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Sample GSM139290 Query DataSets for GSM139290
Status Public on Oct 31, 2006
Title SRF 24 hour serum induction, replicate 2, array b Jurkat
Sample type other
 
Channel 1
Source name SRF, ChIP enriched DNA, 24hr serum induction Jurkat
Organism Homo sapiens
Characteristics SRF enriched ChIP DNA 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 0.223 1.08E-01 3.92E-02 198.04 330.85 1.21E+01 4.39E+01 0 0 0 0 29 29 101.52 85 101 84 7.09E+00 1.05E+01 230 230 4.41E+01 6.49E+01 44 65 3.09E+00 6.22E+00 0 0 0 0 0.24235 -0.0105746 0 0 0 0 0 0 0 0 0 21.6314 14.7586 1.31646 1.95705 0 1 1 3.31E-16 2.88E-08 1 1 1 0 79.8858 70.2414 3.08616 6.21512 0 198.043 330.85 12.0526 43.872 0 1 0 0
2 0.000 2.65E-01 1.00E+00 46.86 149.03 6.81E+00 3.50E+01 2 0 0 0 27 27 85.07 72.48 85 73 3.86E+00 8.12E+00 204 204 4.46E+01 6.51E+01 44 65 3.49E+00 6.65E+00 0 0 0 0 0.0797496 -0.0290424 0 0 0 0 0 0 0 1 0 5.11787 2.22751 0.7433 1.5629 0 1 0 2.33E-07 0.18185 1 1 0 0 79.9562 70.254 3.49188 6.6481 0 46.8559 49.9351 6.80517 35.0362 0 1 1 1
3 -0.170 1.07E-01 1.12E-01 314.11 212.24 1.95E+01 2.95E+01 0 0 0 0 30 30 114.33 79.73 116 80.5 1.17E+01 7.20E+00 210 210 4.44E+01 6.39E+01 44 64 3.39E+00 5.79E+00 0 0 0 0 0.254161 -0.0125715 0 0 0 0 0 0 0 0 0 34.3085 9.46754 2.1315 1.31476 0 1 1 3.84E-16 5.66E-08 1 1 1 0 80.0249 70.2658 3.3897 5.79048 0 314.106 212.238 19.5146 29.4734 0 1 0 0
4 0.391 1.74E-01 2.49E-02 86.69 213.42 1.23E+01 3.44E+01 0 0 0 0 30 30 89.57 79.8 90.5 81.5 7.38E+00 8.41E+00 208 208 4.40E+01 6.50E+01 44 65 3.16E+00 6.33E+00 0 0 0 0 0.0529749 0.0447353 0 0 0 0 0 0 0 0 0 9.46839 9.52007 1.34821 1.53533 0 1 1 9.67E-08 9.76E-07 1 1 1 0 80.0983 70.2799 3.15816 6.33026 0 86.6864 213.416 12.3433 34.4182 0 1 0 0
5 -0.040 1.16E-01 7.29E-01 238.63 217.53 1.93E+01 3.11E+01 0 1 0 0 29 29 106.24 80 104 79 1.13E+01 7.46E+00 209 209 4.41E+01 6.44E+01 44 64 3.26E+00 6.36E+00 0 0 0 0 0.0899719 0.0225283 0 0 0 0 0 0 0 0 0 26.0648 9.70347 2.1048 1.38518 0 1 1 5.80E-13 1.17E-07 1 1 1 0 80.1766 70.2965 3.25642 6.36246 1 238.632 217.527 19.2702 31.0521 0 1 0 0
6 0.211 2.02E-01 2.96E-01 90.65 147.5 1.06E+01 4.29E+01 2 1 0 0 27 27 90.15 76.89 90 75 6.02E+00 9.94E+00 204 204 4.40E+01 6.40E+01 44 64 3.36E+00 5.69E+00 0 0 0 0 -0.110162 0.0443649 0 0 0 0 0 0 0 0 0 9.90123 6.57954 1.15926 1.91361 0 1 1 3.98E-09 0.00220883 1 1 1 0 80.2469 70.3093 3.35502 5.69098 1 90.6492 147.496 10.6134 42.8983 0 1 0 0
