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Status
Public on Mar 07, 2009
Title
MCF7_NPAS2_Rep1-1
Sample type
genomic
Channel 1
Source name
Input
Organism
Homo sapiens
Characteristics
cell line: MCF7 antibody: rabbit IgG target: control replicate: rep 1, part 1
Biomaterial provider
ATCC
Extracted molecule
genomic DNA
Extraction protocol
GENECLEAN Turbo kit
Label
Cy3
Label protocol
Agilent Genomic DNA Labeling Kit PLUS (Agilent p/n 5188-5309)
Channel 2
Source name
NPAS2 targets
Organism
Homo sapiens
Characteristics
cell line: MCF7 antibody: anti-NPAS2 target: NPAS2 targets, ChIP-enriched replicate: rep 1, part 1
Biomaterial provider
ATCC
Extracted molecule
genomic DNA
Extraction protocol
The ChIP assay was performed using the ChIP Assay Kit ((Millipore, Billerica, MA) according to the manufacturer’s protocol. Briefly, cells were grown in 100 mm cell culture plates to 80% confluence. Cross-linking of protein and DNA was performed using cell culture medium containing 1% formaldehyde at room temperature for 10 minutes. Sonication was performed using an Omni Ruptor 250 Ultrasonic Homogenizer (omni International, Marietta, GA) to generate input material. This input sample was then incubated with primary antibody (anti-NPAS2) and negative control (Rabbit IgG) for immunoprecipitation (IP). Agarose beads were added to the reactions to bind protein-conjugated antibody. The antibody-protein-DNA complex was then eluted from the agarose beads with freshly prepared elution buffer (1% SDS, 0.1 M NaHCO3) and the cross-linking was reversed by adding 5M NaCl for 4 hours at 65ºC followed by proteinase K digestion at 45ºC for one hour. The final DNA, representing NPAS2 target sequences, was purified using the GENECLEAN Turbo kit (Qbiogene, Carlsbad, CA) according to the manufacturer’s instructions. Ligation-mediated PCR (LM-PCR) (Agilent Technologies, Foster City, CA) was used to amplify DNA according to the manufacturer’s protocol.
Label
Cy5
Label protocol
Agilent Genomic DNA Labeling Kit PLUS (Agilent p/n 5188-5309)
Hybridization protocol
SureHyb Hybridization Chamber according to Agilent's Instructions
Scan protocol
Agilent’s Microarray Scanner with SureScan Technology
Description
All Arrays were processed at Mogene, LC; an Agilent-certified service provider
Data processing
A whole-chip error model was used for array data analysis and to call a bound gene (target gene). The neighborhood error model takes into account neighboring probes and calls a region as bound, not just a single probe. Genes associated with significant regions are therefore considered target genes.
Submission date
Mar 01, 2009
Last update date
Mar 06, 2009
Contact name
Aaron Ezra Hoffman
E-mail(s)
aaron.hoffman@yale.edu
Organization name
Yale School of Medicine
Department
LEPH
Lab
702
Street address
60 College St.
City
New Haven
State/province
CT
ZIP/Postal code
06520
Country
USA
Platform ID
GPL4124
Series (1)
GSE15052
NPAS2 ChIP-on-chip in MCF7 cells
Data table header descriptions
ID_REF
VALUE
Log Ratio
LogRatioError
PValueLogRatio
gSurrogateUsed
rSurrogateUsed
gIsFound
rIsFound
gProcessedSignal
rProcessedSignal
gProcessedSigError
rProcessedSigError
gNumPixOLHi
rNumPixOLHi
gNumPixOLLo
rNumPixOLLo
gNumPix
rNumPix
gMeanSignal
rMeanSignal
gMedianSignal
rMedianSignal
gPixSDev
rPixSDev
gPixNormIQR
rPixNormIQR
gBGNumPix
rBGNumPix
gBGMeanSignal
rBGMeanSignal
gBGMedianSignal
rBGMedianSignal
gBGPixSDev
rBGPixSDev
gBGPixNormIQR
rBGPixNormIQR
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
xDev
