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Sample GSM139294 Query DataSets for GSM139294
Status Public on Oct 31, 2006
Title SRF No Treatment, replicate 1, array b Jurkat cells
Sample type other
 
Channel 1
Source name SRF ChIP DNA from Jurkat, no treatment
Organism Homo sapiens
Characteristics ChIP enriched sample Antibody: SRF Santa Cruz sc-335 From 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 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 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 -9.40E-01 1.17E-01 1.11E-15 1.76E+03 2.02E+02 5.84E+01 2.19E+01 0 0 0 0 29 29 2.38E+02 8.45E+01 236 83 3.08E+01 9.55E+00 235 235 4.73E+01 6.49E+01 47 64 3.81E+00 6.33E+00 0 0 0 0 0.207668 0.0382282 0 0 0 0 0 0 0 0 0 172.764 16.42 5.71675 1.77255 0 1 1 5.76E-23 3.42E-10 1 1 1 0 65.6843 68.0628 3.8147 6.32799 0 1764.11 202.428 58.3744 21.8522 0 1 0 0
2 0.00E+00 6.31E-01 1.00E+00 3.74E+01 7.89E+01 1.14E+01 1.33E+01 2 0 1 2 25 25 6.78E+01 7.06E+01 68 71 5.58E+00 5.39E+00 201 201 4.72E+01 6.47E+01 47 64 3.66E+00 6.40E+00 0 0 0 0 -0.500516 -0.0258023 0 0 0 0 0 0 0 0 0 2.08575 2.59949 1.11606 1.07839 0 0 0 0.0798957 0.0331277 1 1 0 0 65.7543 68.0405 3.65893 6.39883 0 21.2978 32.0469 11.3963 13.2946 0 1 1 1
3 -5.85E-01 1.35E-01 1.53E-05 5.89E+02 1.53E+02 2.72E+01 1.97E+01 0 0 0 0 29 29 1.23E+02 8.04E+01 122 83 1.44E+01 8.60E+00 206 206 4.77E+01 6.51E+01 47 65 3.82E+00 5.80E+00 0 0 0 0 0.558711 -0.0880801 0 0 0 0 0 0 0 0 0 57.6634 12.4249 2.66598 1.59632 0 1 1 3.41E-19 1.45E-08 1 1 1 0 65.8193 68.0234 3.81686 5.80168 0 588.808 153.176 27.2226 19.6797 0 1 0 0
4 -7.11E-01 2.20E-01 1.20E-03 3.54E+02 6.88E+01 2.15E+01 1.46E+01 0 1 0 0 29 29 1.01E+02 6.95E+01 100 69 1.13E+01 6.36E+00 192 192 4.81E+01 6.48E+01 48 65 3.88E+00 5.58E+00 0 0 0 0 0.0913205 -0.0689106 0 0 0 0 0 0 0 0 0 34.6599 1.48252 2.10359 1.18136 0 1 0 3.67E-16 0.24297 1 1 1 0 65.8918 68.0002 3.87737 5.58261 0 353.916 18.2767 21.48 14.564 0 1 0 0
5 -4.46E-01 2.60E-01 8.62E-02 2.24E+02 8.01E+01 1.96E+01 1.08E+01 1 2 0 2 23 23 8.79E+01 7.45E+01 87 75 9.19E+00 4.19E+00 225 225 4.78E+01 6.46E+01 48 65 4.16E+00 6.21E+00 0 0 0 0 0.38219 -0.0204067 0 0 0 0 0 0 0 0 0 21.9128 6.49365 1.91551 0.873115 0 1 1 7.26E-11 1.21E-07 1 1 1 0 65.9568 67.9846 4.16246 6.2101 0 223.754 80.0546 19.5595 10.7639 0 1 0 0
6 -8.31E-01 1.31E-01 2.07E-10 9.11E+02 1.34E+02 4.27E+01 2.22E+01 0 0 0 0 30 30 1.55E+02 7.89E+01 150 77.5 2.29E+01 9.88E+00 209 209 4.77E+01 6.52E+01 47 65 3.87E+00 5.69E+00 0 0 0 0 0.393424 0.00434029 0 0 0 0 0 0 0 0 0 89.1843 10.8919 4.17777 1.8034 0 1 1 2.35E-19 1.48E-06 1 1 1 0 66.0157 67.9748 3.86586 5.68539 0 910.671 134.277 42.6597 22.2326 0 1 0 0
