-
1
-
-
38449114551
-
Chop it, ChIP it, check it: The current status of chromatin immunoprecipitation
-
Collas, P. and Dahl, J. A. (2008) Chop it, ChIP it, check it: the current status of chromatin immunoprecipitation. Front Biosci. 13, 929–943.
-
(2008)
Front Biosci
, vol.13
, pp. 929-943
-
-
Collas, P.1
Dahl, J.A.2
-
2
-
-
0029119093
-
Histone H4 acetylation distinguishes coding regions of the human genome from heterochromatin in a differentiation-dependent but transcription-independent manner
-
O’Neill, L. P. and Turner, B. M. (1995) Histone H4 acetylation distinguishes coding regions of the human genome from heterochromatin in a differentiation-dependent but transcription-independent manner. EMBO J. 14, 3946–3957.
-
(1995)
EMBO J
, vol.14
, pp. 3946-3957
-
-
O’Neill, L.P.1
Turner, B.M.2
-
3
-
-
0029827129
-
Immunoprecipitation of chromatin
-
O’Neill, L. P. and Turner, B. M. (1996) Immunoprecipitation of chromatin. Methods Enzymol. 274, 189–197.
-
(1996)
Methods Enzymol
, vol.274
, pp. 189-197
-
-
O’Neill, L.P.1
Turner, B.M.2
-
4
-
-
33745549658
-
Epigenetic characterization of the early embryo with a chromatin immunoprecipitation protocol applicable to small cell populations
-
O’Neill, L. P., Vermilyea, M. D. and Turner, B. M. (2006) Epigenetic characterization of the early embryo with a chromatin immunoprecipitation protocol applicable to small cell populations. Nat. Genet. 38, 835–841.
-
(2006)
Nat. Genet.
, vol.38
, pp. 835-841
-
-
O’Neill, L.P.1
Vermilyea, M.D.2
Turner, B.M.3
-
5
-
-
33646872978
-
Chromatin signatures of pluripotent cell lines
-
Azuara, V., Perry, P., Sauer, S., Spivakov, M., Jorgensen, H. F., John, R. M., Gouti, M., Casanova, M., Warnes, G., Merkenschlager, M. and Fisher, A. G. (2006) Chromatin signatures of pluripotent cell lines. Nat. Cell Biol. 8, 532–538.
-
(2006)
Nat. Cell Biol.
, vol.8
, pp. 532-538
-
-
Azuara, V.1
Perry, P.2
Sauer, S.3
Spivakov, M.4
Jorgensen, H.F.5
John, R.M.6
Gouti, M.7
Casanova, M.8
Warnes, G.9
Merkenschlager, M.10
Fisher, A.G.11
-
6
-
-
31544463601
-
Fast chromatin immunoprecipitation assay
-
Nelson, J. D., Denisenko, O., Sova, P. and Bomsztyk, K. (2006) Fast chromatin immunoprecipitation assay. Nucleic Acids Res. 34, e2.
-
(2006)
Nucleic Acids Res
, vol.34
, pp. e2
-
-
Nelson, J.D.1
Denisenko, O.2
Sova, P.3
Bomsztyk, K.4
-
7
-
-
34147171123
-
2ChIP, a quick and quantitative chromatin immunoprecipitation assay unravels epigenetic dynamics of developmentally regulated genes in human carcinoma cells
-
2ChIP, a quick and quantitative chromatin immunoprecipitation assay unravels epigenetic dynamics of developmentally regulated genes in human carcinoma cells. Stem Cells 25, 1037–1046.
-
(2007)
Stem Cells
, vol.25
, pp. 1037-1046
-
-
Dahl, J.A.1
Collas, P.2
-
8
-
-
34547635995
-
Epigenetic characterization of hematopoietic stem cell differentiation using miniChIP and bisulfite sequencing analysis
-
Attema, J. L., Papathanasiou, P., Forsberg, E. C., Xu, J., Smale, S. T. and Weissman, I. L. (2007) Epigenetic characterization of hematopoietic stem cell differentiation using miniChIP and bisulfite sequencing analysis. Proc. Natl. Acad. Sci U. S. A 104, 12371–12376.
