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Sample GSM139296 Query DataSets for GSM139296
Status Public on Oct 31, 2006
Title SRF No Treatment, replicate 2, array b Jurkat cells
Sample type other
 
Channel 1
Source name SRF ChIP DNA from Jurkat, no treatment
Organism Homo sapiens
Characteristics SRF ChIP enriched 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 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 -1.64E-01 6.52E-02 1.20E-02 3.06E+03 2.10E+03 4.25E+01 4.55E+01 0 0 1 0 28 28 2.32E+02 2.63E+02 231.5 260.5 1.18E+01 2.23E+01 231 231 4.52E+01 6.56E+01 45 66 3.65E+00 5.82E+00 0 0 0 0 0.111748 -0.035735 0 0 0 0 0 0 0 0 0 160.475 194.596 2.2278 4.21722 0 1 1 6.36E-33 1.66E-27 1 1 1 1 71.7034 68.2613 3.65252 5.81642 0 3060.12 2097.97 42.4823 45.4666 0 1 0 0
2 -1.74E-01 4.85E-01 7.19E-01 1.03E+02 6.92E+01 2.43E+01 1.24E+01 0 0 0 0 31 31 7.72E+01 7.02E+01 77 69 7.10E+00 6.38E+00 201 201 4.66E+01 6.64E+01 46 67 3.95E+00 6.42E+00 0 0 0 0 0.499188 -0.0194555 0 0 0 0 0 0 0 1 0 5.42522 1.90226 1.276 1.14602 0 1 0 0.000217685 0.130546 1 1 0 0 71.7361 68.3235 3.94772 6.42158 0 103.454 20.5086 24.3321 12.3554 0 1 1 1
3 1.80E-01 7.19E-02 1.26E-02 9.83E+02 1.49E+03 3.15E+01 3.90E+01 0 0 0 0 30 30 1.23E+02 2.06E+02 124.5 203.5 9.06E+00 1.98E+01 216 216 4.65E+01 6.55E+01 46 66 3.54E+00 6.33E+00 0 0 0 0 -0.04647 -0.00408653 0 0 0 0 0 0 0 0 0 51.5549 137.871 1.65351 3.61508 0 1 1 2.03E-24 8.85E-27 1 1 1 1 71.7784 68.3957 3.53973 6.32959 0 983.109 1486.41 31.531 38.9748 0 1 0 0
4 1.61E-01 8.14E-02 4.82E-02 6.59E+02 9.55E+02 2.65E+01 2.72E+01 0 1 0 0 29 29 1.06E+02 1.57E+02 106 159 7.48E+00 1.36E+01 184 184 4.65E+01 6.37E+01 46 63.5 3.52E+00 5.83E+00 0 0 0 0 0.339934 -0.0448814 0 0 0 0 0 0 0 0 0 34.5702 88.5442 1.3891 2.51938 0 1 1 2.30E-21 1.52E-25 1 1 1 1 71.8091 68.4558 3.51562 5.83064 0 659.225 954.61 26.4889 27.1619 0 1 0 0
5 -3.81E-01 1.64E-01 2.04E-02 4.15E+02 1.73E+02 3.21E+01 1.70E+01 0 0 0 0 28 28 9.36E+01 8.45E+01 94.5 84.5 8.91E+00 8.34E+00 212 212 4.67E+01 6.57E+01 46 65 3.54E+00 6.30E+00 0 0 0 0 -0.178391 -0.00226085 0 0 0 0 0 0 0 0 0 21.7509 16.0022 1.6843 1.57652 0 1 1 3.08E-13 4.99E-11 1 1 1 0 71.8563 68.5335 3.53846 6.29589 0 414.77 172.522 32.1182 16.9967 0 1 0 0
6 2.03E-01 6.78E-02 2.72E-03 1.46E+03 2.33E+03 4.99E+01 5.02E+01 0 2 0 0 28 28 1.48E+02 2.85E+02 147.5 287 1.38E+01 2.46E+01 202 202 4.66E+01 6.50E+01 46 65 3.83E+00 6.02E+00 0 0 0 0 0.60139 -0.055137 0 0 0 0 0 0 0 0 0 76.5559 216.276 2.61633 4.65768 0 1 1 3.05E-22 1.40E-27 1 1 1 1 71.9084 68.617 3.82627 6.01861 0 1459.86 2331.71 49.8912 50.2153 0 1 0 0