7 -7.32E-01 9.87E-02 1.27E-13 1.93E+03 3.57E+02 6.18E+01 2.04E+01 0 2 0 0 28 28 2.55E+02 9.69E+01 256 96 3.20E+01 8.74E+00 214 214 4.78E+01 6.46E+01 48 64 4.15E+00 6.35E+00 0 0 0 0 0.48259 0.0740168 0 0 0 0 0 0 0 0 0 188.557 28.9725 6.0501 1.65146 0 1 1 9.22E-23 3.42E-17 1 1 1 1 66.0857 67.9561 4.14677 6.34774 0 1925.38 357.177 61.7783 20.3594 0 1 0 0
8 0.00E+00 5.93E-01 1.00E+00 4.09E+01 8.21E+01 9.36E+00 1.42E+01 2 0 0 0 30 30 6.55E+01 6.67E+01 66.5 67 5.02E+00 6.30E+00 212 212 4.74E+01 6.54E+01 47 65 4.01E+00 6.66E+00 0 0 0 0 -0.223238 0.0140154 0 0 0 0 0 0 0 0 0 -0.610723 -1.21454 0.916933 1.14965 0 0 0 0.527735 0.332395 1 1 0 0 66.1441 67.9479 4.00684 6.66152 0 -6.23617 -14.973 9.36291 14.173 0 1 0 0
9 -4.57E-01 2.70E-01 8.99E-02 2.18E+02 7.60E+01 1.84E+01 1.45E+01 1 1 0 0 27 27 8.75E+01 6.76E+01 87 67 9.37E+00 6.13E+00 217 217 4.76E+01 6.52E+01 48 65 3.83E+00 6.16E+00 0 0 0 0 0.355303 -0.00678477 0 0 0 0 0 0 0 0 0 21.316 -0.310542 1.80248 1.17929 0 1 0 4.18E-12 0.805543 1 1 1 0 66.2025 67.9402 3.83169 6.16312 0 217.66 -3.82841 18.4053 14.5385 0 1 0 0
10 -3.36E-01 3.09E-01 2.76E-01 1.66E+02 7.68E+01 1.32E+01 1.16E+01 1 1 0 0 28 28 8.26E+01 7.37E+01 82 76 6.86E+00 4.99E+00 209 209 4.73E+01 6.45E+01 47 64 3.74E+00 6.23E+00 0 0 0 0 -0.00850153 0.0682912 0 0 0 0 0 0 0 0 0 16.3031 5.75163 1.29654 0.942884 0 1 1 4.24E-13 2.16E-06 1 1 1 0 66.2683 67.9269 3.73903 6.23274 0 166.473 70.9069 13.2392 11.624 0 1 0 0
11 0.00E+00 6.08E-01 1.00E+00 4.20E+01 7.70E+01 1.45E+01 1.20E+01 0 1 0 2 27 27 7.04E+01 6.97E+01 71 71 7.40E+00 5.07E+00 216 216 4.71E+01 6.53E+01 47 64 3.88E+00 6.25E+00 0 0 0 0 -0.0897249 0.00643346 0 0 0 0 0 0 0 0 0 4.11125 1.78852 1.42358 0.975212 0 1 0 0.00834938 0.101233 1 1 0 0 66.3332 67.9152 3.87871 6.24847 0 41.9804 22.0491 14.5364 12.0226 0 1 0 0
12 -7.18E-01 1.05E-01 8.51E-12 1.33E+03 2.55E+02 6.51E+01 2.14E+01 0 0 0 0 29 29 1.97E+02 8.86E+01 196 86 3.43E+01 9.35E+00 200 200 4.75E+01 6.57E+01 47 65 3.67E+00 6.15E+00 0 0 0 0 0.481944 -0.0556343 0 0 0 0 0 0 0 0 0 130.295 20.6793 6.37152 1.73668 0 1 1 2.12E-18 7.06E-13 1 1 1 1 66.3946 67.9069 3.67218 6.15168 0 1330.46 254.937 65.0604 21.41 0 1 0 0
13 -7.05E-01 1.27E-01 2.72E-08 7.85E+02 1.55E+02 3.95E+01 1.92E+01 0 1 0 0 28 28 1.43E+02 8.05E+01 142 81.5 2.05E+01 8.23E+00 218 218 4.74E+01 6.54E+01 47 65 3.88E+00 6.28E+00 0 0 0 0 -0.0612306 -0.0034212 0 0 0 0 0 0 0 0 0 76.8916 12.5726 3.86793 1.55625 0 1 1 1.00E-17 8.27E-09 1 1 1 0 66.4655 67.8917 3.87592 6.27778 0 785.15 154.996 39.4959 19.1856 0 1 0 0