gSpatialDetrendIsInFilteredSet
rSpatialDetrendIsInFilteredSet
gSpatialDetrendSurfaceValue
rSpatialDetrendSurfaceValue
SpotExtentX
SpotExtentY
gNetSignal
rNetSignal
gMultDetrendSignal
rMultDetrendSignal
gProcessedBackground
rProcessedBackground
gProcessedBkngError
rProcessedBkngError
IsUsedBGAdjust
gInterpolatedNegCtrlSub
rInterpolatedNegCtrlSub
gIsInNegCtrlRange
rIsInNegCtrlRange
gIsUsedInMD
rIsUsedInMD
Data table
ID_REF
VALUE
LogRatioError
PValueLogRatio
gSurrogateUsed
rSurrogateUsed
gIsFound
rIsFound
gProcessedSignal
rProcessedSignal
gProcessedSigError
rProcessedSigError
gNumPixOLHi
rNumPixOLHi
gNumPixOLLo
rNumPixOLLo
gNumPix
rNumPix
gMeanSignal
rMeanSignal
gMedianSignal
rMedianSignal
gPixSDev
rPixSDev
gPixNormIQR
rPixNormIQR
gBGNumPix
rBGNumPix
gBGMeanSignal
rBGMeanSignal
gBGMedianSignal
rBGMedianSignal
gBGPixSDev
rBGPixSDev
gBGPixNormIQR
rBGPixNormIQR
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
xDev
gSpatialDetrendIsInFilteredSet
rSpatialDetrendIsInFilteredSet
gSpatialDetrendSurfaceValue
rSpatialDetrendSurfaceValue
SpotExtentX
SpotExtentY
gNetSignal
rNetSignal
gMultDetrendSignal
rMultDetrendSignal
gProcessedBackground
rProcessedBackground
gProcessedBkngError
rProcessedBkngError
IsUsedBGAdjust
gInterpolatedNegCtrlSub
rInterpolatedNegCtrlSub
gIsInNegCtrlRange
rIsInNegCtrlRange
gIsUsedInMD
rIsUsedInMD
1
-4.06E-01
7.21E-02
1.79E-08
0
0
1
1
4.33E+03
1.70E+03
4.33E+02
1.74E+02
1
2
2
2
59
59
3.26E+02
4.36E+02
323
432
3.20E+01
5.32E+01
3.34E+01
4.19E+01
679
679
3.76E+01
6.33E+01
38
63
6.70E+00
1.25E+01
6.67E+00
1.19E+01
0
0
0
0
0.277434
0.0157666
0
0
0
0
0
0
0
0
0
283.623
315.657
28.3948
32.3496
0
1
1
0
0
1
1
1
1
42.106
120.259
6.69806
12.5238
0
4329.21
1698.92
433.418
174.112
0
1
-5.63E+00
0
0
42.106
120.259
54.7002
54.7002
305.126
415.384
0.772831
1.03896
37.5935
63.3432
6.69806
12.5238
0
283.648
276.944
0
0
0
0
2
0.00E+00
6.67E-01
1.00E+00
1.73735
6.76764
1
1
2.05E+01
3.78E+01
2.07E+01
3.82E+01
1
0
0
0
63
63
4.20E+01
1.25E+02
42
123
7.40E+00
2.35E+01
7.78E+00
2.74E+01
512
512
3.86E+01
6.53E+01
39
64
6.68E+00
1.28E+01
6.86E+00
1.20E+01
0
0
0
0
-0.177501
0.0490056
0
0
0
0
0
0
0
0
0
-0.0507169
4.79557
1.35873
7.09457
0
0
0
0.922701
0.0783821
1
1
0
0
42.0983
120.22
6.68141
12.7927
0
-0.771095
25.8429
20.6579
38.232
0
1
3.99E-01
0
0
42.0983
120.22
50.7771
50.7771
21.4446
104.485
0.775885
1.03766
38.5918
65.2891
6.68141
12.7927
0
-0.0234175
-33.5605
0
0
0
0
3
2.83E-01
6.57E-01
6.67E-01
1.73051
0
1
1
2.04E+01
3.92E+01
2.06E+01
3.84E+01
0
0
0
1
63
63
4.28E+01
1.27E+02
43
128
7.07E+00
2.03E+01
7.41E+00
2.08E+01
512
512
3.85E+01
6.53E+01
39
65
6.34E+00
1.29E+01
6.67E+00
1.33E+01
0
0
0
0
-0.0944488
0.00893446
0
0
0
0
0
0
0
0
0
0.749862
7.26236
1.36079
7.11551
0
0
1
0.151544
0.00773171
1
1
0
1
42.0914
120.182
6.33568
12.8506
0
11.3559
39.187
20.6079
38.3946
0
1
4.31E-01
0
0
42.0914
120.182
48.2044
48.2044
22.2383
106.913
0.778952
1.03632
38.502
65.2891
6.33568
12.8506
0
0.780436
-30.7243
0
0
0
0
4
5.97E-02
6.94E-02
3.90E-01
0
0
1
1
5.51E+02
6.33E+02
5.88E+01
7.39E+01
2
0
1
0
59
59
7.86E+01
2.37E+02
79
230
1.25E+01
4.02E+01
1.07E+01
4.26E+01
495
495
3.87E+01
6.67E+01
39
67
6.05E+00
1.36E+01
5.93E+00
1.48E+01
0
0
0
0
0.280514
-0.0132626
0
0
0
0
0
0
0
0
0
36.5418
117.077
3.89861
13.6811
0
1
1
0
1.18E-254
1
1
1
1
42.0853
120.144
6.04862
13.5529
0
551.325
632.508
58.8204
73.9123
0
1
8.59E-01
0
0
42.0853
120.144
51.0895
51.0895
58.0241
216.689
0.78187
1.03505
38.7394
66.6505
6.04862
13.5529
0
36.576
79.4421
0
0
1
1
5
-2.49E-01
7.56E-02
9.95E-04
0
0
1
1
6.55E+02
