-
1
-
-
84886808679
-
Chromatin proteins and modifications as drug targets
-
Helin, K., and Dhanak, D. (2013) Chromatin proteins and modifications as drug targets. Nature 502, 480-488
-
(2013)
Nature
, vol.502
, pp. 480-488
-
-
Helin, K.1
Dhanak, D.2
-
2
-
-
80054787805
-
Targeting Histone Demethylases: A New Avenue for the Fight against Cancer
-
Rotili, D., and Mai, A. (2011) Targeting Histone Demethylases: A New Avenue for the Fight against Cancer. Genes Cancer 2, 663-679
-
(2011)
Genes Cancer
, vol.2
, pp. 663-679
-
-
Rotili, D.1
Mai, A.2
-
3
-
-
80052942443
-
Identification of 67 Histone Marks and Histone Lysine Crotonylation as a New Type of Histone Modification
-
Tan, M., Luo, H., Lee, S., Jin, F., Yang, J. S., Montellier, E., Buchou, T., Cheng, Z., Rousseaux, S., Rajagopal, N., Lu, Z., Ye, Z., Zhu, Q., Wysocka, J., Ye, Y., Khochbin, S., Ren, B., and Zhao, Y. (2011) Identification of 67 Histone Marks and Histone Lysine Crotonylation as a New Type of Histone Modification. Cell 146, 1016-1028
-
(2011)
Cell
, vol.146
, pp. 1016-1028
-
-
Tan, M.1
Luo, H.2
Lee, S.3
Jin, F.4
Yang, J.S.5
Montellier, E.6
Buchou, T.7
Cheng, Z.8
Rousseaux, S.9
Rajagopal, N.10
Lu, Z.11
Ye, Z.12
Zhu, Q.13
Wysocka, J.14
Ye, Y.15
Khochbin, S.16
Ren, B.17
Zhao, Y.18
-
4
-
-
78650985680
-
An assessment of histone-modification antibody quality
-
Egelhofer, T. A., Minoda, A., Klugman, S., Lee, K., Kolasinska-Zwierz, P., Alekseyenko, A. A., Cheung, M. S., Day, D. S., Gadel, S., Gorchakov, A. A., Gu, T., Kharchenko, P. V., Kuan, S., Latorre, I., Linder-Basso, D., Luu, Y., Ngo, Q., Perry, M., Rechtsteiner, A., Riddle, N. C., Schwartz, Y. B., Shanower, G. A., Vielle, A., Ahringer, J., Elgin, S. C., Kuroda, M. I., Pirrotta, V., Ren, B., Strome, S., Park, P. J., Karpen, G. H., Hawkins, R. D., and Lieb, J. D. (2011) An assessment of histone-modification antibody quality. Nat. Struct. Mol. Biol. 18, 91-93
-
(2011)
Nat. Struct. Mol. Biol.
, vol.18
, pp. 91-93
-
-
Egelhofer, T.A.1
Minoda, A.2
Klugman, S.3
Lee, K.4
Kolasinska-Zwierz, P.5
Alekseyenko, A.A.6
Cheung, M.S.7
Day, D.S.8
Gadel, S.9
Gorchakov, A.A.10
Gu, T.11
Kharchenko, P.V.12
Kuan, S.13
Latorre, I.14
Linder-Basso, D.15
Luu, Y.16
Ngo, Q.17
Perry, M.18
Rechtsteiner, A.19
Riddle, N.C.20
Schwartz, Y.B.21
Shanower, G.A.22
Vielle, A.23
Ahringer, J.24
Elgin, S.C.25
Kuroda, M.I.26
Pirrotta, V.27
Ren, B.28
Strome, S.29
Park, P.J.30
Karpen, G.H.31
Hawkins, R.D.32
Lieb, J.D.33
more..
