biostudies-literatureHan MNational Institute of General Medical SciencesNIH HHSNIGMS NIH HHS500https://www.ebi.ac.uk/biostudies/studies/S-EPMC6580472biostudies-literatureUnknown20(1)<h4>Background</h4>The wide variety of specialized permissive and repressive mechanisms by which germ cells regulate developmental gene expression are not well understood genome-wide. Isolation of germ cells with high integrity and purity from living animals is necessary to address these open questions, but no straightforward methods are currently available.<h4>Results</h4>Here we present an experimental paradigm that permits the isolation of nuclei from C. elegans germ cells at quantities sufficient for genomic analyses. We demonstrate that these nuclei represent a very pure population and are suitable for both transcriptome analysis (RNA-seq) and chromatin immunoprecipitation (ChIP-seq) of histone modifications. From these data, we find unexpected germline- and soma-specific patterns of BMC genomicsIsolated C. elegans germ nuclei exhibit distinct genomic profiles of histone modification and gene expression.PMC6580472R35 GM131776R01 GM108663P40 OD010440R01GM108663Han MReinke VWei GMcManus CEHillier LWfalseIsolated C. elegans germ nuclei exhibit distinct genomic profiles of histone modification and gene expression.<h4>Background</h4>The wide variety of specialized permissive and repressive mechanisms by which germ cells regulate developmental gene expression are not well understood genome-wide. Isolation of germ cells with high integrity and purity from living animals is necessary to address these open questions, but no straightforward methods are currently available.<h4>Results</h4>Here we present an experimental paradigm that permits the isolation of nuclei from C. elegans germ cells at quantities sufficient for genomic analyses. We demonstrate that these nuclei represent a very pure population and are suitable for both transcriptome analysis (RNA-seq) and chromatin immunoprecipitation (ChIP-seq) of histone modifications. From these data, we find unexpected germline- and soma-specific patterns of 2019-01-01T00:00:00Z2019 Jun2026-07-14T15:02:24.364Z2019-07-24T07:20:32ZS-EPMC65804723120833210.1186/s12864-019-5893-9