3.69E+02
6.86E+01
5.32E+01
1
1
0
0
65
65
8.56E+01
1.88E+02
86
187
1.75E+01
3.02E+01
1.93E+01
3.04E+01
518
518
3.90E+01
6.61E+01
39
66
6.64E+00
1.36E+01
6.67E+00
1.41E+01
0
0
0
0
0.2673
0.0075166
0
0
0
0
0
0
0
0
0
43.5686
68.2506
4.56381
9.83282
0
1
1
0
4.60E-114
1
1
1
1
42.0776
120.103
6.6432
13.6402
0
654.904
369.147
68.6011
53.1828
0
1
-3.29E+00
0
0
42.0776
120.103
50.7771
50.7771
65.0432
167.823
0.78478
1.03387
38.9633
66.0598
6.6432
13.6402
0
43.6049
30.957
0
0
1
0
6
7.88E-02
6.22E-02
2.05E-01
0
0
1
1
2.61E+03
3.12E+03
2.61E+02
3.15E+02
2
0
1
0
61
61
2.16E+02
6.97E+02
216
699
2.77E+01
1.16E+02
2.82E+01
1.15E+02
513
513
3.87E+01
6.62E+01
39
66
6.67E+00
1.32E+01
6.67E+00
1.33E+01
0
0
0
0
0.463856
0.0514971
0
0
0
0
0
0
0
0
0
174.028
577.036
17.4558
58.1361
0
1
1
0
0
1
1
1
1
42.0699
120.062
6.67135
13.2298
1
2606.08
3124.76
261.401
314.818
0
1
1.27E+00
0
0
42.0699
120.062
49.8279
49.8279
195.495
676.567
0.787744
1.03263
38.6803
66.2203
6.67135
13.2298
0
174.067
540.099
0
0
1
1
7
-5.50E-02
6.17E-02
3.72E-01
0
0
1
1
6.36E+03
5.60E+03
6.36E+02
5.62E+02
0
0
0
0
66
66
4.68E+02
1.15E+03
472.5
1122.5
5.99E+01
1.38E+02
5.21E+01
1.28E+02
514
514
3.83E+01
6.57E+01
38
65
6.58E+00
1.32E+01
7.23E+00
1.46E+01
0
0
0
0
0.468573
-0.0166527
0
0
0
0
0
0
0
0
0
426.347
1033.63
42.6563
103.605
0
1
1
0
0
1
1
1
1
42.0621
120.021
6.57962
13.174
0
6360.85
5603.84
636.408
561.697
0
1
-8.92E-01
0
0
42.0621
120.021
49.5074
49.5074
447.806
1133.12
0.790679
1.03142
38.2665
65.6751
6.57962
13.174
0
426.388
997.047
0
0
1
1
8
-1.57E-01
7.81E-02
4.48E-02
0
0
1
1
4.87E+02
3.39E+02
5.27E+01
5.13E+01
2
1
0
0
61
61
7.48E+01
1.82E+02
73
185
1.16E+01
3.13E+01
1.19E+01
3.11E+01
510
510
3.85E+01
6.46E+01
38
64
6.49E+00
1.17E+01
6.67E+00
1.19E+01
0
0
0
0
0.0210586
-0.0052008
0
0
0
0
0
0
0
0
0
32.7489
62.5122
3.54557
9.44356
0
1
1
0
1.14E-98
1
1
1
1
42.0544
119.98
6.49445
11.69
1
486.801
339.295
52.7037
51.2564
0
1
-2.01E+00
0
0
42.0544
119.98
51.4001
51.4001
54.2003
161.961
0.793591
1.03026
38.5431
64.6353
6.49445
11.69
0
32.7918
26.2784
0
0
1
0
9
3.34E-02
6.18E-02
5.88E-01
0
0
1
1
3.04E+03
3.29E+03
3.05E+02
3.31E+02
2
5
0
0
59
59
2.48E+02
7.25E+02
238
709
3.86E+01
9.90E+01
3.52E+01
6.60E+01
510
510
3.84E+01
6.59E+01
38
66
6.76E+00
1.29E+01
7.41E+00
1.26E+01
0
0
0
0
0.622838
-0.0224835
0
0
0
0
0
0
0
0
0
205.58
605.147
20.6029
60.9273
0
1
1
0
0
1
1
1
1
42.0466
119.937
6.75548
12.8591
0
3044.66
3288.24
305.131
331.066
0
1
5.41E-01
0
0
42.0466
119.937
52.9257
52.9257
227.024
704.554
0.796517
1.02909
38.3706
65.9373
6.75548
12.8591
0
205.626
569.267
0
0
1
1
10
2.95E-01
6.71E-02
1.09E-05
0
0
1
1
9.21E+03
1.82E+04
9.22E+02
1.82E+03
0
0
2
0
63
63
6.66E+02
3.46E+03
662
3425
5.55E+01
3.80E+02
6.34E+01
3.64E+02
513
513
3.83E+01
6.57E+01
38
65
6.74E+00
1.33E+01
7.41E+00
1.33E+01
0
0
0
0
0.497005
-0.0357743
0
0
0
0
0
0
0
0
0
624.373
3342.11
62.4521
334.286
0
1
1
0
0
1
1
1
1
42.0395
119.894
6.74255
13.2877
1
9213.69
18179.9
921.587
1818.4
0
1
4.40E+00
0
0
42.0395
119.894
51.0895
51.0895
645.81
3441.47
0.799397
1.02798
38.2943
65.7485
6.74255
13.2877
0
624.421
3306.57
0
0
1
1
11
-2.97E-01
9.15E-02
1.18E-03
0
0
1
1
4.19E+02
2.11E+02
4.64E+01
4.40E+01
2
0
0
0
62
62
7.05E+01
1.59E+02
70.5
159
1.35E+01
2.21E+01
1.32E+01
2.43E+01
507
507
3.88E+01
6.59E+01
39
65
6.92E+00
1.30E+01
7.41E+00
1.33E+01
0
0
0
0
0.0186176
-0.0124266
0
0
0
0
0
0
0
0
0
28.4839
38.8268
3.15586
8.0733
0
1
1
0
4.51E-43
1
1
1
1
42.0322
119.851
6.91836
13.0049
0
418.838
211.434
46.405
43.9636
0
1
-3.24E+00
0
0
42.0322
119.851
57.259
57.259
49.9131