-
5
-
-
84861174704
-
Quantitative assessment of chromatin immunoprecipitation grade antibodies directed against histone modifications reveals patterns of co-occurring marks on histone protein molecules
-
Peach, S. E., Rudomin, E. L., Udeshi, N. D., Carr, S. A., and Jaffe, J. D. (2012) Quantitative assessment of chromatin immunoprecipitation grade antibodies directed against histone modifications reveals patterns of co-occurring marks on histone protein molecules. Mol. Cell. Proteomics 11, 128-137
-
(2012)
Mol. Cell. Proteomics
, vol.11
, pp. 128-137
-
-
Peach, S.E.1
Rudomin, E.L.2
Udeshi, N.D.3
Carr, S.A.4
Jaffe, J.D.5
-
6
-
-
80054774747
-
Breaking the histone code with quantitative mass spectrometry
-
Britton, L. M., Gonzales-Cope, M., Zee, B. M., and Garcia, B. A. (2011) Breaking the histone code with quantitative mass spectrometry. Expert Rev. Proteomics 8, 631-643
-
(2011)
Expert Rev. Proteomics
, vol.8
, pp. 631-643
-
-
Britton, L.M.1
Gonzales-Cope, M.2
Zee, B.M.3
Garcia, B.A.4
-
7
-
-
0037402422
-
Mass spectrometric quantification of acetylation at specific lysines within the amino-terminal tail of histone H4
-
Smith, C. M., Gafken, P. R., Zhang, Z., Gottschling, D. E., Smith, J. B., and Smith, D. L. (2003) Mass spectrometric quantification of acetylation at specific lysines within the amino-terminal tail of histone H4. Anal. Biochem. 316, 23-33
-
(2003)
Anal. Biochem.
, vol.316
, pp. 23-33
-
-
Smith, C.M.1
Gafken, P.R.2
Zhang, Z.3
Gottschling, D.E.4
Smith, J.B.5
Smith, D.L.6
-
8
-
-
3042765151
-
Novel linear quadrupole ion trap/FT mass spectrometer: Performance characterization and use in the comparative analysis of histone H3 post-translational modifications
-
Syka, J. E., Marto, J. A., Bai, D. L., Horning, S., Senko, M. W., Schwartz, J. C., Ueberheide, B., Garcia, B., Busby, S., Muratore, T., Shabanowitz, J., and Hunt, D. F. (2004) Novel linear quadrupole ion trap/FT mass spectrometer: performance characterization and use in the comparative analysis of histone H3 post-translational modifications. J. Proteome Res. 3, 621-626
-
(2004)
J. Proteome Res.
, vol.3
, pp. 621-626
-
-
Syka, J.E.1
Marto, J.A.2
Bai, D.L.3
Horning, S.4
Senko, M.W.5
Schwartz, J.C.6
Ueberheide, B.7
Garcia, B.8
Busby, S.9
Muratore, T.10
Shabanowitz, J.11
Hunt, D.F.12
-
9
-
-
34248577604
-
Chemical derivatization of histones for facilitated analysis by mass spectrometry
-
Garcia, B. A., Mollah, S., Ueberheide, B. M., Busby, S. A., Muratore, T. L., Shabanowitz, J., and Hunt, D. F. (2007) Chemical derivatization of histones for facilitated analysis by mass spectrometry. Nat. Protocols 2, 933-938
-
(2007)
Nat. Protocols
, vol.2
, pp. 933-938
-
-
Garcia, B.A.1
Mollah, S.2
Ueberheide, B.M.3
Busby, S.A.4
Muratore, T.L.5
Shabanowitz, J.6
Hunt, D.F.7
-
10
-
-
70449450290
-
One-pot shotgun quantitative mass spectrometry characterization of histones
-
Plazas-Mayorca, M. D., Zee, B. M., Young, N. L., Fingerman, I. M., LeRoy, G., Briggs, S. D., and Garcia, B. A. (2009) One-pot shotgun quantitative mass spectrometry characterization of histones. J. Proteome Res. 8, 5367-5374
-
(2009)
J. Proteome Res.
, vol.8
, pp. 5367-5374
-
-
Plazas-Mayorca, M.D.1
Zee, B.M.2
Young, N.L.3
Fingerman, I.M.4
LeRoy, G.5
Briggs, S.D.6
Garcia, B.A.7
-
11
-
-
51549115454
-
Comprehensive Profiling of Histone Modifications Using a Label-Free Approach and Its Applications in Determining Structure-Function Relationships
-
Drogaris, P., Wurtele, H., Masumoto, H., Verreault, A., and Thibault, P. (2008) Comprehensive Profiling of Histone Modifications Using a Label-Free Approach and Its Applications in Determining Structure-Function Relationships. Anal. Chem. 80, 6698-6707
-
(2008)
Anal. Chem.
