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Method Article
Matthew C Lorincz
Lorincz Lab
Corresponding Author
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Combined chromatin immunoprecipitation and next generation sequencing (ChIP-seq) has become an extremely popular method to generate genome-wide epigenetic profiles from numerous cell lines and tissue types. Typical ChIP-seq experiments require large number of cells, making them ill-adapted to the study of rare cell populations. This procedure describes an ultra-low-input (ULI) micrococcal nuclease-based native ChIP (NChIP) and sequencing library construction method to generate genome-wide chromatin profiles from as few as 103 cells (Brind’Amour et al., 10.1038/ncomms7033). In addition, ULI-NChIP-seq has been validated in vivo, by generation of H3K9me3 and H3K27me3 profiles from E13.5 primordial germ cells isolated from single embryos (Liu, Brind’Amour et al., 10.1101/gad.244848.114).
ULI-NChIP-seq should be useful to generate high quality and complexity libraries from rare cell populations, allowing to decrease colony breeding size or to analyze rare clinical samples. Due to often variable cell numbers obtained during isolation of in vivo cell population, the procedure described here allows for flexibility, with some suggestions on adaptation of buffer or volume conditions at various points during the procedure.
Keywords
ChIP sequencing, H3K27me3, H3K9me3, germ cells, low input
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The authors declare no competing financial interests.
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Associated Publications
An ultra-low-input native ChIP-seq protocol for genome-wide profiling of rare cell populations
by Julie Brind’Amour, Sheng Liu, Matthew Hudson, +3
Nature Communications (22 January, 2015)
An open repository of community-contributed protocols sponsored by Nature Research.
Learn more about Protocol Exchange
Method Article
Matthew C Lorincz
Lorincz Lab
Corresponding Author
Version History
CURRENT STATUS: Posted
Version 1
Posted 27 Jan, 2015
No community comments so far
Metrics
Comments: 0
HTML Views: ...
License:
This work is licensed under a CC BY-NC 3.0 License. Read Full License
Combined chromatin immunoprecipitation and next generation sequencing (ChIP-seq) has become an extremely popular method to generate genome-wide epigenetic profiles from numerous cell lines and tissue types. Typical ChIP-seq experiments require large number of cells, making them ill-adapted to the study of rare cell populations. This procedure describes an ultra-low-input (ULI) micrococcal nuclease-based native ChIP (NChIP) and sequencing library construction method to generate genome-wide chromatin profiles from as few as 103 cells (Brind’Amour et al., 10.1038/ncomms7033). In addition, ULI-NChIP-seq has been validated in vivo, by generation of H3K9me3 and H3K27me3 profiles from E13.5 primordial germ cells isolated from single embryos (Liu, Brind’Amour et al., 10.1101/gad.244848.114).
ULI-NChIP-seq should be useful to generate high quality and complexity libraries from rare cell populations, allowing to decrease colony breeding size or to analyze rare clinical samples. Due to often variable cell numbers obtained during isolation of in vivo cell population, the procedure described here allows for flexibility, with some suggestions on adaptation of buffer or volume conditions at various points during the procedure.
Figure 1
Figure 2
Figure 3
Figure 4
Figure 5
Figure 6
Figure 7
Figure 8
Figure 9
Figure 10
Figure 11
Figure 12
The authors declare no competing financial interests.
Loading...
Associated Publications
An ultra-low-input native ChIP-seq protocol for genome-wide profiling of rare cell populations
by Julie Brind’Amour, Sheng Liu, Matthew Hudson, +3
Nature Communications (22 January, 2015)