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Sample GSM139305 Query DataSets for GSM139305
Status Public on Oct 31, 2006
Title SRF replicate 2, array a, CRL-1999 cells
Sample type other
 
Channel 1
Source name SRF ChIP DNA from CRL-1999 Smooth Muscle Cells
Organism Homo sapiens
Characteristics SRF ChIP enriched using Santa Cruz antibody sc-335
Extracted molecule other
Extraction protocol ChIP enriched DNA
Label alexa Fluor 647
 
Channel 2
Source name mock IP DNA CRL-1999 cells
Organism Homo sapiens
Characteristics Mock IP, no antibody control, sheared genomic DNA
Extracted molecule other
Label Alexa fluor 555
 
 
Description Agilent Array CGH hybridization and wash buffers, following protocol as directed.
Data processing Agilent Feature Extraction 8.5
 
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 -4.75E-02 6.27E-02 4.49E-01 2.76E+03 2.47E+03 5.50E+01 6.85E+01 0 1 0 0 29 29 3.00E+02 2.90E+02 298 295 2.32E+01 3.26E+01 231 231 4.62E+01 6.41E+01 46 63 4.03E+00 6.18E+00 0 0 0 0 0.0611377 0.0532836 0 0 0 0 0 0 0 0 0 215.834 218.489 4.3046 6.05063 0 1 1 4.20E-29 3.66E-25 1 1 1 1 84.1664 71.3731 4.02772 6.17946 0 2758.68 2473.1 55.0193 68.4878 0 1 0 0
2 0.00E+00 5.14E-01 1.00E+00 4.98E+01 7.10E+01 1.74E+01 1.06E+01 1 3 0 1 25 25 8.73E+01 7.22E+01 87 72 6.81E+00 4.69E+00 207 207 4.65E+01 6.37E+01 46 63 3.90E+00 6.28E+00 0 0 0 0 0.0799465 -0.0746645 0 0 0 0 0 0 0 0 0 3.09284 0.835137 1.36201 0.93858 0 0 0 0.0348276 0.425116 1 1 0 0 84.1872 71.4049 3.89505 6.27502 0 39.5312 9.45302 17.4085 10.6239 0 1 1 1
3 -1.68E-01 6.58E-02 1.08E-02 2.03E+03 1.38E+03 3.19E+01 3.40E+01 0 0 0 0 28 28 2.43E+02 1.93E+02 244.5 196 1.32E+01 1.59E+01 219 219 4.61E+01 6.37E+01 46 63 3.34E+00 6.07E+00 0 0 0 0 0.19231 -0.173977 0 0 0 0 0 0 0 0 0 159.006 121.992 2.49304 3.00019 0 1 1 2.50E-31 2.38E-26 1 1 1 1 84.2084 71.4361 3.34237 6.07226 0 2032.34 1380.85 31.8648 33.9595 0 1 0 0
4 -1.16E-01 6.97E-02 9.68E-02 1.11E+03 8.51E+02 3.40E+01 4.64E+01 0 0 0 0 28 28 1.71E+02 1.47E+02 168.5 146 1.41E+01 2.17E+01 185 185 4.59E+01 6.34E+01 46 63 3.90E+00 5.68E+00 0 0 0 0 -0.237375 0.0245225 0 0 0 0 0 0 0 0 0 86.9495 75.2112 2.65775 4.0977 0 1 1 1.43E-23 6.27E-17 1 1 1 1 84.229 71.4674 3.9016 5.68341 0 1111.35 851.324 33.9701 46.3824 0 1 0 0
5 1.15E-01 6.34E-02 7.04E-02 2.30E+03 2.99E+03 4.71E+01 9.29E+01 0 0 0 0 30 30 2.64E+02 3.36E+02 260.5 340.5 2.02E+01 4.49E+01 204 204 4.66E+01 6.37E+01 46 63 3.65E+00 6.18E+00 0 0 0 0 0.135904 -0.0675004 0 0 0 0 0 0 0 0 0 179.65 264.169 3.68762 8.20391 0 1 1 1.50E-29 2.51E-24 1 1 1 1 84.2497 71.498 3.64575 6.18306 1 2296.2 2990.16 47.1333 92.8611 0 1 0 0