, vol.80
, pp. 6698-6707
-
-
Drogaris, P.1
Wurtele, H.2
Masumoto, H.3
Verreault, A.4
Thibault, P.5
-
12
-
-
84887108791
-
Global chromatin profiling reveals NSD2 mutations in pediatric acute lymphoblastic leukemia
-
Jaffe, J. D., Wang, Y., Chan, H. M., Zhang, J., Huether, R., Kryukov, G. V., Bhang, H. E., Taylor, J. E., Hu, M., Englund, N. P., Yan, F., Wang, Z., Robert McDonald, E., Wei, L., Ma, J., Easton, J., Yu, Z., deBeaumount, R., Gibaja, V., Venkatesan, K., Schlegel, R., Sellers, W. R., Keen, N., Liu, J., Caponigro, G., Barretina, J., Cooke, V. G., Mullighan, C., Carr, S. A., Downing, J. R., Garraway, L. A., and Stegmeier, F. (2013) Global chromatin profiling reveals NSD2 mutations in pediatric acute lymphoblastic leukemia. Nat. Genet. 45, 1386-1391
-
(2013)
Nat. Genet.
, vol.45
, pp. 1386-1391
-
-
Jaffe, J.D.1
Wang, Y.2
Chan, H.M.3
Zhang, J.4
Huether, R.5
Kryukov, G.V.6
Bhang, H.E.7
Taylor, J.E.8
Hu, M.9
Englund, N.P.10
Yan, F.11
Wang, Z.12
Robert McDonald, E.13
Wei, L.14
Ma, J.15
Easton, J.16
Yu, Z.17
DeBeaumount, R.18
Gibaja, V.19
Venkatesan, K.20
Schlegel, R.21
Sellers, W.R.22
Keen, N.23
Liu, J.24
Caponigro, G.25
Barretina, J.26
Cooke, V.G.27
Mullighan, C.28
Carr, S.A.29
Downing, J.R.30
Garraway, L.A.31
Stegmeier, F.32
more..
-
13
-
-
34147177521
-
Organismal differences in post-translational modifications in histones H3 and H4
-
Garcia, B. A., Hake, S. B., Diaz, R. L., Kauer, M., Morris, S. A., Recht, J., Shabanowitz, J., Mishra, N., Strahl, B. D., Allis, C. D., and Hunt, D. F. (2007) Organismal differences in post-translational modifications in histones H3 and H4. J. Biol. Chem. 282, 7641-7655
-
(2007)
J. Biol. Chem.
, vol.282
, pp. 7641-7655
-
-
Garcia, B.A.1
Hake, S.B.2
Diaz, R.L.3
Kauer, M.4
Morris, S.A.5
Recht, J.6
Shabanowitz, J.7
Mishra, N.8
Strahl, B.D.9
Allis, C.D.10
Hunt, D.F.11
-
14
-
-
1642272372
-
Shotgun annotation of histone modifications: A new approach for streamlined characterization of proteins by top down mass spectrometry
-
Pesavento, J. J., Kim, Y. B., Taylor, G. K., and Kelleher, N. L. (2004) Shotgun annotation of histone modifications: A new approach for streamlined characterization of proteins by top down mass spectrometry. J. Am. Chem. Soc. 126, 3386-3387
-
(2004)
J. Am. Chem. Soc.
, vol.126
, pp. 3386-3387
-
-
Pesavento, J.J.1
Kim, Y.B.2
Taylor, G.K.3
Kelleher, N.L.4
-
15
-
-
71049122240
-
High throughput characterization of combinatorial histone codes
-
Young, N. L., DiMaggio, P. A., Plazas-Mayorca, M. D., Baliban, R. C., Floudas, C. A., and Garcia, B. A. (2009) High throughput characterization of combinatorial histone codes. Mol. Cell. Proteomics 8, 2266-2284
-
(2009)
Mol. Cell. Proteomics
, vol.8
, pp. 2266-2284
-
-
Young, N.L.1
DiMaggio, P.A.2
Plazas-Mayorca, M.D.3
Baliban, R.C.4
Floudas, C.A.5
Garcia, B.A.6
-
16
-
-
84901785321
-
Multiplexed Parallel Reaction Monitoring Targeting Histone Modifications on the QExactive Mass Spectrometer
-
Tang, H., Fang, H., Yin, E., Brasier, A. R., Sowers, L. C., and Zhang, K. (2014) Multiplexed Parallel Reaction Monitoring Targeting Histone Modifications on the QExactive Mass Spectrometer. Anal. Chem. 86, 5526-5534
-
(2014)
Anal. Chem.
