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Status
Public on Mar 07, 2009
Title
MCF7_NPAS2_Rep2-2
Sample type
genomic
Channel 1
Source name
Input
Organism
Homo sapiens
Characteristics
cell line: MCF7 antibody: rabbit IgG target: control replicate: rep 2, part 2
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 2, part 2
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
GPL4125
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
gIsLowPMTScaledUp
rIsLowPMTScaledUp
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
gIsLowPMTScaledUp
rIsLowPMTScaledUp
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
-1.85E-01
6.38E-02
3.80E-03
0
0
1
1
4.95E+03
3.23E+03
4.96E+02
3.25E+02
1
0
3
1
60
60
3.41E+02
4.02E+02
343.5
398.5
3.74E+01
6.51E+01
2.93E+01
7.06E+01
688
688
3.74E+01
4.46E+01
37
44
6.62E+00
1.02E+01
6.67E+00
1.11E+01
0
0
0
0
0
0
0.320985
-0.00601873
0
0
0
0
0
0
0
0
0
298.764
353.214
29.9165
35.4503
0
1
1
0
0
1
1
1
1
42.0357
48.6522
6.61834
10.189
0
4948.44
3233.9
495.508
324.569
0
1
-2.89E+00
0
0
42.0357
48.6522
54.7002
54.7002
319.935
381.588
0.622729
0.673135
37.3939
44.564
6.61834
10.189
0
299.094
350.105
0
0
0
0
2
0.00E+00
5.26E-01
1.00E+00
2.4484
4.42234
0
0
2.53E+01
2.73E+01
1.60E+01
2.75E+01
0
5
0
0
63
63
4.23E+01
4.60E+01
41
46
7.72E+00
8.45E+00
7.41E+00
8.52E+00
514
514
3.77E+01
4.52E+01
37
45
6.71E+00
9.63E+00
6.67E+00
9.64E+00
0
0
0
0
0
0
0.034078
-0.100632
0
0
0
0
0
0
0
0
0
0.270706
-2.70143
0.973177
3.01946
0
0
0
0.649391
0.0201586
1
1
0
0
42.0309
48.6538
6.70507
9.62758
0
4.45166
-24.5779
16.0035
27.4714
0
1
6.29E-02
0
0
42.0309
48.6538
65
65
21.4366
25.6734
0.627214
0.677392
37.6595
45.2198
6.70507
9.62758
0
0.593208
-5.81124
0
0
0
0
3
-6.24E-02
5.37E-01
9.07E-01
0
4.39461
1
1
3.13E+01
2.71E+01
2.33E+01
2.74E+01
13
8
0
0
51
51
4.39E+01
5.12E+01
43
51
1.02E+01
1.06E+01
7.41E+00
1.04E+01
504
504
3.75E+01
4.43E+01
37.5
44
6.64E+00
9.21E+00
5.93E+00
9.64E+00
0
0
0
0
0
0
0.1003
-0.00385923
0
0
0
0
0
0
0
0
0
1.915
2.54166
1.4295
3.03014
0
1
0
0.00132767
0.0287994
1
1
1
0
42.0262
48.6544
6.64085
9.21172
0
31.2673
22.9793
23.3401
27.3957
0
1
-1.16E-01
0
0
42.0262
48.6544
56.9804
56.9804
23.0762
30.9171
0.631711
0.681665
37.4504
44.25
6.64085
9.21172
0
2.22999
-0.570186
0
0
0
0
4
-1.24E-01
7.20E-02
8.49E-02
0
0
1
1
5.14E+02
3.86E+02
5.72E+01
4.72E+01
2
0
0
0
63
63
7.37E+01
9.17E+01
75
92
1.31E+01
2.15E+01
1.15E+01
2.37E+01
513
513
3.72E+01
4.53E+01
37
45
6.58E+00
9.61E+00
6.67E+00
1.04E+01
0
0
0
0
0
0
-0.0575016
-0.0140045
0
0
0
0
0
0
0
0
0
31.7243
43.0128
3.52991
5.2553
0
1
1
0
1.41E-207
1
1
1
1
42.0217
48.6539
6.57952
9.61185
1
514.294
386.451
57.2246
47.2165
0
1
-1.72E+00
0
0
42.0217
48.6539
50.1463
50.1463
52.881
71.3877
0.636239
0.685952
37.1949
45.2846
6.57952
9.61185
0
32.0319
39.8981
0
0
1
1
5
2.13E-01
6.46E-02
9.95E-04
0
0
1
1
2.36E+03
3.85E+03
2.37E+02
3.86E+02
1
3
0
0
60
60
1.89E+02
4.80E+02
184.5
477.5
2.93E+01
6.30E+01
2.87E+01
5.95E+01
505
505
3.81E+01
4.50E+01
38
45
6.69E+00
9.30E+00
6.67E+00
8.90E+00
0
0
0
0
0
0
-0.0747834
-0.115537
0
0
0
0
0
0
0
0
0
146.683
431.644
14.7497
43.2699
0
1
1
0
0
1
1
1
1
42.0169
48.6555
6.6889
9.29667
1
2361.73
3854.77
237.484
386.419
0
1
3.29E+00
0
0
42.0169
48.6555
49.8279
49.8279
167.835
460.021
