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CGS: Spike-In Cooperative

The S.I.C. is a group of like-minded investigators who sometimes need to borrow a little bit of sequencing, and who are sometimes willing to lend a little sequencing. The S.I.C. is made possible by the Center for Genome Sciences & Systems Biology.

The short version:

  • Make a library using unique 9bp indexes assigned to your lab.
  • Submit the library to Jess at the CGS&SB to spike-into a MiSeq 2×250 sequencing run.
  • You will receive demultiplexed fastq files of your spike-in sample.
  • Cost? $150, for about 500,000 reads.

Details could be found: https://genomesciences.wustl.edu/sic

An ultra-low-input native ChIP-seq protocol for genome-wide profiling 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. 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. 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 103 cells. We demonstrate that ULI-NChIP-seq generates high-quality maps of covalent histone marks from 103 to 106 embryonic stem cells. 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. 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.