14 -6.34E-01 9.79E-02 9.09E-11 1.36E+03 3.15E+02 5.14E+01 1.58E+01 0 2 0 1 29 29 2.00E+02 9.34E+01 201 93 2.71E+01 6.90E+00 199 199 4.77E+01 6.48E+01 48 64 3.76E+00 6.19E+00 0 0 0 0 -0.00702127 -0.0561851 0 0 0 0 0 0 0 0 0 132.983 25.5694 5.03085 1.28038 0 1 1 2.09E-21 6.61E-20 1 1 1 1 66.5344 67.8789 3.76313 6.19313 0 1357.9 315.223 51.3706 15.7847 0 1 0 0
15 -4.04E-01 1.48E-01 6.24E-03 4.15E+02 1.64E+02 2.37E+01 3.19E+01 6 4 0 0 25 25 1.07E+02 8.12E+01 107 79 1.16E+01 1.29E+01 191 191 4.76E+01 6.54E+01 48 66 4.01E+00 5.76E+00 0 0 0 0 0.0690607 -0.035835 0 0 0 0 0 0 0 0 0 40.6441 13.2874 2.32327 2.58694 0 1 1 2.28E-15 3.02E-05 1 1 1 0 66.5959 67.8726 4.0096 5.75534 0 415.021 163.808 23.7232 31.8922 0 1 0 0
16 0.00E+00 6.69E-01 1.00E+00 4.06E+01 6.63E+01 1.22E+01 1.27E+01 0 3 0 0 27 27 7.04E+01 6.61E+01 70 66 6.20E+00 5.34E+00 192 192 4.77E+01 6.51E+01 47 65 3.97E+00 5.37E+00 0 0 0 0 0.0367701 0.0434476 0 0 0 0 0 0 0 0 0 3.78711 -1.75602 1.19273 1.02856 0 1 0 0.00441091 0.119462 1 1 0 0 66.6573 67.8671 3.97352 5.37415 0 38.6706 -21.6485 12.1791 12.6802 0 1 0 0
17 -5.01E-01 2.60E-01 5.43E-02 2.36E+02 7.46E+01 1.63E+01 1.87E+01 2 0 0 0 29 29 8.99E+01 7.30E+01 88 73 8.60E+00 8.16E+00 208 208 4.72E+01 6.45E+01 47 64 3.93E+00 6.05E+00 0 0 0 0 0.106373 0.13253 0 0 0 0 0 0 0 0 0 23.1372 5.10796 1.59643 1.51469 0 1 1 7.85E-15 0.00268972 1 1 1 0 66.7249 67.8576 3.93075 6.04876 0 236.257 62.9716 16.3013 18.6733 0 1 0 0
18 -5.99E-01 1.19E-01 4.53E-07 7.53E+02 1.89E+02 3.07E+01 1.83E+01 0 1 0 0 29 29 1.41E+02 8.32E+01 141 82 1.62E+01 8.00E+00 192 192 4.72E+01 6.47E+01 47 64 3.75E+00 6.28E+00 0 0 0 0 0.333551 0.0325528 0 0 0 0 0 0 0 0 0 73.7241 15.3588 3.00641 1.48588 0 1 1 1.23E-20 1.88E-11 1 1 1 0 66.7931 67.8481 3.74702 6.27753 0 752.806 189.345 30.6988 18.3181 0 1 0 0
19 -4.56E-01 3.15E-01 1.47E-01 1.84E+02 6.44E+01 1.11E+01 1.27E+01 3 0 0 0 27 27 8.49E+01 7.18E+01 85 72 5.67E+00 5.37E+00 204 204 4.74E+01 6.46E+01 47 64 3.99E+00 5.23E+00 0 0 0 0 -0.190369 -0.0233221 0 0 0 0 0 0 0 0 0 18.0376 3.93065 1.09171 1.0327 0 1 1 4.39E-16 0.00106995 1 1 1 0 66.8513 67.8471 3.98538 5.22507 0 184.184 48.4576 11.1476 12.7313 0 1 0 0
20 -5.66E-01 1.50E-01 1.71E-04 4.91E+02 1.33E+02 2.25E+01 2.09E+01 1 1 0 0 27 27 1.15E+02 7.87E+01 113 80 1.14E+01 8.81E+00 199 199 4.77E+01 6.45E+01 48 64 3.72E+00 6.27E+00 0 0 0 0 -0.444724 0.0810382 0 0 0 0 0 0 0 0 0 48.0521 10.821 2.20236 1.69632 0 1 1 1.71E-18 9.06E-07 1 1 1 0 66.9108 67.8457 3.71803 6.27153 0 490.666 133.403 22.4885 20.9124 0 1 0 0

Total number of rows: 43959

Table truncated, full table size 15482 Kbytes.




Supplementary file Size Download File type/resource
GSM139294.txt.gz 10.1 Mb (ftp)(http) TXT

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