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Sample GSM139288 Query DataSets for GSM139288
Status Public on Oct 31, 2006
Title SRF 24 hour serum induction, replicate 1, array b Jurkat
Sample type other
 
Channel 1
Source name SRF, ChIP enriched DNA, 24hr serum induction Jurkat
Organism Homo sapiens
Characteristics ChIP enriched DNA, SRF 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 sheared genomic DNA, no antibody control
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
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 gNumBGUsed rNumBGUsed gIsWellAboveBG rIsWellAboveBG gBGUsed rBGUsed gBGSDUsed rBGSDUsed IsNormalization gDyeNormSignal rDyeNormSignal gDyeNormError rDyeNormError DyeNormCorrelation ErrorModel gIsInNegCtrlRange rIsInNegCtrlRange
1 -0.132 6.55E-02 4.42E-02 1057.03 780.49 4.31E+01 2.04E+01 0 0 0 0 30 30 367.47 634.43 386 624 6.45E+01 7.86E+01 228 228 4.40E+01 6.65E+01 44 66 4.00E+00 6.26E+00 0 0 0 0 0.709274 0.0491499 0 0 0 0 0 0 0 0 0 289.172 549.728 11.7844 14.3567 0 1 1 1 1 1 1 78.2947 84.705 4.00269 6.25768 0 1057.03 780.487 43.0766 20.3832 0 1 0 0
2 0.000 1.56E+00 1.00E+00 12.9 9.74 6.19E+00 2.49E+00 0 1 0 0 28 28 79.61 78.93 79.5 77.5 8.96E+00 9.28E+00 197 197 4.48E+01 6.61E+01 45 65 3.53E+00 6.86E+00 0 0 0 0 0.038404 0.10107 0 0 0 0 0 0 0 0 0 1.2617 -5.85073 1.6937 1.75325 0 0 0 1 1 0 0 78.3454 84.7793 3.52883 6.86229 0 4.612 -8.30668 6.19112 2.48921 0 1 1 1
3 -0.197 6.88E-02 4.19E-03 866.09 550.44 3.83E+01 2.02E+01 0 0 0 0 30 30 315.33 472.57 332 493 5.74E+01 7.80E+01 200 200 4.46E+01 6.54E+01 45 65 3.54E+00 5.65E+00 0 0 0 0 0.834589 0.0363497 0 0 0 0 0 0 0 0 0 236.936 387.694 10.4773 14.2476 0 1 1 1 1 1 1 78.3978 84.8728 3.54378 5.64947 0 866.09 550.436 38.2984 20.2283 0 1 0 0
4 -0.378 8.63E-02 1.20E-05 526.25 220.5 2.61E+01 1.03E+01 0 0 1 0 29 29 222.41 240.24 225 241 3.85E+01 3.89E+01 206 206 4.54E+01 6.47E+01 45 64 4.21E+00 5.59E+00 0 0 0 0 0.624066 -0.00103353 0 0 0 0 0 0 0 0 0 143.967 155.309 7.1479 7.22367 0 1 1 1 1 1 1 78.4469 84.9329 4.21189 5.59203 0 526.254 220.502 26.1283 10.2559 0 1 0 0
5 0.043 7.03E-02 5.46E-01 489.85 540.2 2.11E+01 1.10E+01 0 0 0 0 30 30 212.5 465.5 225.5 473.5 3.16E+01 4.24E+01 191 191 4.51E+01 6.49E+01 45 64 4.10E+00 6.23E+00 0 0 0 0 0.572643 -0.0896119 0 0 0 0 0 0 0 0 0 134.008 380.481 5.76808 7.73598 0 1 1 1 1 1 1 78.4921 85.0188 4.09813 6.23223 1 489.85 540.195 21.0845 10.9833 0 1 0 0