, vol.86
, pp. 5526-5534
-
-
Tang, H.1
Fang, H.2
Yin, E.3
Brasier, A.R.4
Sowers, L.C.5
Zhang, K.6
-
17
-
-
84875059660
-
Mass spectrometry-based proteomics for the analysis of chromatin structure and dynamics
-
Soldi, M., Cuomo, A., Bremang, M., and Bonaldi, T. (2013) Mass spectrometry-based proteomics for the analysis of chromatin structure and dynamics. Int. J. Mol. Sci. 14, 5402-5431
-
(2013)
Int. J. Mol. Sci.
, vol.14
, pp. 5402-5431
-
-
Soldi, M.1
Cuomo, A.2
Bremang, M.3
Bonaldi, T.4
-
18
-
-
33847334699
-
Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome
-
Heintzman, N. D., Stuart, R. K., Hon, G., Fu, Y., Ching, C. W., Hawkins, R. D., Barrera, L. O., Van Calcar, S., Qu, C., Ching, K. A., Wang, W., Weng, Z., Green, R. D., Crawford, G. E., and Ren, B. (2007) Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome. Nat. Genet. 39, 311-318
-
(2007)
Nat. Genet.
, vol.39
, pp. 311-318
-
-
Heintzman, N.D.1
Stuart, R.K.2
Hon, G.3
Fu, Y.4
Ching, C.W.5
Hawkins, R.D.6
Barrera, L.O.7
Van Calcar, S.8
Qu, C.9
Ching, K.A.10
Wang, W.11
Weng, Z.12
Green, R.D.13
Crawford, G.E.14
Ren, B.15
-
19
-
-
34249026300
-
High-Resolution Profiling of Histone Methylations in the Human Genome
-
Barski, A., Cuddapah, S., Cui, K., Roh, T.-Y., Schones, D. E., Wang, Z., Wei, G., Chepelev, I., and Zhao, K. High-Resolution Profiling of Histone Methylations in the Human Genome. Cell 129, 823-837
-
Cell
, vol.129
, pp. 823-837
-
-
Barski, A.1
Cuddapah, S.2
Cui, K.3
Roh, T.-Y.4
Schones, D.E.5
Wang, Z.6
Wei, G.7
Chepelev, I.8
Zhao, K.9
-
20
-
-
78649698079
-
Global turnover of histone post-translational modifications and variants in human cells
-
Zee, B. M., Levin, R. S., Dimaggio, P. A., and Garcia, B. A. (2010) Global turnover of histone post-translational modifications and variants in human cells. Epigenetics Chromatin 3, 22
-
(2010)
Epigenetics Chromatin
, vol.3
, pp. 22
-
-
Zee, B.M.1
Levin, R.S.2
Dimaggio, P.A.3
Garcia, B.A.4
-
21
-
-
77951855269
-
Quantitative Mass Spectrometry of Histones H3.2 and H3.3 in Suz12-deficient Mouse Embryonic Stem Cells Reveals Distinct, Dynamic Post-translational Modifications at Lys-27 and Lys-36
-
Jung, H. R., Pasini, D., Helin, K., and Jensen, O. N. (2010) Quantitative Mass Spectrometry of Histones H3.2 and H3.3 in Suz12-deficient Mouse Embryonic Stem Cells Reveals Distinct, Dynamic Post-translational Modifications at Lys-27 and Lys-36. Mol. Cell. Proteomics 9, 838-850
-
(2010)
Mol. Cell. Proteomics
, vol.9
, pp. 838-850
-
-
Jung, H.R.1
Pasini, D.2
Helin, K.3
Jensen, O.N.4
-
22
-
-
41949086475
-
Mass spectrometry identifies and quantifies 74 unique histone H4 isoforms in differentiating human embryonic stem cells
-
Phanstiel, D., Brumbaugh, J., Berggren, W. T., Conard, K., Feng, X., Levenstein, M. E., McAlister, G. C., Thomson, J. A., and Coon, J. J. (2008) Mass spectrometry identifies and quantifies 74 unique histone H4 isoforms in differentiating human embryonic stem cells. Proc. Natl. Acad. Sci. U.S.A. 105, 4093-4098
-
(2008)
Proc. Natl. Acad. Sci. U.S.A.
