Whole-genome chromatin profiling from limited numbers of cells using nano-ChIP-seq

Nature Protocols

Volumn 6, Issue 10, 2011, Pages 1656-1668

  Adli, Mazhar ^a,b,c   Bernstein, Bradley E ^a,b,c  

^a BROAD INSTITUTE OF MIT AND HARVARD   (United States)

^b HOWARD HUGHES MEDICAL INSTITUTE   (United States)

^c MASSACHUSETTS GENERAL HOSPITAL   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; PROTEINASE;

ARTICLE; CELL COUNT; CELL CYCLE; CHROMATIN IMMUNOPRECIPITATION; CLINICAL PROTOCOL; DNA CROSS LINKING; DNA ISOLATION; DNA LIBRARY; DNA SEQUENCE; GENE MAPPING; HIGH THROUGHPUT SEQUENCING; NANOCHIP; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; SENSITIVITY AND SPECIFICITY; SEQUENCE ANALYSIS;

ANIMALS; CELLS, CULTURED; CHROMATIN IMMUNOPRECIPITATION; GENE LIBRARY; GENOME; GENOMICS; HEMATOPOIETIC STEM CELLS; MICE; NANOTECHNOLOGY; SEQUENCE ANALYSIS, DNA; STEM CELLS;

EID: 80053388216     PISSN: 17542189     EISSN: 17502799     Source Type: Journal    
DOI: 10.1038/nprot.2011.402     Document Type: Article

References (10)

1. Park, P.J. ChIP-seq: Advantages and challenges of a maturing technology. Nat. Rev. Genet. 10, 669-680 (2009).
2. Dahl, J.A. & Collas, P. Q2ChIP, a quick and quantitative chromatin immunoprecipitation assay, unravels epigenetic dynamics of developmentally regulated genes in human carcinoma cells. Stem Cells 25, 1037-1046 (2007). (Pubitemid 46572602)
3. Acevedo, L.G. et al. Genome-scale ChIP-chip analysis using 10,000 human cells. Biotechniques 43, 791-797 (2007). (Pubitemid 350303586)
4. O'Neill, L.P., VerMilyea, M.D. & Turner, B.M. Epigenetic characterization of the early embryo with a chromatin immunoprecipitation protocol applicable to small cell populations. Nat. Genet. 38, 835-841 (2006). (Pubitemid 43980607)
5. Attema, J.L. et al. Epigenetic characterization of hematopoietic stem cell differentiation using miniChIP and bisulfite sequencing analysis. Proc. Natl. Acad. Sci. USA 104, 12371-12376 (2007). (Pubitemid 47206144)
6. Goren, A. et al. Chromatin profiling by directly sequencing small quantities of immunoprecipitated DNA. Nat. Methods 7, 47-49 (2009).
7. Adli, M., Zhu, J. & Bernstein, B.E. Genome-wide chromatin maps derived from limited numbers of hematopoietic progenitors. Nat. Methods 7, 615-618 (2010).
8. Shankaranarayanan, P. et al. Single-tube linear DNA amplification (LinDA) for robust ChIP-seq. Nat. Methods 8, 565-567 (2011).
9. Dahl, J.A. & Collas, P. A rapid micro chromatin immunoprecipitation assay (microChIP). Nat. Protoc. 3, 1032-1045 (2008). (Pubitemid 351818692)
10. Lieb, J.D., Liu, X., Botstein, D. & Brown, P.O. Promoter-specific binding of Rap1 revealed by genome-wide maps of protein-DNA association. Nat. Genet. 28, 327-334 (2001). (Pubitemid 32702421)