+01 1.06E+01 231 231 4.77E+01 7.15E+01 48 71 4.32E+00 9.04E+00 0 0 0 0 -0.0276941 -0.0149014 0 0 0 0 1 1 0 1 0 125.314 55.1763 4.00296 1.97089 0 1 1 1.82E-23 4.09E-24 1 1 1 1 74.2033 71.6513 4.32281 9.03658 0 1622.24 787.343 51.82 28.1238 0 1 0 0
2 0.00E+00 6.31E-01 1.00E+00 6.56E+01 1.07E+02 2.00E+01 1.84E+01 1 1 0 0 26 26 7.93E+01 7.48E+01 80 73 7.89E+00 6.56E+00 217 217 4.72E+01 7.14E+01 47 71 3.72E+00 7.50E+00 0 0 0 0 0.515886 -0.0875017 0 0 0 0 0 0 0 1 0 5.0687 3.15924 1.54698 1.28625 0 1 0 0.0032787 0.0288758 1 1 0 0 74.239 71.6869 3.72301 7.49717 0 65.6165 45.081 20.0263 18.3542 0 1 1 1
3 -2.93E-02 7.25E-02 6.86E-01 1.43E+03 1.33E+03 5.62E+01 4.33E+01 0 0 0 0 29 29 1.85E+02 1.65E+02 187 163 2.34E+01 1.63E+01 194 194 4.78E+01 7.64E+01 47 75.5 4.32E+00 9.82E+00 0 0 0 0 0.216518 0.180243 0 0 0 0 0 0 0 1 0 110.276 93.5201 4.34492 3.03333 0 1 1 5.61E-21 1.56E-24 1 1 1 1 74.2758 71.7213 4.32226 9.82272 1 1427.57 1334.49 56.2468 43.2844 0 1 0 0
4 7.72E-02 8.60E-02 3.69E-01 8.12E+02 9.70E+02 3.32E+01 4.49E+01 0 0 0 0 30 30 1.37E+02 1.40E+02 135 140.5 1.41E+01 1.72E+01 201 201 4.76E+01 8.99E+01 48 90 3.61E+00 1.65E+01 0 0 0 0 0.272767 0.0494207 0 0 0 0 0 0 0 1 0 62.7537 68.009 2.56543 3.14795 0 1 1 4.08E-21 9.63E-22 1 1 1 1 74.313 71.7577 3.60521 16.4674 0 812.373 970.46 33.2106 44.92 0 1 0 0
5 -8.06E-02 7.99E-02 3.13E-01 1.15E+03 9.58E+02 4.05E+01 3.36E+01 0 1 0 1 28 28 1.63E+02 1.39E+02 165.5 138 1.65E+01 1.24E+01 213 213 4.76E+01 6.88E+01 47 69 3.81E+00 6.93E+00 0 0 0 0 -0.123321 -0.0191075 0 0 0 0 0 0 0 1 0 89.0417 67.1009 3.12666 2.35272 0 1 1 7.65E-22 1.20E-22 1 1 1 1 74.3512 71.792 3.80925 6.92976 0 1152.68 957.501 40.476 33.5723 0 1 0 0
6 -1.91E-01 1.55E-01 2.20E-01 4.63E+02 2.99E+02 2.46E+01 2.02E+01 3 1 0 0 28 28 1.10E+02 9.28E+01 108 93.5 1.01E+01 7.49E+00 208 208 4.92E+01 6.79E+01 49 68 3.98E+00 5.84E+00 0 0 0 0 -0.0441721 -0.0339475 0 0 0 0 0 0 1 1 0 35.7886 20.9254 1.89963 1.4148 0 1 1 2.23E-17 2.83E-15 1 1 1 1 74.39 71.8246 3.9817 5.84002 0 463.298 298.597 24.5916 20.1886 0 1 0 0
7 5.69E-02 6.90E-02 4.10E-01 1.60E+03 1.82E+03 6.81E+01 1.03E+02 0 0 0 0 31 31 1.98E+02 2.00E+02 202 197 2.93E+01 4.02E+01 149 149 5.17E+01 6.48E+01 49 64 8.66E+00 8.23E+00 0 0 0 0 0.478934 0.343812 0 0 0 0 0 0 1 0 0 123.538 127.753 5.26062 7.22565 0 1 1 3.09E-21 1.55E-17 1 1 1 1 74.4293 71.8602 8.65904 8.23214 1 1599.26 1822.98 68.101 103.107 0 1 0 0