, vol.105
, pp. 4093-4098
-
-
Phanstiel, D.1
Brumbaugh, J.2
Berggren, W.T.3
Conard, K.4
Feng, X.5
Levenstein, M.E.6
McAlister, G.C.7
Thomson, J.A.8
Coon, J.J.9
-
23
-
-
35448953287
-
A method to determine the ionization efficiency change of peptides caused by phosphorylation
-
Gao, Y., and Wang, Y. (2007) A method to determine the ionization efficiency change of peptides caused by phosphorylation. J. Am. Soc. Mass Spectrom. 18, 1973-1976
-
(2007)
J. Am. Soc. Mass Spectrom.
, vol.18
, pp. 1973-1976
-
-
Gao, Y.1
Wang, Y.2
-
24
-
-
0034845380
-
Phosphopeptide analysis by positive and negative ion matrix-assisted laser desorption/ionization mass spectrometry
-
Janek, K., Wenschuh, H., Bienert, M., and Krause, E. (2001) Phosphopeptide analysis by positive and negative ion matrix-assisted laser desorption/ionization mass spectrometry. Rapid Commun. Mass Spectrom. 15, 1593-1599
-
(2001)
Rapid Commun. Mass Spectrom.
, vol.15
, pp. 1593-1599
-
-
Janek, K.1
Wenschuh, H.2
Bienert, M.3
Krause, E.4
-
25
-
-
84878868806
-
Manipulating the mass spectrometric properties of peptides through selective chemical modification
-
Ivanov, A. R., and Lazarev, A. V., eds. Springer Netherlands
-
Arnott, D., Liu, P., Molina, P., Phu, L., and Sandoval, W. (2011) Manipulating the mass spectrometric properties of peptides through selective chemical modification. In: Ivanov, A. R., and Lazarev, A. V., eds. Sample preparation in biological mass spectrometry, pp. 19-40, Springer Netherlands
-
(2011)
Sample Preparation in Biological Mass Spectrometry
, pp. 19-40
-
-
Arnott, D.1
Liu, P.2
Molina, P.3
Phu, L.4
Sandoval, W.5
-
26
-
-
25444442032
-
Modifications of human histone H3 variants during mitosis
-
Garcia, B. A., Barber, C. M., Hake, S. B., Ptak, C., Turner, F. B., Busby, S. A., Shabanowitz, J., Moran, R. G., Allis, C. D., and Hunt, D. F. (2005) Modifications of human histone H3 variants during mitosis. Biochemistry 44, 13202-13213
-
(2005)
Biochemistry
, vol.44
, pp. 13202-13213
-
-
Garcia, B.A.1
Barber, C.M.2
Hake, S.B.3
Ptak, C.4
Turner, F.B.5
Busby, S.A.6
Shabanowitz, J.7
Moran, R.G.8
Allis, C.D.9
Hunt, D.F.10
-
27
-
-
42349105213
-
Relative quantification of proteins in human cerebrospinal fluids by MS/MS Using 6-Plex Isobaric Tags
-
Dayon, L., Hainard, A., Licker, V., Turck, N., Kuhn, K., Hochstrasser, D. F., Burkhard, P. R., and Sanchez, J. C. (2008) Relative quantification of proteins in human cerebrospinal fluids by MS/MS Using 6-Plex Isobaric Tags. Anal. Chem. 80, 2921-2931
-
(2008)
Anal. Chem.
, vol.80
, pp. 2921-2931
-
-
Dayon, L.1
Hainard, A.2
Licker, V.3
Turck, N.4
Kuhn, K.5
Hochstrasser, D.F.6
Burkhard, P.R.7
Sanchez, J.C.8
-
28
-
-
79952143091
-
PICquant: A quantitative platform to measure differential peptide abundance using dual-isotopic labeling with 12C6- and 13C6-phenyl isocyanate
-
Lyons, C. E., Victor, K. G., Moshnikov, S. A., Bachmann, L. M., Baras, A. S., Dettmann, K. M., Cross, J. V., and Templeton, D. J. (2011) PICquant: a quantitative platform to measure differential peptide abundance using dual-isotopic labeling with 12C6- and 13C6-phenyl isocyanate. Anal. Chem. 83, 856-865
-
(2011)
Anal. Chem.
