A quality control system for profiles obtained by ChIP sequencing

Nucleic Acids Research

Volumn 41, Issue 21, 2013, Pages

  Mendoza Parra, Marco Antonio ^a   Van Gool, Wouter ^a   Saleem, Mohamed Ashick Mohamed ^a   Ceschin, Danilo Guillermo ^a   Gronemeyer, Hinrich ^a  

^a UNIVERSITÉ DE STRASBOURG   (France)

Author keywords

[No Author keywords available]

Indexed keywords

RNA POLYMERASE;

ARTICLE; CHROMATIN; CHROMATIN IMMUNOPRECIPITATION; COMBINATORIAL CHEMISTRY; DATA MINING; DNA METHYLATION; DNA MODIFICATION; DNA SEQUENCE; EPIGENETICS; GENETIC DATABASE; PRIORITY JOURNAL; QUALITY CONTROL; RNA TRANSCRIPTION;

CHROMATIN IMMUNOPRECIPITATION; COMPUTER SIMULATION; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; QUALITY CONTROL; SEQUENCE ANALYSIS, DNA;

EID: 84890108019     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkt829     Document Type: Article

References (34)

1. Harris, R.A., Wang, T., Coarfa, C., Nagarajan, R.P., Hong, C., Downey, S.L., Johnson, B.E., Fouse, S.D., Delaney, A., Zhao, Y. et al. (2010) Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications. Nat. Biotechnol., 28, 1097-1105.
2. Laird, P.W. (2010) Principles and challenges of genomewide DNA methylation analysis. Nat. Rev. Genet., 11, 191-203.
3. Ceschin, D.G., Walia, M., Wenk, S.S., Duboe, C., Gaudon, C., Xiao, Y., Fauquier, L., Sankar, M., Vandel, L. and Gronemeyer, H. (2011) Methylation specifies distinct estrogen-induced binding site repertoires of CBP to chromatin. Genes Dev., 25, 1132-1146.
4. Sims, R.J. III, Rojas, L.A., Beck, D., Bonasio, R., Schuller, R., Drury, W.J. III, Eick, D. and Reinberg, D. (2011) The C-terminal domain of RNA polymerase II is modified by site-specific methylation. Science, 332, 99-103.
5. Park, P.J. (2009) ChIP-seq: advantages and challenges of a maturing technology. Nat. Rev. Genet., 10, 669-680.
6. Law, J.A. and Jacobsen, S.E. (2010) Establishing, maintaining and modifying DNA methylation patterns in plants and animals. Nat. Rev. Genet., 11, 204-220.
7. Margueron, R. and Reinberg, D. (2010) Chromatin structure and the inheritance of epigenetic information. Nat. Rev. Genet., 11, 285-296.
8. Ernst, J. and Kellis, M. (2010) Discovery and characterization of chromatin states for systematic annotation of the human genome. Nat. Biotechnol., 28, 817-825.
9. Ernst, J., Kheradpour, P., Mikkelsen, T.S., Shoresh, N., Ward, L.D., Epstein, C.B., Zhang, X., Wang, L., Issner, R., Coyne, M. et al. (2011) Mapping and analysis of chromatin state dynamics in nine human cell types. Nature, 473, 43-49.
10. Wang, Z., Gerstein, M. and Snyder, M. (2009) RNA-Seq: a revolutionary tool for transcriptomics. Nat. Rev. Genet., 10, 57-63.
11. Mamanova, L., Andrews, R.M., James, K.D., Sheridan, E.M., Ellis, P.D., Langford, C.F., Ost, T.W., Collins, J.E. and Turner, D.J. (2010) FRT-seq: amplification-free, strand-specific transcriptome sequencing. Nat. Methods, 7, 130-132.
12. Wang, Z., Zang, C., Cui, K., Schones, D.E., Barski, A., Peng, W. and Zhao, K. (2009) Genome-wide mapping of HATs and HDACs reveals distinct functions in active and inactive genes. Cell, 138, 1019-1031.
13. Ozsolak, F. and Milos, P.M. (2011) RNA sequencing: advances, challenges and opportunities. Nat. Rev. Genet., 12, 87-98.
14. Hah, N., Danko, C.G., Core, L., Waterfall, J.J., Siepel, A., Lis, J.T. and Kraus, W.L. (2011) A rapid, extensive, and transient transcriptional response to estrogen signaling in breast cancer cells. Cell, 145, 622-634.
15. Ingolia, N.T. (2010) Genome-wide translational profiling by ribosome footprinting. Methods Enzymol., 470, 119-142.
16. Lieberman-Aiden, E., van Berkum, N.L., Williams, L., Imakaev, M., Ragoczy, T., Telling, A., Amit, I., Lajoie, B.R., Sabo, P.J., Dorschner, M.O. et al. (2009) Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science, 326, 289-293.