8 0.00E+00 6.10E-01 1.00E+00 7.90E+01 9.69E+01 1.32E+01 1.93E+01 0 0 0 0 30 30 7.59E+01 7.49E+01 77.5 76.5 5.58E+00 7.42E+00 181 181 5.01E+01 6.44E+01 49 63 6.10E+00 6.79E+00 0 0 0 0 -0.0527863 0.192932 0 0 0 0 0 0 1 0 0 1.39764 3.0077 1.01905 1.35473 0 0 0 0.217226 0.0443627 1 1 0 0 74.469 71.8923 6.10089 6.78771 0 18.0931 42.9186 13.1921 19.3314 0 1 0 0
9 -1.34E-01 7.35E-02 6.92E-02 1.61E+03 1.18E+03 6.36E+01 4.32E+01 0 1 0 0 30 30 1.99E+02 1.55E+02 196.5 156 2.69E+01 1.66E+01 197 197 4.81E+01 6.46E+01 48 64 4.04E+00 5.73E+00 0 0 0 0 0.365057 -0.0151218 0 0 0 0 0 0 0 0 0 123.991 82.7091 4.91228 3.02954 0 1 1 2.32E-21 1.16E-22 1 1 1 1 74.509 71.9242 4.03981 5.7322 0 1605.12 1180.22 63.5915 43.2303 0 1 0 0
10 3.17E-01 6.78E-01 6.40E-01 5.35E+01 1.11E+02 2.64E+01 2.86E+01 3 0 0 0 27 27 7.85E+01 7.97E+01 79 80 1.06E+01 1.04E+01 204 204 4.81E+01 6.50E+01 48 65 4.13E+00 6.29E+00 0 0 0 0 -0.364812 0.0677177 0 0 0 0 0 0 0 0 0 3.93169 7.78247 2.03836 2.00113 0 0 1 0.0668271 0.000702651 1 1 0 0 74.5498 71.9583 4.13327 6.2921 0 50.8974 111.053 26.3874 28.5553 0 1 0 0
11 -1.10E-01 7.06E-02 1.19E-01 1.80E+03 1.40E+03 6.92E+01 4.27E+01 0 0 0 0 30 30 2.14E+02 1.70E+02 210.5 171 2.93E+01 1.64E+01 194 194 4.81E+01 6.64E+01 48 66.5 3.85E+00 6.35E+00 0 0 0 0 -0.00569549 0.0480356 0 0 0 0 0 0 0 1 0 139.176 97.9748 5.34482 2.99174 0 1 1 1.01E-21 4.23E-25 1 1 1 1 74.591 71.9919 3.85296 6.35132 0 1801.69 1398.06 69.1909 42.6909 0 1 0 0
12 0.00E+00 7.95E-01 1.00E+00 4.81E+01 9.05E+01 1.42E+01 2.20E+01 1 0 0 0 30 30 7.72E+01 7.06E+01 76 69.5 6.03E+00 8.46E+00 195 195 4.61E+01 6.63E+01 46 66 3.72E+00 6.34E+00 0 0 0 0 0.0634144 -0.105574 0 0 0 0 0 0 0 1 0 2.53434 -1.39078 1.10077 1.54509 0 0 0 0.0322112 0.393832 1 1 0 0 74.6323 72.0241 3.71608 6.34251 0 32.8081 -19.8459 14.2499 22.0479 0 1 0 0
13 -3.28E-01 1.89E-01 8.31E-02 4.29E+02 2.02E+02 2.20E+01 3.35E+01 3 1 0 0 27 27 1.08E+02 8.62E+01 108 82 8.81E+00 1.22E+01 186 186 4.71E+01 6.61E+01 47 66 3.18E+00 6.14E+00 0 0 0 0 -0.13815 -0.0641534 0 0 0 0 0 0 0 1 0 33.1398 14.1258 1.69635 2.34675 0 1 1 2.36E-17 2.34E-06 1 1 1 0 74.675 72.0594 3.17962 6.13557 0 429.008 201.569 21.96 33.4871 0 1 0 0
14 6.35E-02 8.88E-02 4.74E-01 7.73E+02 8.95E+02 4.81E+01 3.60E+01 0 0 0 0 30 30 1.34E+02 1.35E+02 132 134 2.03E+01 1.38E+01 194 194 4.76E+01 6.62E+01 48 66 3.67E+00 6.06E+00 0 0 0 0 0.169106 0.0726142 0 0 0 0 0 0 0 1 0 59.7153 62.7061 3.71443 2.52455 0 1 1 4.81E-16 1.01E-21 1 1 1 1 74.7181 72.0939 3.67119 6.05833 0 773.039 894.79 48.0848 36.0242 0 1 0 0