7 -0.031 6.27E-02 6.26E-01 1854.43 1728.27 5.57E+01 8.02E+01 0 0 0 0 29 29 282.86 147.41 285 151 3.28E+01 1.93E+01 214 214 4.39E+01 6.38E+01 44 64 3.22E+00 6.24E+00 0 0 0 0 0.520432 -0.122933 0 0 0 0 0 0 0 0 0 202.551 77.0949 6.08858 3.57899 0 1 1 4.32E-24 3.19E-19 1 1 1 1 80.3107 70.3189 3.21524 6.24458 1 1854.43 1728.27 55.743 80.2317 0 1 0 0
8 0.000 3.32E-01 1.00E+00 29.23 137.85 1.15E+01 3.57E+01 0 0 0 0 30 30 79.77 70.4 79.5 69 6.90E+00 8.73E+00 199 199 4.38E+01 6.50E+01 44 65 3.19E+00 6.15E+00 0 0 0 0 0.00962392 0.0174842 0 0 0 0 0 0 0 0 0 -0.618193 0.0664457 1.25916 1.59352 0 0 0 0.632351 0.968157 1 1 0 0 80.3849 70.3336 3.19292 6.14919 0 -5.65977 1.48954 11.528 35.7226 0 1 0 0
9 0.000 3.07E-01 1.00E+00 33.66 143.86 1.45E+01 3.72E+01 0 0 0 0 29 29 84.34 71.69 85 72 8.52E+00 8.94E+00 216 216 4.44E+01 6.52E+01 44 64 3.68E+00 6.42E+00 0 0 0 0 0.332148 0.124577 0 0 0 0 0 0 0 1 0 3.88278 1.33973 1.58291 1.66099 0 0 0 0.0217766 0.441078 1 1 0 0 80.462 70.3499 3.67684 6.41749 0 35.5482 30.0333 14.4921 37.235 0 1 0 0
10 0.044 9.97E-02 6.57E-01 271.25 300.4 1.62E+01 4.14E+01 2 0 0 0 30 30 110.17 83.77 109.5 83.5 9.70E+00 1.01E+01 199 199 4.45E+01 6.41E+01 44 64 3.89E+00 5.57E+00 0 0 0 0 -0.0888043 -0.0977739 0 0 0 0 0 0 0 0 0 29.6276 13.4003 1.77018 1.84869 0 1 1 9.43E-17 5.11E-08 1 1 1 0 80.5391 70.3664 3.8869 5.5729 1 271.25 300.4 16.2066 41.4429 0 1 0 0
11 0.000 3.13E-01 1.00E+00 33.14 140.1 1.22E+01 2.59E+01 1 0 0 1 29 29 80.55 75.97 79 77 7.16E+00 6.21E+00 214 214 4.38E+01 6.33E+01 44 63 3.62E+00 6.25E+00 0 0 0 0 0.0718478 0.0422421 0 0 0 0 0 0 0 0 0 -0.0613933 5.5843 1.33038 1.15379 0 0 1 0.964114 6.06E-05 1 1 0 0 80.6131 70.3812 3.61959 6.24957 0 -0.562076 125.186 12.1801 25.8651 0 1 0 0
12 0.142 6.38E-02 2.59E-02 1656.91 2298.52 3.42E+01 7.30E+01 1 0 1 0 26 26 261.65 172.92 263 173 1.91E+01 1.66E+01 195 195 4.39E+01 6.38E+01 44 64 2.87E+00 6.13E+00 0 0 0 0 0.288628 -0.086862 0 0 0 0 0 0 0 0 0 180.977 102.533 3.7404 3.25526 0 1 1 2.50E-26 4.34E-22 1 1 1 1 80.6768 70.3903 2.87117 6.12742 0 1656.91 2298.52 34.2446 72.9744 0 1 0 0
13 -0.053 6.52E-02 4.17E-01 1109.41 982.07 2.26E+01 4.36E+01 0 1 0 1 28 28 201.93 114.21 201.5 111.5 1.31E+01 1.03E+01 206 206 4.35E+01 6.40E+01 44 64 3.67E+00 6.06E+00 0 0 0 0 0.255331 -0.0665429 0 0 0 0 0 0 0 0 0 121.176 43.8083 2.47256 1.94525 0 1 1 2.65E-28 6.77E-20 1 1 1 1 80.7523 70.406 3.6688 6.05893 1 1109.41 982.07 22.6372 43.6076 0 1 0 0