17. Fullwood, M.J., Liu, M.H., Pan, Y.F., Liu, J., Xu, H., Mohamed, Y.B., Orlov, Y.L., Velkov, S., Ho, A., Mei, P.H. et al. (2009) An oestrogen-receptor- alpha-bound human chromatin interactome. Nature, 462, 58-64.
18. Yaffe, E. and Tanay, A. (2011) Probabilistic modeling of Hi-C contact maps eliminates systematic biases to characterize global chromosomal architecture. Nat. Genet., 43, 1059-1065.
19. Down, T.A., Rakyan, V.K., Turner, D.J., Flicek, P., Li, H., Kulesha, E., Graf, S., Johnson, N., Herrero, J., Tomazou, E.M. et al. (2008) A Bayesian deconvolution strategy for immunoprecipitation-based DNA methylome analysis. Nat. Biotechnol., 26, 779-785.
20. Weber, M., Davies, J.J., Wittig, D., Oakeley, E.J., Haase, M., Lam, W.L. and Schubeler, D. (2005) Chromosome-wide and promoter-specific analyses identify sites of differential DNA methylation in normal and transformed human cells. Nat. Genet., 37, 853-862.
21. Core, L.J., Waterfall, J.J. and Lis, J.T. (2008) Nascent RNA sequencing reveals widespread pausing and divergent initiation at human promoters. Science, 322, 1845-1848.
22. Landt, S.G., Marinov, G.K., Kundaje, A., Kheradpour, P., Pauli, F., Batzoglou, S., Bernstein, B.E., Bickel, P., Brown, J.B., Cayting, P. et al. (2012) ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia. Genome Res., 22, 1813-1831.
23. Ji, H., Jiang, H., Ma, W., Johnson, D.S., Myers, R.M. and Wong, W.H. (2008) An integrated software system for analyzing ChIP-chip and ChIP-seq data. Nat. Biotechnol., 26, 1293-1300.
24. Li, Q., Brown, J.B., Huang, H. and Bickel, P.J. (2011) Measuring reproducibility of high-throughput experiments. Ann. Appl. Stat., 5, 1752.
25. Barrett, T., Wilhite, S.E., Ledoux, P., Evangelista, C., Kim, I.F., Tomashevsky, M., Marshall, K.A., Phillippy, K.H., Sherman, P.M., Holko, M. et al. (2013) NCBI GEO: archive for functional genomics data sets-update. Nucleic Acids Res., 41, D991-D995.
26. Langmead, B. and Salzberg, S.L. (2012) Fast gapped-read alignment with Bowtie 2. Nat. Methods, 9, 357-359.
27. Zhang, Y., Liu, T., Meyer, C.A., Eeckhoute, J., Johnson, D.S., Bernstein, B.E., Nusbaum, C., Myers, R.M., Brown, M., Li, W. et al. (2008) Model-based analysis of ChIP-Seq (MACS). Genome Biol., 9, R137.
28. Reiss, D.J., Facciotti, M.T. and Baliga, N.S. (2008) Model-based deconvolution of genome-wide DNA binding. Bioinformatics, 24, 396-403.
29. Kharchenko, P.V., Tolstorukov, M.Y. and Park, P.J. (2008) Design and analysis of ChIP-seq experiments for DNA-binding proteins. Nat. Biotechnol., 26, 1351-1359.
30. Rozowsky, J., Euskirchen, G., Auerbach, R.K., Zhang, Z.D., Gibson, T., Bjornson, R., Carriero, N., Snyder, M. and Gerstein, M.B. (2009) PeakSeq enables systematic scoring of ChIP-seq experiments relative to controls. Nat. Biotechnol., 27, 66-75.
31. Goecks, J., Nekrutenko, A. and Taylor, J. (2010) Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences. Genome Biol., 11, R86.
32. Blankenberg, D., Von Kuster, G., Coraor, N., Ananda, G., Lazarus, R., Mangan, M., Nekrutenko, A. and Taylor, J. (2010) Galaxy: a web-based genome analysis tool for experimentalists. Curr. Protoc. Mol. Biol., Chapter 19, Unit 19 10 11-21.
33. Giardine, B., Riemer, C., Hardison, R.C., Burhans, R., Elnitski, L., Shah, P., Zhang, Y., Blankenberg, D., Albert, I., Taylor, J. et al. (2005) Galaxy: a platform for interactive large-scale genome analysis. Genome Res., 15, 1451-1455.
34. Ho, J.W., Bishop, E., Karchenko, P.V., Negre, N., White, K.P. and Park, P.J. (2011) ChIP-chip versus ChIP-seq: lessons for experimental design and data analysis. BMC Genomics, 12, 134.