0.640604
0.69011
38.0812
45.0495
6.6889
9.29667
0
146.983
428.528
0
0
1
1
6
3.34E-01
1.09E-01
2.14E-03
0
0
1
1
1.25E+02
2.69E+02
2.77E+01
3.80E+01
1
0
0
0
63
63
4.98E+01
7.90E+01
50
82
8.85E+00
2.02E+01
8.15E+00
2.26E+01
504
504
3.82E+01
4.58E+01
38
46
6.82E+00
9.50E+00
6.67E+00
9.82E+00
0
0
0
0
0
0
0.074787
-0.0632071
0
0
0
0
0
0
0
0
0
7.8132
30.3428
1.73389
4.28066
0
1
1
4.06E-37
4.85E-122
1
1
1
1
42.0122
48.6572
6.81799
9.50462
0
124.918
269.303
27.7216
37.9923
0
1
3.07E+00
0
0
42.0122
48.6572
56.9804
56.9804
28.9604
58.721
0.645124
0.694394
38.1548
45.7599
6.81799
9.50462
0
8.10584
27.2259
0
0
0
0
7
-6.34E-02
6.20E-02
3.07E-01
0
0
1
1
2.54E+03
2.20E+03
2.56E+02
2.21E+02
0
1
1
0
66
66
2.02E+02
2.98E+02
201.5
300.5
3.02E+01
5.18E+01
3.11E+01
6.41E+01
512
512
3.90E+01
4.59E+01
39
45
7.21E+00
9.51E+00
7.41E+00
9.64E+00
0
0
0
0
0
0
0.253357
-0.0310024
0
0
0
0
0
0
0
0
0
160.235
249.22
16.0981
25.1043
0
1
1
0
0
1
1
1
1
42.0075
48.6587
7.20743
9.50767
0
2544.34
2198.59
255.618
221.467
0
1
-1.02E+00
0
0
42.0075
48.6587
57.5363
57.5363
181.377
277.6
0.649563
0.698601
38.9863
45.9141
7.20743
9.50767
0
160.52
246.102
0
0
1
1
8
3.35E-01
6.87E-02
1.07E-06
0
0
1
1
3.41E+03
7.39E+03
3.42E+02
7.39E+02
2
0
0
0
63
63
2.58E+02
8.91E+02
258
868
3.77E+01
1.53E+02
3.52E+01
1.58E+02
512
512
3.83E+01
4.61E+01
38
45
6.72E+00
9.57E+00
6.67E+00
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0
0
0
0
0
0
0.236495
0.00784309
0
0
0
0
0
0
0
0
0
216.458
842.419
21.701
84.296
0
1
1
0
0
1
1
1
1
42.0027
48.6602
6.71596
9.56784
1
3414.04
7387.88
342.275
739.262
0
1
4.88E+00
0
0
42.0027
48.6602
52.0157
52.0157
237.595
870.8
0.653949
0.702747
38.3359
46.1016
6.71596
9.56784
0
216.735
839.3
0
0
1
1
9
-2.63E-01
7.60E-02
5.46E-04
0
0
1
1
5.47E+02
2.99E+02
5.99E+01
3.98E+01
0
0
0
0
65
65
7.69E+01
8.29E+01
76
83
1.28E+01
2.14E+01
1.11E+01
2.30E+01
515
515
3.84E+01
4.56E+01
38
45
7.32E+00
9.34E+00
7.41E+00
9.64E+00
0
0
0
0
0
0
0.058469
0.0331241
0
0
0
0
0
0
0
0
0
34.9404
34.2767
3.82155
4.56794
0
1
1
0
4.92E-148
1
1
1
1
41.998
48.6617
7.31721
9.34003
0
547.455
298.846
59.877
39.8262
0
1
-3.46E+00
0
0
41.998
48.6617
48.2044
48.2044
56.0735
62.6595
0.658293
0.706875
38.4078
45.6019
7.31721
9.34003
0
35.2108
31.1563
0
0
1
1
10
-6.39E-02
6.79E-02
3.47E-01
0
0
1
1
5.84E+02
5.04E+02
6.31E+01
5.68E+01
0
0
0
0
65
65
7.95E+01
1.07E+02
82
101
1.55E+01
2.22E+01
1.33E+01
2.22E+01
497
497
3.86E+01
4.52E+01
38
44
6.71E+00
9.78E+00
6.67E+00
1.04E+01
0
0
0
0
0
0
0.180231
0.00192455
0
0
0
0
0
0
0
0
0
37.4987
58.1222
4.05678
6.54974
0
1
1
0
0.00E+00
1
1
1
1
41.9936
48.6624
6.70851
9.7754
1
583.568
503.745
63.133
56.7665
0
1
-9.40E-01
0
0
41.9936
48.6624
48.5334
48.5334
58.6273
86.5056
0.662772
0.711086
38.6117
45.2414
6.70851
9.7754
0
37.7616
55.0006
0
0
1
1
11
5.81E-02
6.91E-02
4.00E-01
0
0
1
1
4.61E+02
5.27E+02
5.19E+01
5.87E+01
0
0
0
0
62
62
7.18E+01
1.10E+02
71
110
1.23E+01
2.14E+01
1.32E+01
2.32E+01
512
512
3.79E+01
4.49E+01
38
45
6.56E+00
8.91E+00
6.86E+00
8.15E+00
0
0
0
0
0
0
0.0211006
-0.0733992
0
0
0
0
0
0
0
0
0
29.8013
61.127
3.35814
6.81779
0
1
1
7.35717e-310
0
1
1
1
1
41.9891
48.6633
6.55828
8.91406
0
460.738
526.715
51.9179
58.747
0
1
8.42E-01
0
0
41.9891
48.6633
55.8519
55.8519
50.9253
89.5113
0.667144