14 -0.131 6.47E-02 4.35E-02 1582.6 1171.68 3.85E+01 5.69E+01 0 0 0 0 32 32 253.69 122.69 256.5 123.5 2.38E+01 1.43E+01 209 209 4.39E+01 6.42E+01 44 64 3.91E+00 5.78E+00 0 0 0 0 0.188112 -0.0467555 0 0 0 0 0 0 0 0 0 172.861 52.2664 4.20384 2.5366 0 1 1 9.37E-29 4.38E-20 1 1 1 1 80.8267 70.4211 3.90661 5.77955 0 1582.6 1171.68 38.4876 56.8641 0 1 0 0
15 0.024 7.39E-02 7.47E-01 529.99 559.97 1.65E+01 3.53E+01 3 0 2 1 24 24 138.79 95.42 138 96.5 8.84E+00 7.72E+00 210 210 4.41E+01 6.41E+01 44 64 3.36E+00 5.85E+00 0 0 0 0 0.048445 0.0155405 0 0 0 0 0 0 0 0 0 57.8885 24.9791 1.80476 1.57645 0 1 1 5.42E-21 1.39E-14 1 1 1 1 80.9032 70.4375 3.36089 5.85072 1 529.989 559.968 16.5232 35.34 0 1 0 0
16 0.000 3.46E-01 1.00E+00 27.95 131.71 1.30E+01 3.07E+01 1 0 0 0 28 28 78.5 71.64 79.5 69.5 7.52E+00 7.25E+00 192 192 4.40E+01 6.48E+01 44 65 3.05E+00 5.88E+00 0 0 0 0 0.0904301 0.0843545 0 0 0 0 0 0 0 0 0 -2.47965 1.18883 1.42028 1.36975 0 0 0 0.0953819 0.413121 1 1 0 0 80.9797 70.454 3.05248 5.87545 0 -22.7021 26.6504 13.0032 30.7064 0 1 0 0
17 0.261 1.18E-01 2.71E-02 166.75 304.07 1.57E+01 3.49E+01 0 2 0 0 30 30 99.27 84.03 100 84.5 9.40E+00 8.54E+00 200 200 4.39E+01 6.50E+01 44 64 3.26E+00 6.04E+00 0 0 0 0 0.159282 0.00618317 0 0 0 0 0 0 0 0 0 18.213 13.5642 1.71668 1.55843 0 1 1 1.37E-11 9.49E-10 1 1 1 0 81.0537 70.4691 3.25897 6.04364 0 166.746 304.074 15.7167 34.9359 0 1 0 0
18 -0.217 6.72E-02 1.23E-03 1516.04 919.47 3.48E+01 4.65E+01 0 0 0 0 32 32 246.72 111.5 247 111 2.15E+01 1.17E+01 201 201 4.35E+01 6.39E+01 43 64 3.60E+00 5.72E+00 0 0 0 0 -0.0390633 -0.163499 0 0 0 0 0 0 0 0 0 165.591 41.0157 3.80079 2.07423 0 1 1 1.54E-29 9.33E-20 1 1 1 1 81.1278 70.4843 3.59853 5.7238 0 1516.04 919.466 34.7976 46.4988 0 1 0 0
19 -0.065 9.23E-02 4.83E-01 351.32 302.62 1.39E+01 3.99E+01 2 1 0 0 26 26 119.58 84 119.5 83 7.74E+00 9.09E+00 207 207 4.38E+01 6.35E+01 44 63 3.62E+00 5.27E+00 0 0 0 0 0.221202 -0.0846941 0 0 0 0 0 0 0 0 0 38.373 13.4991 1.51827 1.78196 0 1 1 7.13E-20 5.36E-08 1 1 1 0 81.2039 70.5009 3.6154 5.2684 1 351.318 302.615 13.9003 39.947 0 1 0 0
20 0.150 6.61E-02 2.34E-02 930.34 1313.5 2.17E+01 5.72E+01 2 0 2 0 28 28 182.89 129.11 181 133 1.26E+01 1.35E+01 205 205 4.42E+01 6.42E+01 44 64 3.87E+00 6.62E+00 0 0 0 0 -0.238029 -0.0177767 0 0 0 0 0 0 0 0 0 101.618 58.5927 2.37232 2.5502 0 1 1 8.74E-27 7.06E-20 1 1 1 1 81.2752 70.5145 3.86537 6.62446 0 930.344 1313.5 21.7194 57.169 0 1 0 0

Total number of rows: 44259

Table truncated, full table size 15065 Kbytes.




Supplementary file Size Download File type/resource
GSM139290.txt.gz 11.2 Mb (ftp)(http) TXT

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