7 -4.56E-02 6.43E-02 4.78E-01 2.30E+03 2.07E+03 5.20E+01 4.61E+01 0 0 0 0 30 30 1.93E+02 2.61E+02 196.5 259 1.49E+01 2.34E+01 210 210 4.63E+01 6.53E+01 46 65 3.75E+00 5.75E+00 0 0 0 0 -0.0410585 -0.078297 0 0 0 0 0 0 0 0 0 120.852 192.447 2.72637 4.27361 0 1 1 1.64E-28 1.07E-28 1 1 1 1 71.9475 68.6864 3.74525 5.74645 0 2304.55 2074.8 51.9896 46.0745 0 1 0 0
8 -2.34E-01 5.08E-01 6.44E-01 1.05E+02 6.13E+01 2.38E+01 1.51E+01 0 0 0 1 29 29 7.75E+01 7.26E+01 78 72 6.72E+00 7.56E+00 213 213 4.59E+01 6.44E+01 46 64 3.71E+00 5.69E+00 0 0 0 0 -0.118301 -0.0216449 0 0 0 0 0 0 0 0 0 5.51656 3.77966 1.24827 1.40336 0 1 0 0.000149832 0.0140843 1 1 0 0 72.0007 68.7721 3.71286 5.68761 0 105.196 40.7491 23.8034 15.1299 0 1 0 0
9 -8.36E-02 1.26E-01 5.08E-01 4.10E+02 3.38E+02 3.03E+01 1.59E+01 1 1 0 0 30 30 9.35E+01 1.00E+02 93.5 101 8.71E+00 8.10E+00 206 206 4.62E+01 6.47E+01 46 64 3.79E+00 6.27E+00 0 0 0 0 0.0776294 -0.029888 0 0 0 0 0 0 0 0 0 21.4798 31.342 1.59073 1.47812 0 1 1 2.80E-14 1.07E-20 1 1 1 1 72.0536 68.858 3.79408 6.273 1 409.601 337.903 30.3339 15.9358 0 1 0 0
10 -1.93E-01 1.46E-01 1.87E-01 3.86E+02 2.47E+02 2.60E+01 2.29E+01 1 0 0 0 31 31 9.23E+01 9.19E+01 91 93 7.59E+00 1.18E+01 189 189 4.63E+01 6.48E+01 47 64 3.54E+00 5.95E+00 0 0 0 0 -0.0833978 -0.0601005 0 0 0 0 0 0 0 0 0 20.2255 22.9379 1.36341 2.12499 0 1 1 1.00E-15 4.63E-12 1 1 1 1 72.0971 68.9331 3.54076 5.94504 0 385.683 247.297 25.9991 22.9098 0 1 0 0
11 -3.38E-01 3.40E-01 3.21E-01 1.77E+02 8.11E+01 1.84E+01 1.46E+01 2 1 2 0 24 24 8.14E+01 7.65E+01 81 76 4.72E+00 6.63E+00 225 225 4.64E+01 6.44E+01 46 64 3.69E+00 6.41E+00 0 0 0 0 0.405151 -0.0366252 0 0 0 0 0 0 0 0 0 9.27062 7.52657 0.96293 1.35398 0 1 1 8.56E-10 1.25E-05 1 1 0 0 72.146 69.0151 3.69165 6.40566 1 176.783 81.1452 18.3623 14.5975 0 1 0 0
12 -1.14E-02 6.52E-02 8.62E-01 1.91E+03 1.86E+03 5.20E+01 4.93E+01 0 0 0 0 29 29 1.72E+02 2.41E+02 172 241 1.47E+01 2.46E+01 201 201 4.60E+01 6.48E+01 46 65 3.75E+00 6.43E+00 0 0 0 0 0.369267 0.0321242 0 0 0 0 0 0 0 0 0 100.045 172.383 2.72855 4.57333 0 1 1 1.71E-25 7.67E-26 1 1 1 1 72.1966 69.0995 3.74961 6.43216 1 1907.77 1858.49 52.031 49.3058 0 1 0 0
13 -9.19E-03 7.00E-02 8.96E-01 1.23E+03 1.20E+03 3.14E+01 3.67E+01 0 0 0 0 30 30 1.37E+02 1.81E+02 136.5 181 9.03E+00 1.87E+01 208 208 4.60E+01 6.40E+01 46 63 3.37E+00 6.45E+00 0 0 0 0 0.261533 -0.0671611 0 0 0 0 0 0 0 0 0 64.4592 111.625 1.64851 3.4077 0 1 1 2.76E-27 6.15E-25 1 1 1 1 72.2408 69.1753 3.37202 6.44704 1 1229.18 1203.44 31.4357 36.739 0 1 0 0
