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Sample GSM139295 Query DataSets for GSM139295
Status Public on Oct 31, 2006
Title SRF No Treatment, replicate 2, array a Jurkat cells
Sample type other
 
Channel 1
Source name SRF ChIP DNA from Jurkat, no treatment
Organism Homo sapiens
Characteristics ChIP enriched DNA from Jurkat cells, Antibody :Santa Cruz sc-335
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 control, 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 -1.56E-01 6.41E-02 1.53E-02 3.69E+03 2.58E+03 7.33E+01 6.94E+01 0 0 1 0 28 28 2.37E+02 2.65E+02 235 266 1.70E+01 2.72E+01 229 229 4.45E+01 6.59E+01 44 66 3.60E+00 6.30E+00 0 0 0 0 0.273909 -0.0639631 0 0 0 0 0 0 0 1 0 161.765 190.816 3.21634 5.13946 0 1 1 2.02E-28 6.62E-25 1 1 1 1 75.4497 73.6837 3.59655 6.29513 0 3685.89 2575.85 73.286 69.3782 0 1 0 0
2 0.00E+00 4.44E-01 1.00E+00 8.30E+01 8.33E+01 3.37E+01 2.06E+01 1 0 0 0 30 30 7.60E+01 7.51E+01 75 75 8.11E+00 8.35E+00 202 202 4.48E+01 6.56E+01 45 66 3.64E+00 6.17E+00 0 0 0 0 0.139114 0.0788105 0 0 0 0 0 0 0 1 0 0.423392 1.37648 1.48051 1.52431 0 0 0 0.779996 0.391265 1 1 0 0 75.5433 73.7569 3.64334 6.17385 0 9.6472 18.5813 33.7342 20.5769 0 1 1 1
3 5.42E-02 6.36E-02 3.94E-01 2.16E+03 2.45E+03 4.77E+01 5.00E+01 1 0 0 1 30 30 1.70E+02 2.55E+02 170.5 255 1.15E+01 2.03E+01 215 215 4.51E+01 6.47E+01 45 65 3.37E+00 6.39E+00 0 0 0 0 -0.144406 0.0320441 0 0 0 0 0 0 0 0 0 94.7675 181.242 2.09191 3.70149 0 1 1 6.74E-29 5.93E-30 1 1 1 1 75.6325 73.8248 3.37363 6.38794 1 2159.32 2446.61 47.6652 49.9668 0 1 0 0
4 -2.20E-01 7.81E-02 4.89E-03 1.06E+03 6.41E+02 3.88E+01 2.35E+01 1 0 0 0 31 31 1.22E+02 1.21E+02 123 120 9.49E+00 9.69E+00 181 181 4.51E+01 6.47E+01 45 64 3.20E+00 6.71E+00 0 0 0 0 0.0512864 0.131772 0 0 0 0 0 0 0 0 0 46.6916 47.5201 1.705 1.74058 0 1 1 3.02E-23 1.18E-24 1 1 1 1 75.7278 73.8992 3.195 6.71204 0 1063.89 641.48 38.8494 23.4963 0 1 0 0
5 -6.56E-02 6.56E-02 3.17E-01 1.78E+03 1.53E+03 5.93E+01 5.02E+01 1 0 0 0 29 29 1.54E+02 1.87E+02 152 188 1.40E+01 2.00E+01 211 211 4.52E+01 6.45E+01 45 64 4.00E+00 6.93E+00 0 0 0 0 0.494046 0.0610248 0 0 0 0 0 0 0 0 0 78.1492 113.413 2.60422 3.72001 0 1 1 4.07E-23 1.93E-23 1 1 1 1 75.8164 73.9659 3.99988 6.92697 0 1780.67 1530.98 59.3385 50.2169 0 1 0 0
6 -1.06E-01 9.79E-02 2.77E-01 5.46E+02 4.27E+02 2.97E+01 2.75E+01 0 0 1 1 28 28 9.99E+01 1.06E+02 99.5 103 6.89E+00 1.08E+01 200 200 4.53E+01 6.45E+01 45 64 3.46E+00 6.34E+00 0 0 0 0 0.0123127 0.0276788 0 0 0 0 0 0 0 0 0 23.9574 31.652 1.30193 2.03933 0 1 1 2.60E-17 1.65E-15 1 1 1 1 75.8997 74.0266 3.45829 6.34038 1 545.881 427.274 29.665 27.5292 0 1 0 0