0.715234
37.9316
44.8945
6.55828
8.91406
0
30.057
58.0033
0
0
1
1
12
4.90E-02
6.22E-02
4.31E-01
0
0
1
1
1.59E+03
1.78E+03
1.60E+02
1.79E+02
1
1
1
0
62
62
1.45E+02
2.56E+02
147.5
255.5
1.47E+01
4.19E+01
1.48E+01
4.56E+01
519
519
3.82E+01
4.56E+01
38
45
6.74E+00
9.30E+00
7.41E+00
9.64E+00
0
0
0
0
0
0
0.119906
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0
0
0
0
0
0
0
0
0
103.274
207.255
10.4427
20.9443
0
1
1
0
0
1
1
1
1
41.9844
48.6646
6.74138
9.299
1
1586.3
1775.67
160.402
179.442
0
1
7.87E-01
0
0
41.9844
48.6646
50.4627
50.4627
124.393
235.64
0.671495
0.719337
38.2004
45.5549
6.74138
9.299
0
103.522
204.13
0
0
1
1
13
1.79E-01
6.36E-02
4.90E-03
0
0
1
1
7.76E+03
1.17E+04
7.76E+02
1.17E+03
0
0
3
1
62
62
5.50E+02
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538
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11715.9
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82.5198
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60
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459
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2847.27
3453.74
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1.35E+00
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41.9705
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189.172
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41.9663
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302.581
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38.1162
28.288
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1
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41.9663
48.6688
57.259
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0.688763
0.735632
37.6808
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20.4249
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4.14E-02
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1
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64
64
1.29E+02
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221
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41.962
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1298.26
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1
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1
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1
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63
63
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124
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44.5
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41.9577
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49.1849
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10.2014
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64.8506
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1
1
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0
1
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0
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66
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1
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441.979
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Total number of rows: 243485 Table truncated, full table size 125219 Kbytes .Supplementary data files not provided
Processed data included within Sample table