6 -1.13E-01 7.09E-02 1.10E-01 1.02E+03 7.89E+02 3.27E+01 4.00E+01 0 0 1 0 30 30 1.64E+02 1.41E+02 166 138.5 1.40E+01 1.94E+01 196 196 4.65E+01 6.38E+01 46 63 3.55E+00 6.14E+00 0 0 0 0 -0.168935 0.040942 0 0 0 0 0 0 0 0 0 80.0592 69.672 2.55574 3.5381 0 1 1 3.55E-24 1.41E-18 1 1 1 1 84.2741 71.528 3.54819 6.14386 0 1023.28 788.625 32.6662 40.0482 0 1 0 0
7 -9.76E-02 6.38E-02 1.26E-01 2.29E+03 1.83E+03 6.25E+01 5.40E+01 0 1 0 0 29 29 2.63E+02 2.33E+02 266 239 2.63E+01 2.57E+01 216 216 4.63E+01 6.26E+01 46 62 4.07E+00 6.47E+00 0 0 0 0 0.00529039 0.0220261 0 0 0 0 0 0 0 0 0 178.947 161.407 4.88807 4.77382 0 1 1 2.73E-25 1.74E-24 1 1 1 1 84.2942 71.5581 4.07479 6.46919 0 2287.22 1826.99 62.477 54.0354 0 1 0 0
8 0.00E+00 5.59E-01 1.00E+00 4.76E+01 6.27E+01 1.73E+01 1.36E+01 2 1 0 0 28 28 8.55E+01 7.09E+01 85 71 7.17E+00 6.37E+00 205 205 4.58E+01 6.33E+01 45 63 3.73E+00 5.54E+00 0 0 0 0 0.186346 0.0313703 0 0 0 0 0 0 0 0 0 1.14693 -0.730244 1.35545 1.20374 0 0 0 0.412769 0.567499 1 1 0 0 84.3174 71.5874 3.72605 5.53779 0 14.6595 -8.26572 17.3248 13.6252 0 1 0 0
9 -4.80E-02 6.58E-02 4.65E-01 1.39E+03 1.25E+03 3.41E+01 6.38E+01 0 0 0 0 32 32 1.93E+02 1.82E+02 192.5 179 1.51E+01 3.19E+01 207 207 4.58E+01 6.27E+01 46 63 3.28E+00 6.29E+00 0 0 0 0 -0.113746 0.0161783 0 0 0 0 0 0 0 0 0 109.002 110.196 2.66496 5.63658 0 1 1 8.57E-29 4.31E-19 1 1 1 1 84.3413 71.6162 3.27763 6.29102 0 1393.22 1247.32 34.0623 63.8011 0 1 0 0
10 -9.75E-02 4.25E-01 8.18E-01 8.10E+01 6.47E+01 2.16E+01 1.53E+01 0 0 0 0 30 30 9.07E+01 7.69E+01 88 73.5 9.24E+00 7.41E+00 192 192 4.58E+01 6.35E+01 46 64 3.99E+00 5.72E+00 0 0 0 0 -0.0219462 0.0606086 0 0 0 0 0 0 0 0 0 6.33714 5.28833 1.6871 1.35353 0 1 1 0.000836784 0.000670639 1 1 0 0 84.3629 71.645 3.98771 5.71755 1 80.9983 59.8592 21.5638 15.3207 0 1 0 0
11 4.42E-02 6.19E-02 4.76E-01 4.15E+03 4.59E+03 7.07E+01 1.64E+02 0 0 2 0 28 28 4.09E+02 4.78E+02 411.5 490 2.93E+01 7.69E+01 206 206 4.61E+01 6.21E+01 46 62 4.22E+00 5.79E+00 0 0 0 0 -0.160374 0.0290987 0 0 0 0 0 0 0 0 0 324.654 405.862 5.53045 14.5326 0 1 1 3.94E-30 1.79E-21 1 1 1 1 84.3819 71.6733 4.21521 5.79289 1 4149.57 4594 70.6876 164.496 0 1 0 0
12 0.00E+00 5.51E-01 1.00E+00 5.04E+01 6.11E+01 1.78E+01 1.41E+01 0 0 0 0 31 31 8.69E+01 7.17E+01 86 72 7.75E+00 6.91E+00 200 200 4.66E+01 6.33E+01 47 63 3.95E+00 5.40E+00 0 0 0 0 0.237537 -0.114394 0 0 0 0 0 0 0 0 0 2.46763 0.00866623 1.39179 1.24191 0 0 0 0.0916229 0.994715 1 1 0 0 84.4033 71.701 3.94626 5.39961 0 31.54 0.0980941 17.7892 14.0574 0 1 0 0
13 -2.14E-01 9.87E-02 3.04E-02 5.16E+02 3.16E+02 3.64E+01 2.09E+01 0 2 0 2 26 26 1.25E+02 9.96E+01 123 100.5 1.45E+01 9.42E+00 210 210 4.63E+01 6.31E+01 46 63 3.95E+00 6.11E+00 0 0 0 0 0.283009 -0.0589934 0 0 0 0 0 0 0 0 0 40.3875 27.8868 2.84417 1.84647 0 1 1 1.46E-13 1.29E-14 1 1 1 1 84.4202 71.7286 3.95037 6.11417 0 516.214 315.654 36.3528 20.9005 0 1 0 0
