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Sample GSM139298 Query DataSets for GSM139298
Status Public on Oct 31, 2006
Title SRF replicate 1, array b, Be(2)-C cells
Sample type other
 
Channel 1
Source name SRF ChIP DNA from Be(2)-C
Organism Homo sapiens
Characteristics ChIP enriched DNA, from Be(2)-C, neuronal cell line
Extracted molecule other
Extraction protocol ChIP enriched DNA
Label Alexa Fluor 647
 
Channel 2
Source name Mock IP DNA Be(2)-Ccells
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 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

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 2.97E-02 6.85E-02 6.65E-01 1.01E+03 1.09E+03 2.23E+01 5.46E+01 2 0 2 0 26 26 2.51E+02 1.38E+02 248 137.5 1.83E+01 1.74E+01 210 210 6.26E+01 6.64E+01 52 65.5 2.35E+01 8.36E+00 0 0 0 0 -0.0136447 0.553367 0 0 0 0 1 0 1 1 0 163.355 67.922 3.59498 3.41864 0 1 1 5.45E-32 2.87E-17 1 1 1 1 87.1448 69.8472 23.5001 8.35742 0 1013.69 1085.47 22.3084 54.6339 0 1 0 0
2 1.14E-02 1.68E-01 9.46E-01 2.00E+02 2.06E+02 1.45E+01 2.48E+01 1 2 0 0 28 28 1.19E+02 8.27E+01 119 81.5 1.24E+01 8.21E+00 178 178 8.38E+01 7.34E+01 83 72 2.03E+01 8.95E+00 0 0 0 0 0.442958 0.460378 0 0 0 0 1 1 1 1 0 32.2923 12.8727 2.33692 1.55146 0 1 1 3.60E-16 3.77E-09 1 1 0 0 87.1006 69.8416 20.2946 8.95396 0 200.387 205.721 14.5016 24.7941 0 1 1 1
3 -6.00E-03 7.97E-02 9.40E-01 6.29E+02 6.20E+02 2.24E+01 3.18E+01 0 3 0 0 28 28 1.88E+02 1.09E+02 189 108 1.91E+01 1.05E+01 189 189 6.90E+01 6.88E+01 67 67 1.63E+01 8.45E+00 0 0 0 0 0.232565 0.467315 0 0 0 0 0 0 1 1 0 101.343 38.8115 3.60938 1.98754 0 1 1 5.99E-24 6.94E-19 1 1 1 1 87.086 69.8314 16.2972 8.45436 1 628.875 620.252 22.3977 31.7632 0 1 0 0
4 -5.79E-02 1.26E-01 6.45E-01 3.09E+02 2.71E+02 1.40E+01 3.19E+01 1 0 0 0 29 29 1.37E+02 8.68E+01 140 87 1.22E+01 1.08E+01 185 185 6.83E+01 6.91E+01 67 68 1.73E+01 1.03E+01 0 0 0 0 0.152217 0.60812 0 0 0 0 0 0 1 1 0 49.8506 16.9407 2.25904 1.99671 0 1 1 3.60E-24 1.85E-09 1 1 1 0 87.0804 69.8179 17.3493 10.3078 1 309.345 270.733 14.0183 31.9097 0 1 0 0
5 -6.25E-02 9.48E-02 5.10E-01 4.74E+02 4.10E+02 1.65E+01 4.39E+01 1 0 0 0 28 28 1.63E+02 9.55E+01 164.5 94.5 1.41E+01 1.46E+01 193 193 6.88E+01 6.83E+01 69 68 1.63E+01 8.49E+00 0 0 0 0 0.00674825 0.458788 0 0 0 0 0 0 1 1 0 76.3065 25.6601 2.6628 2.74993 0 1 1 4.63E-26 4.18E-10 1 1 1 1 87.0506 69.8042 16.2694 8.48787 1 473.515 410.078 16.5238 43.9471 0 1 0 0
6 -6.17E-02 7.92E-02 4.36E-01 6.85E+02 5.95E+02 1.68E+01 3.84E+01 0 0 0 0 30 30 1.97E+02 1.07E+02 199 106 1.48E+01 1.31E+01 187 187 6.47E+01 6.77E+01 61 67 1.80E+01 8.93E+00 0 0 0 0 0.467215 0.488556 0 0 0 0 0 0 1 1 0 110.431 37.2047 2.70748 2.40067 0 1 1 1.29E-34 2.28E-16 1 1 1 1 87.0361 69.7953 18.0188 8.93338 1 685.27 594.575 16.8011 38.3655 0 1 0 0