15 4.59E-02 1.38E-01 7.40E-01 4.06E+02 4.52E+02 1.83E+01 2.77E+01 1 0 0 0 27 27 1.06E+02 1.04E+02 105 104 7.36E+00 1.01E+01 202 202 4.86E+01 6.59E+01 48 66 4.49E+00 6.00E+00 0 0 0 0 0.132122 0.163237 0 0 0 0 0 0 0 1 0 31.3875 31.6523 1.41693 1.93949 0 1 1 2.78E-19 9.67E-16 1 1 1 1 74.7606 72.1255 4.4915 6.00265 0 406.325 451.664 18.3428 27.6758 0 1 0 0
16 -1.37E-01 2.98E-01 6.45E-01 2.13E+02 1.55E+02 1.61E+01 2.54E+01 1 0 0 0 28 28 9.13E+01 8.30E+01 91 83 6.56E+00 9.41E+00 204 204 4.88E+01 6.60E+01 49 66 4.70E+00 6.96E+00 0 0 0 0 0.0850319 -0.0182009 0 0 0 0 0 0 0 1 0 16.4466 10.8789 1.24044 1.77764 0 1 1 6.61E-14 1.59E-06 1 1 1 0 74.8034 72.1568 4.69619 6.95712 1 212.908 155.237 16.058 25.3662 0 1 0 0
17 -1.64E-01 1.79E-01 3.60E-01 3.81E+02 2.62E+02 2.33E+01 1.44E+01 0 0 0 2 27 27 1.04E+02 9.05E+01 104 90 9.33E+00 5.26E+00 202 202 4.77E+01 6.67E+01 48 66.5 3.80E+00 6.11E+00 0 0 0 0 -0.0839661 -0.0422405 0 0 0 0 0 0 0 1 0 29.4488 18.3283 1.79649 1.01185 0 1 1 1.71E-15 1.57E-18 1 1 1 1 74.8474 72.1902 3.80321 6.10729 0 381.228 261.537 23.2564 14.4387 0 1 0 0
18 -3.82E-01 1.77E-01 3.14E-02 4.91E+02 2.04E+02 3.35E+01 1.99E+01 0 0 0 0 32 32 1.13E+02 8.65E+01 112 85 1.46E+01 7.90E+00 197 197 4.83E+01 6.64E+01 48 66 4.52E+00 6.89E+00 0 0 0 0 -0.0365646 0.0479882 0 0 0 0 0 0 0 1 0 37.9205 14.2763 2.58658 1.39628 0 1 1 1.20E-15 6.96E-12 1 1 1 0 74.892 72.2237 4.51522 6.88784 0 490.897 203.716 33.4844 19.9243 0 1 0 0
19 -3.58E-02 6.45E-01 9.56E-01 8.63E+01 7.95E+01 1.75E+01 2.43E+01 0 0 0 0 30 30 8.16E+01 7.66E+01 81 77 7.42E+00 9.32E+00 204 204 4.79E+01 6.50E+01 48 65 4.18E+00 5.57E+00 0 0 0 0 0.133758 0.0335832 0 0 0 0 0 0 0 0 0 6.6649 4.34707 1.35494 1.70098 0 1 0 3.53E-05 0.0180951 1 1 0 0 74.9351 72.2529 4.1787 5.56859 0 86.28 62.0308 17.5403 24.2723 0 1 0 0
20 -1.71E-01 1.50E-01 2.57E-01 4.71E+02 3.18E+02 2.62E+01 2.75E+01 0 0 0 0 30 30 1.11E+02 9.46E+01 110 93 1.11E+01 1.05E+01 196 196 4.82E+01 6.44E+01 48 65 4.11E+00 5.59E+00 0 0 0 0 0.265999 0.165629 0 0 0 0 0 0 0 0 0 36.3881 22.2844 2.0254 1.92604 0 1 1 1.47E-17 1.19E-12 1 1 1 1 74.9786 72.2822 4.1136 5.58587 0 471.06 317.99 26.2197 27.4837 0 1 0 0

Total number of rows: 43963

Table truncated, full table size 15485 Kbytes.




Supplementary file Size Download File type/resource
GSM139293.txt.gz 10.1 Mb (ftp)(http) TXT

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