14 -1.91E-01 1.25E-01 1.29E-01 3.49E+02 2.25E+02 3.54E+01 1.38E+01 0 0 0 0 30 30 1.12E+02 9.16E+01 113 90.5 1.52E+01 6.68E+00 197 197 4.65E+01 6.34E+01 47 63 3.51E+00 6.00E+00 0 0 0 0 0.108391 0.0308953 0 0 0 0 0 0 0 0 0 27.2977 19.8778 2.76677 1.21909 0 1 1 8.27E-11 1.57E-17 1 1 1 1 84.4356 71.7555 3.5118 5.99929 0 348.906 224.999 35.3635 13.799 0 1 0 0
15 -1.10E-02 7.71E-02 8.86E-01 6.62E+02 6.45E+02 2.94E+01 2.81E+01 1 0 0 0 29 29 1.36E+02 1.29E+02 134 130 1.24E+01 1.34E+01 206 206 4.64E+01 6.19E+01 46 62 3.64E+00 5.51E+00 0 0 0 0 0.00505482 0.0713303 0 0 0 0 0 0 0 0 0 51.7858 57.0113 2.30156 2.48214 0 1 1 1.07E-19 3.63E-20 1 1 1 1 84.4556 71.7818 3.63908 5.51134 1 661.901 645.318 29.4174 28.0957 0 1 0 0
16 2.24E-01 1.14E-01 5.00E-02 2.48E+02 4.15E+02 2.32E+01 2.94E+01 0 0 0 0 32 32 1.04E+02 1.08E+02 101.5 109 1.03E+01 1.47E+01 192 192 4.64E+01 6.23E+01 46 62 3.72E+00 5.50E+00 0 0 0 0 0.390386 0.0279523 0 0 0 0 0 0 0 0 0 19.3998 36.6612 1.81601 2.59341 0 1 1 5.03E-12 2.76E-15 1 1 1 1 84.4752 71.8075 3.72216 5.50313 0 247.958 414.973 23.2113 29.3551 0 1 0 0
17 -1.99E-01 8.71E-02 2.26E-02 6.42E+02 4.07E+02 2.66E+01 3.17E+01 0 0 0 0 29 29 1.35E+02 1.08E+02 132 104 1.12E+01 1.51E+01 213 213 4.54E+01 6.33E+01 45 63 3.76E+00 6.74E+00 0 0 0 0 0.231748 -0.0231276 0 0 0 0 0 0 0 0 0 50.2675 35.9259 2.07949 2.80159 0 1 1 1.30E-20 1.87E-13 1 1 1 1 84.4911 71.8327 3.76068 6.7364 0 642.495 406.649 26.579 31.7115 0 1 0 0
18 -1.37E-01 4.07E-01 7.37E-01 8.83E+01 6.45E+01 1.96E+01 1.25E+01 0 0 0 0 29 29 9.14E+01 7.76E+01 92 77 8.28E+00 5.93E+00 207 207 4.64E+01 6.25E+01 46 62 3.79E+00 5.35E+00 0 0 0 0 -0.181729 0.0660416 0 0 0 0 0 0 0 0 0 6.90893 5.6945 1.53732 1.10037 0 1 1 0.000118339 2.19E-05 1 1 0 0 84.5049 71.8572 3.79403 5.35053 1 88.3066 64.4567 19.6492 12.4552 0 1 0 0
19 -1.95E-01 3.53E-01 5.81E-01 1.09E+02 6.94E+01 2.26E+01 1.46E+01 0 1 1 2 25 25 9.30E+01 7.62E+01 91 77 8.86E+00 6.44E+00 214 214 4.59E+01 6.28E+01 46 62 4.12E+00 6.14E+00 0 0 0 0 -0.15132 0.0667053 0 0 0 0 0 0 0 0 0 8.51659 4.27879 1.77152 1.288 0 1 1 7.01E-05 0.00365746 1 1 0 0 84.5234 71.8812 4.12486 6.13512 1 108.855 48.4322 22.6427 14.579 0 1 0 0
20 3.07E-01 8.10E-02 1.49E-04 4.69E+02 9.51E+02 2.26E+01 4.65E+01 1 0 1 0 27 27 1.21E+02 1.56E+02 120 156 9.19E+00 2.13E+01 200 200 4.59E+01 6.23E+01 46 62 3.77E+00 5.60E+00 0 0 0 0 0.124262 0.0608719 0 0 0 0 0 0 0 0 0 36.6802 84.0213 1.76894 4.10508 0 1 1 4.51E-18 1.04E-17 1 1 1 1 84.5421 71.9046 3.76967 5.59522 0 468.828 951.048 22.6098 46.4658 0 1 0 0

Total number of rows: 43963

Table truncated, full table size 15488 Kbytes.




Supplementary file Size Download File type/resource
GSM139305.txt.gz 10.1 Mb (ftp)(http) TXT

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