7 -1.81E-01 6.48E-02 5.18E-03 3.18E+03 2.09E+03 4.73E+01 7.24E+01 0 0 0 0 29 29 5.99E+02 2.01E+02 597 198 4.11E+01 2.44E+01 193 193 5.48E+01 6.42E+01 51 63 1.17E+01 6.87E+00 0 0 0 0 0.12145 0.335484 0 0 0 0 0 0 1 1 0 512.185 131.076 7.63037 4.53142 0 1 1 5.06E-33 1.08E-22 1 1 1 1 87.0221 69.7863 11.7364 6.86553 0 3178.33 2094.74 47.3498 72.4174 0 1 0 0
8 -6.86E-02 2.43E-01 7.78E-01 1.46E+02 1.25E+02 2.34E+01 2.42E+01 1 1 0 1 28 28 1.11E+02 7.69E+01 109 77.5 2.00E+01 8.01E+00 200 200 5.46E+01 6.40E+01 50 63 1.23E+01 7.81E+00 0 0 0 0 0.408299 0.454503 0 0 0 0 0 0 1 1 0 23.5629 7.15138 3.77174 1.51442 0 1 1 1.10E-06 8.87E-05 1 1 0 0 87.0085 69.7772 12.2629 7.81339 0 146.218 114.287 23.4053 24.2022 0 1 0 0
9 1.60E-02 1.83E-01 9.30E-01 1.81E+02 1.88E+02 1.05E+01 3.20E+01 0 0 0 0 30 30 1.16E+02 8.15E+01 116.5 78 9.29E+00 1.10E+01 189 189 4.75E+01 6.06E+01 47 61 4.91E+00 5.81E+00 0 0 0 0 0.085543 0.120009 0 0 0 0 0 0 0 0 0 29.2047 11.7654 1.69611 2.00272 0 1 1 2.37E-17 2.35E-06 1 1 1 0 86.9953 69.768 4.90821 5.80664 1 181.228 188.024 10.5251 32.0058 0 1 0 0
10 -9.60E-02 1.09E-01 3.80E-01 3.93E+02 3.15E+02 2.27E+01 3.08E+01 0 0 0 0 29 29 1.50E+02 8.94E+01 156 91 1.97E+01 1.04E+01 190 190 5.26E+01 6.35E+01 48 63 1.17E+01 7.03E+00 0 0 0 0 0.408402 0.459192 0 0 0 0 0 0 1 1 0 63.2588 19.6896 3.66506 1.92762 0 1 1 3.71E-17 3.05E-11 1 1 1 1 86.9826 69.7587 11.7149 7.03098 1 392.548 314.663 22.7433 30.8057 0 1 0 0
11 1.30E-01 2.14E-01 5.45E-01 1.33E+02 1.79E+02 1.49E+01 2.47E+01 0 0 0 0 29 29 1.08E+02 8.10E+01 109 81 1.29E+01 8.33E+00 190 190 5.54E+01 6.47E+01 52 64 1.15E+01 8.27E+00 0 0 0 0 0.298574 0.521754 0 0 0 0 0 0 1 1 0 21.4606 11.2301 2.39427 1.54767 0 1 1 5.32E-10 5.89E-08 1 1 0 0 86.9187 69.7354 11.5203 8.26553 0 133.172 179.47 14.8575 24.7335 0 1 0 0
12 7.02E-02 6.31E-02 2.66E-01 2.27E+03 2.67E+03 4.83E+01 9.21E+01 0 0 0 0 29 29 4.53E+02 2.37E+02 458 236 4.19E+01 3.10E+01 189 189 7.08E+01 6.91E+01 69 69 1.58E+01 9.37E+00 0 0 0 0 0.430533 0.512267 0 0 0 0 0 0 1 1 0 366.112 167.107 7.77992 5.76512 0 1 1 5.57E-29 9.11E-23 1 1 1 1 86.8876 69.7209 15.8351 9.3691 1 2271.89 2670.56 48.2777 92.1334 0 1 0 0
13 1.54E-02 6.46E-02 8.11E-01 1.56E+03 1.62E+03 3.37E+01 6.41E+01 1 2 0 0 27 27 3.38E+02 1.71E+02 327 173 2.82E+01 2.09E+01 190 190 7.52E+01 7.12E+01 71 69.5 2.03E+01 9.64E+00 0 0 0 0 0.208026 0.606615 0 0 0 0 0 0 1 1 0 251.573 101.216 5.43397 4.01348 0 1 1 5.83E-29 2.00E-20 1 1 1 1 86.8719 69.7095 20.2835 9.64332 1 1561.12 1617.56 33.7201 64.1402 0 1 0 0