6 -0.026 7.08E-02 7.16E-01 511.41 481.91 3.42E+01 1.98E+01 0 0 0 0 29 29 218.45 424.52 236 425 5.04E+01 7.51E+01 193 193 4.56E+01 6.55E+01 45 65 4.13E+00 7.12E+00 0 0 0 0 0.874816 0.0161281 0 0 0 0 0 0 0 0 0 139.905 339.429 9.36238 13.9376 0 1 1 1 1 1 1 78.5436 85.0884 4.1311 7.12253 1 511.405 481.911 34.2231 19.7882 0 1 0 0
7 0.000 6.16E-02 1.00E+00 3320.02 3319.86 9.15E+01 5.10E+01 0 0 2 2 28 28 986.86 2423.46 1031 2462.5 1.32E+02 1.90E+02 196 196 4.53E+01 6.50E+01 45 64 3.99E+00 5.87E+00 0 0 0 0 0.836295 0.136857 0 0 0 0 0 0 0 0 0 908.256 2338.31 25.0332 35.9208 0 1 1 1 1 1 1 78.6011 85.1564 3.99021 5.8716 1 3320.02 3319.86 91.5061 50.9993 0 1 0 0
8 0.000 1.40E+00 1.00E+00 14.39 10.85 5.80E+00 2.47E+00 0 0 0 0 30 30 79.9 82.27 79 83 8.69E+00 9.54E+00 186 186 4.54E+01 6.52E+01 45 64 3.94E+00 7.64E+00 0 0 0 0 0.349507 0.174316 0 0 0 0 0 0 0 0 0 1.25036 -2.94399 1.58611 1.74127 0 0 0 1 1 0 0 78.6496 85.2107 3.93556 7.64207 0 4.57053 -4.17978 5.79784 2.4722 0 1 0 0
9 0.339 4.13E-01 4.12E-01 28.34 61.86 8.38E+00 4.26E+00 0 0 0 0 29 29 86.45 128.86 90 134 1.23E+01 1.62E+01 201 201 4.56E+01 6.47E+01 45 65 3.74E+00 6.60E+00 0 0 0 0 0.680572 0.013953 0 0 0 0 0 0 0 0 0 7.7535 43.5719 2.29295 3.0003 0 1 1 1 1 0 1 78.6948 85.2902 3.741 6.59654 1 28.342 61.862 8.3816 4.25973 0 1 0 0
10 -0.144 8.59E-02 9.42E-02 350.77 251.93 2.24E+01 1.05E+01 0 0 0 0 30 30 174.7 262.83 181.5 259.5 3.36E+01 4.03E+01 192 192 4.53E+01 6.51E+01 45 64.5 3.83E+00 7.35E+00 0 0 0 0 0.681498 -0.0621447 0 0 0 0 0 0 0 0 0 95.9607 177.444 6.14034 7.36645 0 1 1 1 1 1 1 78.7393 85.3898 3.83288 7.34514 0 350.773 251.929 22.4453 10.4587 0 1 0 0
11 0.197 5.34E-01 7.12E-01 26.1 41.07 5.28E+00 4.34E+00 0 1 1 0 28 28 84.71 114.39 85 109.5 7.64E+00 1.62E+01 167 167 4.78E+01 6.64E+01 47 65 7.14E+00 8.36E+00 0 0 0 0 0.322154 0.350818 0 0 0 0 0 0 0 0 0 5.9278 28.9262 1.44462 3.05866 0 1 1 1 1 0 1 78.7865 85.4666 7.14092 8.35879 1 21.6684 41.0686 5.28063 4.34259 0 1 0 0
12 0.018 6.18E-02 7.71E-01 2529.6 2636.69 8.26E+01 5.01E+01 0 0 0 1 30 30 770.87 1942.67 800 1995 1.24E+02 1.93E+02 174 174 4.60E+01 6.44E+01 46 64 5.21E+00 6.95E+00 0 0 0 0 0.869889 0.31468 0 0 0 0 0 0 0 0 0 692.021 1857.13 22.6084 35.2783 0 1 1 1 1 1 1 78.8452 85.5381 5.21059 6.95341 1 2529.6 2636.69 82.6425 50.0871 0 1 0 0
13 -0.051 6.31E-02 4.15E-01 1367.67 1214.95 7.61E+01 2.97E+01 3 1 0 4 23 23 453.04 941.35 461 968 9.98E+01 1.00E+02 189 189 4.54E+01 6.57E+01 45 65 4.25E+00 6.94E+00 0 0 0 0 0.73093 0.0449085 0 0 0 0 0 0 0 0 0 374.153 855.74 20.8104 20.9418 0 1 1 1 1 1 1 78.89 85.6082 4.24774 6.94342 1 1367.67 1214.95 76.07 29.7325 0 1 0 0