7 1.03E-01 6.34E-02 1.06E-01 2.56E+03 3.25E+03 6.68E+01 7.62E+01 0 0 0 0 30 30 1.88E+02 3.15E+02 186.5 312.5 1.60E+01 3.09E+01 223 223 4.49E+01 6.42E+01 45 64 3.28E+00 6.30E+00 0 0 0 0 0.301373 -0.000238299 0 0 0 0 0 0 0 0 0 112.475 240.437 2.92973 5.64276 0 1 1 1.36E-26 6.74E-28 1 1 1 1 75.992 74.0967 3.28146 6.30295 1 2562.79 3245.68 66.7553 76.1724 0 1 0 0
8 0.00E+00 4.40E-01 1.00E+00 8.52E+01 8.28E+01 2.73E+01 1.84E+01 2 0 0 0 28 28 7.48E+01 7.58E+01 74.5 77 6.34E+00 7.23E+00 207 207 4.48E+01 6.45E+01 45 65 3.74E+00 6.14E+00 0 0 0 0 0.122128 -0.134184 0 0 0 0 0 0 0 0 0 -1.25284 1.66553 1.1975 1.3667 0 0 0 0.314878 0.253178 1 1 0 0 76.0743 74.1559 3.74022 6.13661 0 -28.5465 22.4832 27.2856 18.4492 0 1 0 0
9 -4.60E-02 6.36E-02 4.70E-01 2.41E+03 2.17E+03 8.40E+01 5.14E+01 0 1 0 0 31 31 1.82E+02 2.35E+02 184 230 2.05E+01 2.12E+01 213 213 4.53E+01 6.43E+01 45 64 3.89E+00 6.63E+00 0 0 0 0 0.436169 -0.0730186 0 0 0 0 0 0 0 0 0 105.973 160.914 3.68803 3.80513 0 1 1 1.61E-23 8.54E-29 1 1 1 1 76.1563 74.2147 3.88876 6.63167 0 2414.64 2172.2 84.0337 51.3659 0 1 0 0
10 4.26E-02 3.79E-01 9.11E-01 9.30E+01 1.03E+02 2.68E+01 1.58E+01 2 1 1 1 25 25 7.79E+01 8.19E+01 76 82 5.88E+00 5.85E+00 211 211 4.48E+01 6.43E+01 44 64 4.08E+00 6.47E+00 0 0 0 0 -0.252671 0.107402 0 0 0 0 0 0 0 0 0 1.63582 7.60065 1.17519 1.1695 0 0 1 0.187104 9.47E-07 1 1 0 0 76.2442 74.2794 4.08201 6.47389 0 37.2729 102.602 26.7772 15.7872 0 1 0 0
11 -1.94E-01 6.63E-02 3.43E-03 2.56E+03 1.63E+03 6.02E+01 6.29E+01 1 1 0 0 28 28 1.89E+02 1.95E+02 184 190.5 1.40E+01 2.46E+01 207 207 4.48E+01 6.45E+01 45 64 3.41E+00 6.18E+00 0 0 0 0 0.205168 0.0268839 0 0 0 0 0 0 0 0 0 112.169 121.086 2.642 4.656 0 1 1 1.60E-26 7.81E-21 1 1 1 1 76.331 74.3425 3.41323 6.18319 0 2555.83 1634.56 60.1993 62.852 0 1 0 0
12 0.00E+00 4.51E-01 1.00E+00 7.93E+01 8.46E+01 2.72E+01 1.69E+01 2 1 0 1 28 28 7.99E+01 7.25E+01 78.5 73 6.31E+00 6.61E+00 202 202 4.50E+01 6.41E+01 45 64 3.16E+00 6.27E+00 0 0 0 0 -0.112975 -0.0120249 0 0 0 0 0 0 0 0 0 3.4783 -1.86642 1.19339 1.24985 0 1 0 0.00768749 0.168123 1 1 0 0 76.4146 74.4021 3.16306 6.26749 0 79.2547 -25.195 27.192 16.8719 0 1 0 0
13 -4.02E-01 1.35E-01 2.95E-03 4.90E+02 1.94E+02 5.52E+01 2.50E+01 0 1 0 0 29 29 9.80E+01 8.89E+01 95 90 1.30E+01 9.97E+00 217 217 4.48E+01 6.43E+01 45 65 3.66E+00 6.10E+00 0 0 0 0 -0.0296627 0.0400778 0 0 0 0 0 0 0 0 0 21.4941 14.3935 2.4227 1.85079 0 1 1 1.17E-09 1.52E-08 1 1 1 0 76.5059 74.4686 3.6585 6.10002 0 489.754 194.299 55.2023 24.9841 0 1 0 0