138.146
0.802242
1.02687
38.7653
65.9014
6.91836
13.0049
0
28.5342
3.63979
0
0
1
0
12
-2.79E-01
7.38E-02
1.58E-04
0
0
1
1
7.97E+02
4.19E+02
8.22E+01
5.70E+01
3
1
0
0
57
57
9.64E+01
1.97E+02
96
197
1.45E+01
2.96E+01
1.19E+01
2.97E+01
503
503
3.81E+01
6.63E+01
38
66
6.28E+00
1.27E+01
5.93E+00
1.26E+01
0
0
0
0
-0.16164
-0.0720048
0
0
0
0
0
0
0
0
0
54.414
76.9477
5.60848
10.4553
0
1
1
0
2.94E-138
1
1
1
1
42.0246
119.807
6.2834
12.7322
0
797.305
419.444
82.1786
56.9919
0
1
-3.78E+00
0
0
42.0246
119.807
50.4627
50.4627
75.8356
176.223
0.805079
1.02584
38.0537
66.2505
6.2834
12.7322
0
54.4665
42.0985
0
0
1
0
13
-2.69E-01
1.03E-01
8.86E-03
0
0
1
1
3.22E+02
1.74E+02
3.79E+01
4.23E+01
0
0
0
0
66
66
6.41E+01
1.52E+02
63
148.5
1.24E+01
2.82E+01
1.26E+01
3.22E+01
510
510
3.79E+01
6.54E+01
38
65
6.50E+00
1.31E+01
7.41E+00
1.33E+01
0
0
0
0
-0.00125856
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0
0
0
0
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64
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64
64
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163
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1
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42.0014
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370.946
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1
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25.6347
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0
1
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1
1
3.64E+02
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61
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1
1
41.9943
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363.558
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1
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0
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41.9943
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57.259
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46.5445
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0.816154
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25.2139
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1
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17
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7.46E-02
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0
1
1
6.92E+02
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0
0
65
65
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194
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489
489
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1
1
41.9872
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66
66
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22.055
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0
1
0
19
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1
1
1.41E+03
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1
0
0
63
63
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138
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503
503
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1
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1
1
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63
63
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41.964
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231.263
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0
0
1
1
Total number of rows: 243494 Table truncated, full table size 125001 Kbytes .Supplementary data files not provided
Processed data included within Sample table