14 -8.28E-03 6.93E-02 9.05E-01 1.29E+03 1.26E+03 3.87E+01 4.80E+01 1 0 0 0 28 28 1.40E+02 1.87E+02 138.5 185.5 1.07E+01 2.36E+01 199 199 4.56E+01 6.38E+01 45 63 3.63E+00 6.42E+00 0 0 0 0 0.164772 -0.0341771 0 0 0 0 0 0 0 0 0 67.6036 117.315 2.02846 4.45508 0 1 1 6.61E-24 5.10E-21 1 1 1 1 72.2893 69.2567 3.62578 6.42131 1 1289.14 1264.79 38.681 48.0309 0 1 0 0
15 -2.22E-01 9.24E-02 1.65E-02 7.92E+02 4.75E+02 2.88E+01 2.47E+01 1 0 0 0 28 28 1.14E+02 1.13E+02 115.5 115 8.00E+00 1.21E+01 209 209 4.58E+01 6.41E+01 46 64 3.86E+00 6.24E+00 0 0 0 0 -0.137529 0.0145653 0 0 0 0 0 0 0 0 0 41.515 44.0838 1.51161 2.2924 0 1 1 5.66E-22 7.94E-18 1 1 1 1 72.3421 69.3448 3.86001 6.24363 0 791.656 475.275 28.8251 24.7148 0 1 0 0
16 0.00E+00 6.22E-01 1.00E+00 7.23E+01 6.03E+01 3.09E+01 1.33E+01 0 1 0 0 28 28 7.51E+01 7.16E+01 74 71.5 8.57E+00 6.55E+00 181 181 4.55E+01 6.46E+01 45 64 3.79E+00 5.60E+00 0 0 0 0 -0.293905 -0.249022 0 0 0 0 0 0 0 0 0 2.67625 2.17342 1.61992 1.23693 0 0 0 0.114555 0.105182 1 1 0 0 72.3952 69.4337 3.79389 5.59688 0 51.0338 23.432 30.8905 13.3356 0 1 0 0
17 2.51E-01 1.08E-01 2.01E-02 3.52E+02 6.28E+02 2.66E+01 2.48E+01 1 0 0 0 29 29 9.09E+01 1.28E+02 91 130 7.51E+00 1.24E+01 209 209 4.61E+01 6.32E+01 46 63 3.10E+00 5.95E+00 0 0 0 0 0.0925884 0.00966563 0 0 0 0 0 0 0 0 0 18.4498 58.2045 1.39435 2.30062 0 1 1 9.05E-14 1.65E-21 1 1 1 1 72.4468 69.5197 3.10102 5.94705 0 351.821 627.512 26.589 24.8034 0 1 0 0
18 1.86E-02 9.14E-02 8.39E-01 5.92E+02 6.18E+02 3.68E+01 2.83E+01 0 0 0 0 30 30 1.04E+02 1.27E+02 103 128 1.06E+01 1.44E+01 201 201 4.59E+01 6.40E+01 46 64 3.95E+00 5.82E+00 0 0 0 0 -0.245794 -0.103575 0 0 0 0 0 0 0 0 0 31.0342 57.2946 1.93202 2.62716 0 1 1 3.19E-16 5.53E-20 1 1 1 1 72.4991 69.6054 3.94502 5.82355 1 591.796 617.702 36.8421 28.3238 0 1 0 0
19 -1.83E-01 1.92E-01 3.41E-01 2.77E+02 1.82E+02 2.81E+01 2.27E+01 0 0 0 0 29 29 8.71E+01 8.66E+01 88 85 7.95E+00 1.13E+01 213 213 4.64E+01 6.44E+01 46 64 3.38E+00 6.49E+00 0 0 0 0 -0.0556196 -0.0109076 0 0 0 0 0 0 0 0 0 14.5147 16.8518 1.47552 2.10242 0 1 1 1.09E-10 8.32E-09 1 1 1 0 72.5543 69.7 3.38407 6.48789 1 276.782 181.682 28.137 22.6665 0 1 0 0
20 -1.68E-01 1.09E-01 1.23E-01 5.57E+02 3.78E+02 4.24E+01 2.42E+01 1 0 0 0 29 29 1.02E+02 1.05E+02 100 104 1.20E+01 1.21E+01 193 193 4.57E+01 6.41E+01 46 63 3.22E+00 6.37E+00 0 0 0 0 0.21578 0.0347322 0 0 0 0 0 0 0 0 0 29.1844 35.0689 2.22136 2.24087 0 1 1 1.38E-13 7.59E-16 1 1 1 1 72.6088 69.7932 3.21662 6.36826 0 556.521 378.083 42.3594 24.1592 0 1 0 0

Total number of rows: 43959

Table truncated, full table size 15482 Kbytes.




Supplementary file Size Download File type/resource
GSM139296.txt.gz 10.1 Mb (ftp)(http) TXT

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