-
(2007)
Proc. Natl. Acad. Sci U. S. A
, vol.104
, pp. 12371-12376
-
-
Attema, J.L.1
Papathanasiou, P.2
Forsberg, E.C.3
Xu, J.4
Smale, S.T.5
Weissman, I.L.6
-
9
-
-
19944430797
-
Genomic maps and comparative analysis of histone modifications in human and mouse
-
Bernstein, B. E., Kamal, M., Lindblad-Toh, K., Bekiranov, S., Bailey, D. K., Huebert, D. J., McMahon, S., Karlsson, E. K., Kulbokas, E. J., III, Gingeras, T. R., Schreiber, S. L. and Lander, E. S. (2005) Genomic maps and comparative analysis of histone modifications in human and mouse. Cell 120, 169–181.
-
(2005)
Cell
, vol.120
, pp. 169-181
-
-
Bernstein, B.E.1
Kamal, M.2
Lindblad-Toh, K.3
Bekiranov, S.4
Bailey, D.K.5
Huebert, D.J.6
McMahon, S.7
Karlsson, E.K.8
Kulbokas, E.J.9
Gingeras, T.R.10
Schreiber, S.L.11
Lander, E.S.12
-
10
-
-
25144525014
-
Core transcriptional regulatory circuitry in human embryonic stem cells
-
Boyer, L. A., Lee, T. I., Cole, M. F., Johnstone, S. E., Levine, S. S., Zucker, J. P., Guenther, M. G., Kumar, R. M., Murray, H. L., Jenner, R. G., Gifford, D. K., Melton, D. A., Jaenisch, R. and Young, R. A. (2005) Core transcriptional regulatory circuitry in human embryonic stem cells. Cell 122, 947–956.
-
(2005)
Cell
, vol.122
, pp. 947-956
-
-
Boyer, L.A.1
Lee, T.I.2
Cole, M.F.3
Johnstone, S.E.4
Levine, S.S.5
Zucker, J.P.6
Guenther, M.G.7
Kumar, R.M.8
Murray, H.L.9
Jenner, R.G.10
Gifford, D.K.11
Melton, D.A.12
Jaenisch, R.13
Young, R.A.14
-
11
-
-
33646070846
-
A bivalent chromatin structure marks key developmental genes in embryonic stem cells
-
Bernstein, B. E., Mikkelsen, T. S., Xie, X., Kamal, M., Huebert, D. J., Cuff, J., Fry, B., Meissner, A., Wernig, M., Plath, K., Jaenisch, R., Wagschal, A., Feil, R., Schreiber, S. L. and Lander, E. S. (2006) A bivalent chromatin structure marks key developmental genes in embryonic stem cells. Cell 125, 315–326.
-
(2006)
Cell
, vol.125
, pp. 315-326
-
-
Bernstein, B.E.1
Mikkelsen, T.S.2
Xie, X.3
Kamal, M.4
Huebert, D.J.5
Cuff, J.6
Fry, B.7
Meissner, A.8
Wernig, M.9
Plath, K.10
Jaenisch, R.11
Wagschal, A.12
Feil, R.13
Schreiber, S.L.14
Lander, E.S.15
-
12
-
-
33645381936
-
The Oct4 and Nanog transcription network regulates pluripotency in mouse embryonic stem cells
-
Loh, Y. H., Wu, Q., Chew, J. L., Vega, V. B., Zhang, W., Chen, X., Bourque, G., George, J., Leong, B., Liu, J., Wong, K. Y., Sung, K. W., Lee, C. W., Zhao, X. D., Chiu, K. P., Lipovich, L., Kuznetsov, V. A., Robson, P., Stanton, L. W., Wei, C. L., Ruan, Y., Lim, B. and Ng, H. H. (2006) The Oct4 and Nanog transcription network regulates pluripotency in mouse embryonic stem cells. Nat. Genet. 38, 431–440.