14 -3.02E-02 6.40E-02 6.37E-01 1.85E+03 1.73E+03 4.42E+01 7.91E+01 1 0 0 0 28 28 3.85E+02 1.78E+02 393.5 174 3.77E+01 2.62E+01 193 193 6.37E+01 6.59E+01 62 65 1.16E+01 6.77E+00 0 0 0 0 0.308866 0.317106 0 0 0 0 0 0 1 1 0 298.514 108.128 7.12812 4.9511 0 1 1 1.52E-26 7.25E-19 1 1 1 1 86.8428 69.6938 11.6164 6.76924 1 1852.41 1728.01 44.2331 79.1243 0 1 0 0
15 1.32E-02 6.58E-02 8.42E-01 1.32E+03 1.36E+03 4.13E+01 4.31E+01 3 3 0 0 27 27 3.00E+02 1.55E+02 297 155 3.46E+01 1.40E+01 180 180 6.34E+01 6.81E+01 60 67 1.51E+01 9.01E+00 0 0 0 0 -0.209628 0.317798 0 0 0 0 0 0 1 1 0 213.104 85.2931 6.65391 2.69931 0 1 1 3.74E-23 8.07E-24 1 1 1 1 86.7848 69.6699 15.1302 9.00777 1 1322.4 1363.08 41.2904 43.1381 0 1 0 0
16 -9.55E-02 2.24E-01 6.70E-01 1.64E+02 1.32E+02 1.23E+01 2.51E+01 0 0 0 0 31 31 1.13E+02 7.79E+01 111 78 1.11E+01 8.76E+00 185 185 5.46E+01 6.57E+01 53 65 9.94E+00 6.79E+00 0 0 0 0 0.00435889 0.186786 0 0 0 0 0 0 1 1 0 26.4478 8.24254 1.98744 1.57354 0 1 1 3.99E-15 1.51E-05 1 1 1 0 86.778 69.6607 9.94248 6.78655 1 164.12 131.725 12.3329 25.147 0 1 0 0
17 -1.49E-01 9.20E-02 1.05E-01 5.59E+02 3.97E+02 2.00E+01 3.33E+01 4 5 0 0 25 25 1.77E+02 9.45E+01 181 95 1.61E+01 1.04E+01 172 172 5.39E+01 6.40E+01 51 63 9.91E+00 7.13E+00 0 0 0 0 -0.097554 0.289745 0 0 0 0 0 0 1 1 0 90.1063 24.8294 3.22041 2.08256 0 1 1 5.11E-21 5.10E-12 1 1 1 1 86.7737 69.6506 9.91025 7.12574 0 559.149 396.804 19.9841 33.2818 0 1 0 0
18 8.44E-02 6.57E-02 1.99E-01 1.31E+03 1.59E+03 1.34E+01 6.27E+01 2 1 0 0 25 25 2.98E+02 1.69E+02 301 167 1.08E+01 1.96E+01 196 196 7.20E+01 6.74E+01 69.5 68 1.83E+01 7.76E+00 0 0 0 0 0.132676 0.438966 0 0 0 0 0 0 1 1 0 211.084 99.5344 2.15329 3.925 0 1 1 2.84E-50 3.10E-19 1 1 1 1 86.7158 69.6256 18.255 7.75781 1 1309.87 1590.68 13.3621 62.726 0 1 0 0
19 -2.88E-02 1.04E-01 7.83E-01 3.89E+02 3.64E+02 1.19E+01 3.02E+01 1 0 0 0 28 28 1.49E+02 9.24E+01 149.5 92.5 1.01E+01 9.99E+00 200 200 7.08E+01 6.75E+01 69 67 1.52E+01 7.18E+00 0 0 0 0 0.197002 0.312455 0 0 0 0 0 0 1 1 0 62.6817 22.7773 1.91578 1.88796 0 1 1 6.04E-31 7.33E-13 1 1 1 1 86.7112 69.6156 15.2262 7.17539 1 388.967 364.008 11.8882 30.1718 0 1 0 0
20 3.61E-02 6.81E-02 5.96E-01 1.04E+03 1.13E+03 1.64E+01 4.20E+01 1 0 1 0 27 27 2.54E+02 1.40E+02 254 141 1.37E+01 1.36E+01 192 192 6.44E+01 6.57E+01 63 66 1.33E+01 7.69E+00 0 0 0 0 0.0467179 0.51937 0 0 0 0 0 0 1 1 0 167.701 70.7648 2.63564 2.62529 0 1 1 1.83E-35 1.68E-21 1 1 1 1 86.7068 69.6056 13.3242 7.68915 1 1040.65 1130.9 16.3553 41.9552 0 1 0 0

Total number of rows: 43959

Table truncated, full table size 15479 Kbytes.




Supplementary file Size Download File type/resource
GSM139298.txt.gz 10.2 Mb (ftp)(http) TXT

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