14 -1.10E-02 6.80E-02 8.72E-01 1.27E+03 1.24E+03 4.82E+01 3.34E+01 0 0 0 0 30 30 1.33E+02 1.67E+02 130.5 166 1.16E+01 1.36E+01 197 197 4.49E+01 6.41E+01 45 64 3.53E+00 6.07E+00 0 0 0 0 0.026859 0.10412 0 0 0 0 0 0 0 0 0 55.938 92.0674 2.11602 2.47544 0 1 1 3.63E-22 5.82E-27 1 1 1 1 76.5953 74.5326 3.52688 6.07334 1 1274.58 1242.83 48.2146 33.4163 0 1 0 0
15 6.29E-03 8.26E-02 9.39E-01 6.58E+02 6.68E+02 4.27E+01 3.54E+01 1 0 0 1 28 28 1.06E+02 1.24E+02 105 123 9.90E+00 1.39E+01 212 212 4.51E+01 6.44E+01 45 64 3.80E+00 5.77E+00 0 0 0 0 0.020725 -0.0181181 0 0 0 0 0 0 0 0 0 28.8934 49.4813 1.87184 2.6206 0 1 1 3.89E-15 1.98E-17 1 1 1 1 76.678 74.5901 3.80353 5.76979 1 658.35 667.954 42.6508 35.3758 0 1 0 0
16 -7.08E-02 1.92E-01 7.13E-01 2.18E+02 1.85E+02 1.85E+01 2.12E+01 1 0 1 0 28 28 8.63E+01 8.84E+01 86 89 4.29E+00 8.30E+00 194 194 4.56E+01 6.41E+01 46 65 3.41E+00 6.48E+00 0 0 0 0 -0.0543787 -0.0747131 0 0 0 0 0 0 0 0 0 9.56107 13.7102 0.810078 1.56788 0 1 1 1.01E-12 1.43E-09 1 1 1 0 76.7604 74.6469 3.40814 6.47832 1 217.854 185.076 18.458 21.165 0 1 0 0
17 -3.29E-02 9.20E-02 7.21E-01 5.55E+02 5.15E+02 2.91E+01 3.39E+01 2 0 0 0 27 27 1.01E+02 1.13E+02 100 112 6.64E+00 1.31E+01 200 200 4.53E+01 6.29E+01 45.5 62 3.95E+00 5.84E+00 0 0 0 0 -0.00182577 -0.0221557 0 0 0 0 0 0 0 0 0 24.3744 38.1445 1.27694 2.51191 0 1 1 1.60E-17 9.90E-15 1 1 1 1 76.8478 74.7073 3.94943 5.83963 1 555.384 514.918 29.0957 33.9086 0 1 0 0
18 -4.12E-01 1.04E-01 7.33E-05 7.57E+02 2.93E+02 4.22E+01 2.69E+01 1 1 0 0 28 28 1.10E+02 9.65E+01 109.5 94 9.80E+00 1.05E+01 197 197 4.48E+01 6.42E+01 45 64 4.07E+00 6.05E+00 0 0 0 0 -0.228953 0.00894486 0 0 0 0 0 0 0 0 0 33.2429 21.7328 1.85168 1.98906 0 1 1 7.02E-17 1.15E-11 1 1 1 1 76.9357 74.7672 4.07047 6.05254 0 757.456 293.374 42.1914 26.8505 0 1 0 0
19 1.63E-01 2.11E-01 4.41E-01 1.49E+02 2.17E+02 2.99E+01 2.28E+01 1 0 0 0 28 28 8.36E+01 9.09E+01 83 90 6.94E+00 8.93E+00 205 205 4.53E+01 6.37E+01 45 64 3.43E+00 6.04E+00 0 0 0 0 -0.120088 -0.0412109 0 0 0 0 0 0 0 0 0 6.55713 16.1091 1.31075 1.6879 0 1 1 3.20E-05 2.30E-10 1 1 0 1 77.0143 74.8195 3.42629 6.04199 0 149.407 217.459 29.8661 22.7852 0 1 0 0
20 -3.00E-02 8.15E-02 7.12E-01 7.08E+02 6.61E+02 3.73E+01 3.21E+01 1 0 0 0 31 31 1.08E+02 1.24E+02 108 125 9.13E+00 1.32E+01 177 177 4.58E+01 6.39E+01 46 64 3.09E+00 4.71E+00 0 0 0 0 0.143924 -0.00722076 0 0 0 0 0 0 0 0 0 31.0675 48.9344 1.63897 2.37479 0 1 1 1.47E-18 1.21E-19 1 1 1 1 77.0938 74.8721 3.08871 4.70942 1 707.887 660.571 37.3448 32.0575 0 1 0 0

Total number of rows: 43963

Table truncated, full table size 15485 Kbytes.




Supplementary file Size Download File type/resource
GSM139295.txt.gz 10.1 Mb (ftp)(http) TXT

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