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Items: 8

1.

ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia.

Landt SG, Marinov GK, Kundaje A, Kheradpour P, Pauli F, Batzoglou S, Bernstein BE, Bickel P, Brown JB, Cayting P, Chen Y, DeSalvo G, Epstein C, Fisher-Aylor KI, Euskirchen G, Gerstein M, Gertz J, Hartemink AJ, Hoffman MM, Iyer VR, Jung YL, Karmakar S, Kellis M, Kharchenko PV, Li Q, Liu T, Liu XS, Ma L, Milosavljevic A, Myers RM, Park PJ, Pazin MJ, Perry MD, Raha D, Reddy TE, Rozowsky J, Shoresh N, Sidow A, Slattery M, Stamatoyannopoulos JA, Tolstorukov MY, White KP, Xi S, Farnham PJ, Lieb JD, Wold BJ, Snyder M.

Genome Res. 2012 Sep;22(9):1813-31. doi: 10.1101/gr.136184.111.

2.

Role of ChIP-seq in the discovery of transcription factor binding sites, differential gene regulation mechanism, epigenetic marks and beyond.

Mundade R, Ozer HG, Wei H, Prabhu L, Lu T.

Cell Cycle. 2014;13(18):2847-52. doi: 10.4161/15384101.2014.949201. Review.

3.

Sequencing depth and coverage: key considerations in genomic analyses.

Sims D, Sudbery I, Ilott NE, Heger A, Ponting CP.

Nat Rev Genet. 2014 Feb;15(2):121-32. doi: 10.1038/nrg3642. Review.

PMID:
24434847
4.

Deciphering transcriptional control mechanisms in hematopoiesis:the impact of high-throughput sequencing technologies.

Wilson NK, Tijssen MR, Gƶttgens B.

Exp Hematol. 2011 Oct;39(10):961-8. doi: 10.1016/j.exphem.2011.07.005. Epub 2011 Jul 23. Review.

PMID:
21781948
5.

Mapping Transcription Regulatory Networks with ChIP-seq and RNA-seq.

Wade JT.

Adv Exp Med Biol. 2015;883:119-34. doi: 10.1007/978-3-319-23603-2_7. Review.

PMID:
26621465
6.

Next-generation genomics: an integrative approach.

Hawkins RD, Hon GC, Ren B.

Nat Rev Genet. 2010 Jul;11(7):476-86. doi: 10.1038/nrg2795. Review.

7.

Beyond the ENCODE project: using genomics and epigenomics strategies to study enhancer evolution.

Sakabe NJ, Nobrega MA.

Philos Trans R Soc Lond B Biol Sci. 2013 Nov 11;368(1632):20130022. doi: 10.1098/rstb.2013.0022. Print 2013 Dec 19. Review.

8.

Deciphering ENCODE.

Diehl AG, Boyle AP.

Trends Genet. 2016 Apr;32(4):238-49. doi: 10.1016/j.tig.2016.02.002. Epub 2016 Mar 5. Review.

PMID:
26962025

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