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Cut&Run of Aldh18a1 using 46C mouse ES cells

ABSTRACT: Cut&Run of Aldh18a1 using 46C mouse ES cells

PROVIDER: PRJEB51482 | ENA |

REPOSITORIES: ENA

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Cut&Run of Aldh18a1 using 46C mouse ES cells

Project description:Using a proteomic approach we identified Aldh18a1 as a protein co-localized with RNA polymerase II. We then carried out Aldh18a1 Cut&Run assays to confirm its co-localization with RNA polymerase II (E-MTAB-11510). As a result, we observed Aldh18a1 is co-localized with RNA polymerase II primarily on transcription start sites.

2022-06-01 | E-MTAB-11513 | biostudies-arrayexpress

Bulk Cut&run and Cut&tag

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Identification of chromatin states during zebrafish gastrulation using CUT&RUN and CUT&Tag

Project description:Here we describe successful implementation of CUT&RUN for profiling protein-DNA interactions in zebrafish embryos. We apply modified a CUT&RUN method to generate high resolution maps of enrichment for H3K4me3, H3K27me3, H3K9me3, and RNA polymerase II during zebrafish gastrulation. Using this data, we identify a conserved subset of developmental genes that are enriched in both H3K4me3 and H3K27me3 during gastrulation, and we demonstrate the increased effectiveness of CUT&RUN for detecting protein enrichment at repetitive sequences with reduced mappability. Our work demonstrates the power of combining CUT&RUN with the strengths of the zebrafish system to better understand the changing embryonic chromatin landscape and its roles in shaping development.

2021-06-17 | GSE178343 | GEO

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Project description:Global Profiling of Histone Modifications in Plasmodium falciparum using CUT&RUN.

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Low-input chromatin profiling in Arabidopsis endosperm using CUT&RUN

Project description:Endosperm is an essential seed tissue with a unique epigenetic landscape. During endosperm development, differential epigenetic regulation of the maternal and paternal genomes plays important roles in regulating gene expression, especially at imprinted genes. Profiling the endosperm epigenetic landscape on a genome-wide scale is challenging due to its small size, mode of development, and close association with maternal tissue. Here, we applied a low input chromatin profiling method, CUT&RUN (cleavage under targets and release using nuclease), to profile parental-specific chromatin modifications using low numbers of Arabidopsis endosperm nuclei. We demonstrate that CUT&RUN generates genome-wide H3K27me3 landscapes with high sensitivity, specificity and reproducibility using around 20,000 endosperm nuclei purified by flow cytometry and fluorescence-activated cell sorting. H3K27me3 peaks identified by CUT&RUN and previous ChIP (chromatin immunoprecipitation) approaches were largely overlapping, with some distinctions in heterochromatin. The versatility and simplicity of CUT&RUN makes it a viable alternative to ChIP, which requires greater amounts of starting material, and will enable the study of tissue or even cell-type specific epigenomes in Arabidopsis and other plant species.

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