14 0.014 6.18E-02 8.23E-01 2521.02 2602.64 8.08E+01 4.51E+01 0 0 1 0 28 28 768.61 1918.82 814.5 1941 1.17E+02 1.68E+02 179 179 4.56E+01 6.57E+01 45 65 3.69E+00 7.50E+00 0 0 0 0 0.853343 0.0929707 0 0 0 0 0 0 0 0 0 689.672 1833.14 22.0948 31.7343 0 1 1 1 1 1 1 78.9352 85.677 3.69343 7.5012 1 2521.01 2602.64 80.765 45.0554 0 1 0 0
15 -0.103 7.02E-02 1.41E-01 601.13 473.7 2.52E+01 1.42E+01 0 0 1 1 28 28 243.43 419.39 255 408.5 3.64E+01 5.30E+01 201 201 4.57E+01 6.52E+01 46 64 4.20E+00 7.52E+00 0 0 0 0 0.515792 0.0920432 0 0 0 0 0 0 0 0 0 164.452 333.642 6.88692 10.0251 0 1 1 1 1 1 1 78.9767 85.7505 4.19981 7.51692 1 601.134 473.695 25.1743 14.2334 0 1 0 0
16 -0.720 2.23E-01 1.27E-03 175.51 33.47 1.91E+01 4.93E+00 0 0 0 0 32 32 127.03 109.38 124 102.5 2.95E+01 1.97E+01 191 191 4.54E+01 6.52E+01 45 64 4.57E+00 6.57E+00 0 0 0 0 0.70433 0.107336 0 0 0 0 0 0 0 0 0 48.0142 23.5734 5.22314 3.47391 0 1 1 1 1 1 1 79.017 85.8016 4.57387 6.56838 0 175.51 33.4688 19.0926 4.93215 0 1 0 0
17 0.134 7.62E-02 7.78E-02 344.65 469.53 1.93E+01 1.64E+01 0 0 0 0 29 29 173.34 416.55 178 429 2.84E+01 6.21E+01 191 191 4.60E+01 6.50E+01 45 64 5.36E+00 6.22E+00 0 0 0 0 0.551866 0.109395 0 0 0 0 0 0 0 0 0 94.2853 330.71 5.26964 11.5336 0 1 1 1 1 1 1 79.0595 85.8413 5.35506 6.21627 0 344.649 469.532 19.2626 16.375 0 1 0 0
18 -0.026 6.20E-02 6.75E-01 2314.12 2179.59 1.00E+02 5.79E+01 0 0 0 1 29 29 712.17 1621.07 766 1653 1.48E+02 2.20E+02 167 167 4.64E+01 6.61E+01 46 66 3.99E+00 7.58E+00 0 0 0 0 0.847021 0.0849489 0 0 0 0 0 0 0 0 0 633.072 1535.17 27.4596 40.7772 0 1 1 1 1 1 1 79.1008 85.8974 3.98876 7.58155 1 2314.12 2179.59 100.376 57.8942 0 1 0 0
19 0.002 9.01E-02 9.81E-01 264.76 266.1 1.44E+01 8.90E+00 0 0 0 0 30 30 151.57 273.37 155.5 265.5 2.15E+01 3.43E+01 190 190 4.52E+01 6.69E+01 45 66 4.21E+00 7.04E+00 0 0 0 0 0.67066 -0.0113404 0 0 0 0 0 0 0 0 0 72.4292 187.425 3.92887 6.26713 0 1 1 1 1 1 1 79.1374 85.942 4.20996 7.04253 1 264.757 266.1 14.3615 8.89788 0 1 0 0
20 -0.104 6.44E-02 1.07E-01 1166.75 918.69 4.17E+01 2.20E+01 0 0 0 2 30 30 398.37 733.07 420 733.5 6.25E+01 8.49E+01 193 193 4.64E+01 6.58E+01 46 65 4.22E+00 6.94E+00 0 0 0 0 0.748601 0.106199 0 0 0 0 0 0 0 0 0 319.186 647.069 11.4172 15.4989 0 1 1 1 1 1 1 79.1804 85.9974 4.22481 6.93936 0 1166.75 918.689 41.7343 22.0049 0 1 0 0

Total number of rows: 44259

Table truncated, full table size 14350 Kbytes.




Supplementary file Size Download File type/resource
GSM139288.txt.gz 11.3 Mb (ftp)(http) TXT

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