In recent years, scaled-down ChIP-Chip 4 and ChIP-seq procedures 5, 6, 7, 8, 9, 10 were developed for inputs ranging from 10 3 to 10 6 cells. While such experiments have yielded significant insights, standard ChIP-seq protocols require ~10 7 cells 1, 2, 3, precluding their use on rare cell populations. Finally, we identify sexually dimorphic H3K27me3 enrichment at specific genic promoters, thereby illustrating the utility of this method for generating high-quality and -complexity libraries from rare cell populations.Ĭhromatin immunoprecipitation followed by next-generation sequencing (ChIP-seq) is a widely used approach to study genome-wide DNA–protein interactions. Subsequently, we show that ULI-NChIP-seq H3K27me3 profiles generated from E13.5 primordial germ cells isolated from single male and female embryos show high similarity to recent data sets generated using 50–180 × more material.
We demonstrate that ULI-NChIP-seq generates high-quality maps of covalent histone marks from 10 3 to 10 6 embryonic stem cells.
Here, we present an ultra-low-input micrococcal nuclease-based native ChIP (ULI-NChIP) and sequencing method to generate genome-wide histone mark profiles with high resolution from as few as 10 3 cells. A major limitation of ChIP-seq, however, is the large number of cells required to generate high-quality data sets, precluding the study of rare cell populations. Combined chromatin immunoprecipitation and next-generation sequencing (ChIP-seq) has enabled genome-wide epigenetic profiling of numerous cell lines and tissue types.
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