-
(2006)
Nat. Genet.
, vol.38
, pp. 431-440
-
-
Loh, Y.H.1
Wu, Q.2
Chew, J.L.3
Vega, V.B.4
Zhang, W.5
Chen, X.6
Bourque, G.7
George, J.8
Leong, B.9
Liu, J.10
Wong, K.Y.11
Sung, K.W.12
Lee, C.W.13
Zhao, X.D.14
Chiu, K.P.15
Lipovich, L.16
Kuznetsov, V.A.17
Robson, P.18
Stanton, L.W.19
Wei, C.L.20
Ruan, Y.21
Lim, B.22
Ng, H.H.23
more..
-
13
-
-
33646865180
-
Control of developmental regulators by Polycomb in human embryonic stem cells
-
Lee, T. I., Jenner, R. G., Boyer, L. A., Guenther, M. G., Levine, S. S., Kumar, R. M., Chevalier, B., Johnstone, S. E., Cole, M. F., Isono, K., Koseki, H., Fuchikami, T., Abe, K., Murray, H. L., Zucker, J. P., Yuan, B., Bell, G. W., Herbolsheimer, E., Hannett, N. M., Sun, K., Odom, D. T., Otte, A. P., Volkert, T. L., Bartel, D. P., Melton, D. A., Gifford, D. K., Jaenisch, R. and Young, R. A. (2006) Control of developmental regulators by Polycomb in human embryonic stem cells. Cell 125, 301–313.
-
(2006)
Cell
, vol.125
, pp. 301-313
-
-
Lee, T.I.1
Jenner, R.G.2
Boyer, L.A.3
Guenther, M.G.4
Levine, S.S.5
Kumar, R.M.6
Chevalier, B.7
Johnstone, S.E.8
Cole, M.F.9
Isono, K.10
Koseki, H.11
Fuchikami, T.12
Abe, K.13
Murray, H.L.14
Zucker, J.P.15
Yuan, B.16
Bell, G.W.17
Herbolsheimer, E.18
Hannett, N.M.19
Sun, K.20
Odom, D.T.21
Otte, A.P.22
Volkert, T.L.23
Bartel, D.P.24
Melton, D.A.25
Gifford, D.K.26
Jaenisch, R.27
Young, R.A.28
more..
-
14
-
-
34447098370
-
A chromatin landmark and transcription initiation at most promoters in human cells
-
Guenther, M. G., Levine, S. S., Boyer, L. A., Jaenisch, R. and Young, R. A. (2007) A chromatin landmark and transcription initiation at most promoters in human cells. Cell 130, 77–88.
-
(2007)
Cell
, vol.130
, pp. 77-88
-
-
Guenther, M.G.1
Levine, S.S.2
Boyer, L.A.3
Jaenisch, R.4
Young, R.A.5
-
15
-
-
37349081961
-
Genome-scale ChIP-chip analysis using 10,000 human cells
-
Acevedo, L. G., Iniguez, A. L., Holster, H. L., Zhang, X., Green, R. and Farnham, P. J. (2007) Genome-scale ChIP-chip analysis using 10,000 human cells. Biotechniques 43, 791–797.
-
(2007)
Biotechniques
, vol.43
, pp. 791-797
-
-
Acevedo, L.G.1
Iniguez, A.L.2
Holster, H.L.3
Zhang, X.4
Green, R.5
Farnham, P.J.6
-
16
-
-
34548424709
-
Whole-genome mapping of histone H3 Lys4 and 27 trimethylations reveals distinct genomic compartments in human embryonic stem cells
-
Zhao, X. D., Han, X., Chew, J. L., Liu, J., Chiu, K. P., Choo, A., Orlov, Y. L., Sung, W. K., Shahab, A., Kuznetsov, V. A., Bourque, G., Oh, S., Ruan, Y., Ng, H. H. and Wei, C. L. (2007) Whole-genome mapping of histone H3 Lys4 and 27 trimethylations reveals distinct genomic compartments in human embryonic stem cells. Cell Stem Cell 1, 286–298.