, vol.83
, pp. 856-865
-
-
Lyons, C.E.1
Victor, K.G.2
Moshnikov, S.A.3
Bachmann, L.M.4
Baras, A.S.5
Dettmann, K.M.6
Cross, J.V.7
Templeton, D.J.8
-
29
-
-
0041877476
-
Quantitative analysis of modified proteins by LC-MS/MS of peptides labeled with phenyl isocyanate
-
Mason, D. E., and Liebler, D. C. (2003) Quantitative analysis of modified proteins by LC-MS/MS of peptides labeled with phenyl isocyanate. J. Proteome Res. 2, 265-272
-
(2003)
J. Proteome Res.
, vol.2
, pp. 265-272
-
-
Mason, D.E.1
Liebler, D.C.2
-
30
-
-
84874032401
-
Specific and efficient N-propionylation of histones with propionic acid N-hydroxysuccinimide ester for histone marks characterization by LC-MS
-
Liao, R., Wu, H., Deng, H., Yu, Y., Hu, M., Zhai, H., Yang, P., Zhou, S., and Yi, W. (2013) Specific and efficient N-propionylation of histones with propionic acid N-hydroxysuccinimide ester for histone marks characterization by LC-MS. Anal. Chem. 85, 2253-2259
-
(2013)
Anal. Chem.
, vol.85
, pp. 2253-2259
-
-
Liao, R.1
Wu, H.2
Deng, H.3
Yu, Y.4
Hu, M.5
Zhai, H.6
Yang, P.7
Zhou, S.8
Yi, W.9
-
31
-
-
84861870951
-
The COMPASS family of histone H3K4 methylases: Mechanisms of regulation in development and disease pathogenesis
-
Shilatifard, A. (2012) The COMPASS family of histone H3K4 methylases: Mechanisms of regulation in development and disease pathogenesis. Ann. Rev. Biochem. 81, 65-95
-
(2012)
Ann. Rev. Biochem.
, vol.81
, pp. 65-95
-
-
Shilatifard, A.1
-
32
-
-
84926450115
-
Building the Connectivity Map of epigenetics: Chromatin profiling by quantitative targeted mass spectrometry
-
Creech, A. L., Taylor, J. E., Maier, V. K., Wu, X., Feeney, C. M., Udeshi, N. D., Peach, S. E., Boehm, J. S., Lee, J. T., Carr, S. A., and Jaffe, J. D. (2015) Building the Connectivity Map of epigenetics: Chromatin profiling by quantitative targeted mass spectrometry. Methods 72, 57-64
-
(2015)
Methods
, vol.72
, pp. 57-64
-
-
Creech, A.L.1
Taylor, J.E.2
Maier, V.K.3
Wu, X.4
Feeney, C.M.5
Udeshi, N.D.6
Peach, S.E.7
Boehm, J.S.8
Lee, J.T.9
Carr, S.A.10
Jaffe, J.D.11
-
33
-
-
84907195499
-
Stable Isotope labeled histone peptide library for histone post-translational modification and variant quantification by mass spectrometry
-
Lin, S., Wein, S., Gonzales-Cope, M., Otte, G. L., Yuan, Z. F., Afjehi-sadat, L., Maile, T., Berger, S. L., Rush, J., Lill, J. R., Arnott, D., and Garcia, B. A. (2014) Stable Isotope labeled histone peptide library for histone post-translational modification and variant quantification by mass spectrometry. Mol. Cell. Proteomics Mol. Cell. Proteomics 13, 2450-2466
-
(2014)
Mol. Cell. Proteomics Mol. Cell. Proteomics
, vol.13
, pp. 2450-2466
-
-
Lin, S.1
Wein, S.2
Gonzales-Cope, M.3
Otte, G.L.4
Yuan, Z.F.5
Afjehi-sadat, L.6
Maile, T.7
Berger, S.L.8
Rush, J.9
Lill, J.R.10
Arnott, D.11
Garcia, B.A.12
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