-
(2007)
Cell Stem Cell
, vol.1
, pp. 286-298
-
-
Zhao, X.D.1
Han, X.2
Chew, J.L.3
Liu, J.4
Chiu, K.P.5
Choo, A.6
Orlov, Y.L.7
Sung, W.K.8
Shahab, A.9
Kuznetsov, V.A.10
Bourque, G.11
Oh, S.12
Ruan, Y.13
Ng, H.H.14
Wei, C.L.15
-
17
-
-
0041668072
-
Immunoprecipitation of native chromatin: NChIP
-
O’Neill, L. P. and Turner, B. M. (2003) Immunoprecipitation of native chromatin: NChIP. Methods 31, 76–82.
-
(2003)
Methods
, vol.31
, pp. 76-82
-
-
O’Neill, L.P.1
Turner, B.M.2
-
18
-
-
85138996980
-
High-throughput methods of regulatory element discovery
-
Hudson, M. E. and Snyder, M. (2006) High-throughput methods of regulatory element discovery. Biotechniques 41, 673, 675, 677.
-
(2006)
Biotechniques 41
, vol.673
, Issue.675
, pp. 677
-
-
Hudson, M.E.1
Snyder, M.2
-
19
-
-
36448975122
-
Paired-end genomic signature tags: A method for the functional analysis of genomes and epigenomes
-
Dunn, J. J., McCorkle, S. R., Everett, L. and Anderson, C. W. (2007) Paired-end genomic signature tags: a method for the functional analysis of genomes and epigenomes. Genet. Eng. 28, 159–173.
-
(2007)
Genet. Eng
, vol.28
, pp. 159-173
-
-
Dunn, J.J.1
McCorkle, S.R.2
Everett, L.3
Anderson, C.W.4
-
20
-
-
33845306470
-
Genomic approaches to early embryogenesis and stem cell biology
-
Aiba, K., Carter, M. G., Matoba, R. and Ko, M. S. (2006) Genomic approaches to early embryogenesis and stem cell biology. Semin. Reprod. Med. 24, 330–339.
-
(2006)
Semin. Reprod. Med.
, vol.24
, pp. 330-339
-
-
Aiba, K.1
Carter, M.G.2
Matoba, R.3
Ko, M.S.4
-
21
-
-
33747869931
-
Mapping histone modifications by nucleosome immunoprecipitation
-
Clark, D. J. and Shen, C. H. (2006) Mapping histone modifications by nucleosome immunoprecipitation. Methods Enzymol. 410, 416–430.
-
(2006)
Methods Enzymol
, vol.410
, pp. 416-430
-
-
Clark, D.J.1
Shen, C.H.2
-
22
-
-
33747835616
-
Mapping the distribution of chromatin proteins by ChIP on chip
-
Negre, N., Lavrov, S., Hennetin, J., Bellis, M. and Cavalli, G. (2006) Mapping the distribution of chromatin proteins by ChIP on chip. Methods Enzymol. 410, 316–341.
-
(2006)
Methods Enzymol
, vol.410
, pp. 316-341
-
-
Negre, N.1
Lavrov, S.2
Hennetin, J.3
Bellis, M.4
Cavalli, G.5
-
23
-
-
33746864004
-
ChIP-chip comes of age for genome-wide functional analysis
-
Wu, J., Smith, L. T., Plass, C. and Huang, T. H. (2006) ChIP-chip comes of age for genome-wide functional analysis. Cancer Res. 66, 6899–6902.
-
(2006)
Cancer Res
, vol.66
, pp. 6899-6902
-
-
Wu, J.1
Smith, L.T.2
Plass, C.3
Huang, T.H.4
-
24
-
-
33746829957
-
DNA microarray technologies for measuring protein-DNA interactions
-
Bulyk, M. L. (2006) DNA microarray technologies for measuring protein-DNA interactions. Curr. Opin. Biotechnol. 17, 422–430.
-
(2006)
Curr. Opin. Biotechnol.
, vol.17
, pp. 422-430
-
-
Bulyk, M.L.1
-
25
-
-
34047211996
-
Comparison of sample preparation methods for ChIP-chip assays
-
O’Geen, H., Nicolet, C. M., Blahnik, K., Green, R. and Farnham, P. J. (2006) Comparison of sample preparation methods for ChIP-chip assays. Biotechniques 41, 577–580.
-
(2006)
Biotechniques
, vol.41
, pp. 577-580
-
-
O’Geen, H.1
Nicolet, C.M.2
Blahnik, K.3
Green, R.4
Farnham, P.J.5
-
26
-
-
33847661809
-
Protocol for the fast chromatin immunoprecipitation (ChIP) method
-
Nelson, J. D., Denisenko, O. and Bomsztyk, K. (2006) Protocol for the fast chromatin immunoprecipitation (ChIP) method. Nat. Protoc. 1, 179–185.
-
(2006)
Nat. Protoc.
, vol.1
, pp. 179-185
-
-
Nelson, J.D.1
Denisenko, O.2
Bomsztyk, K.3
-
27
-
-
39449114225
-
Microplate-based chromatin immunoprecipitation method, Matrix ChIP: A platform to study signaling of complex genomic events
-
Flanagin, S., Nelson, J. D., Castner, D. G., Denisenko, O. and Bomsztyk, K. (2008) Microplate-based chromatin immunoprecipitation method, Matrix ChIP: a platform to study signaling of complex genomic events. Nucleic Acids Res. 36, e17.
-
(2008)
Nucleic Acids Res
, vol.36
, pp. e17
-
-
Flanagin, S.1
Nelson, J.D.2
Castner, D.G.3
Denisenko, O.4
Bomsztyk, K.5
-
28
-
-
74049115531
-
Chromatin profiling by directly sequencing small quantities of immunoprecipitated DNA
-
Goren, A., Ozsolak, F., Shoresh, N., Ku, M., Adli, M., Hart, C., Gymrek, M., Zuk, O., Regev, A., Milos, P. M. and Bernstein, B. E. (2010) Chromatin profiling by directly sequencing small quantities of immunoprecipitated DNA. Nat. Methods 7, 47–49.
-
(2010)
Nat. Methods
, vol.7
, pp. 47-49
-
-
Goren, A.1
Ozsolak, F.2
Shoresh, N.3
Ku, M.4
Adli, M.5
Hart, C.6
Gymrek, M.7
Zuk, O.8
Regev, A.9
Milos, P.M.10
Bernstein, B.E.11
-
29
-
-
39449101500
-
MicroChIP – A rapid micro chromatin immunoprecipitation assay for small cell samples and biopsies
-
Dahl, J. A. and Collas, P. (2008) MicroChIP – A rapid micro chromatin immunoprecipitation assay for small cell samples and biopsies. Nucleic Acids Res. 36, e15.
-
(2008)
Nucleic Acids Res
, vol.36
, pp. e15
-
-
Dahl, J.A.1
Collas, P.2
-
30
-
-
44949138461
-
A rapid micro chromatin immunoprecipitation assay (mChIP)
-
Dahl, J. A. and Collas, P. (2008) A rapid micro chromatin immunoprecipitation assay (mChIP). Nat. Protoc. 3, 1032–1045.
-
(2008)
Nat. Protoc.
, vol.3
, pp. 1032-1045
-
-
Dahl, J.A.1
Collas, P.2
-
31
-
-
0034161329
-
Mapping chromosomal proteins in vivo by formaldehyde-crosslinked-chromatin immunoprecipitation
-
Orlando, V. (2000) Mapping chromosomal proteins in vivo by formaldehyde-crosslinked-chromatin immunoprecipitation. Trends Biochem. Sci. 25, 99–104.
-
(2000)
Trends Biochem. Sci.
, vol.25
, pp. 99-104
-
-
Orlando, V.1
|