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Systematic alteration of ATAC-seq for profiling open chromatin in cryopreserved nuclei preparations from livestock tissues

posted on 2024-06-11, 06:19 authored by University of California, Davis, Functional Annotation of Animal Genomes (FAANG)
The use of Assay for Transposase-Accessible Chromatin (ATAC-seq) to profile chromatin accessibility has surged over the past years, but its applicability to tissues has been very limited. With the intent of preserving nuclear architecture during long-term storage, cryopreserved nuclei preparations from chicken lung were used to optimize ATAC-seq. Sequencing data were compared with existing DNase-seq, ChIP-seq, and RNA-seq data to evaluate library quality, ultimately resulting in a modified ATAC-seq method capable of generating high quality chromatin accessibility data from cryopreserved nuclei preparations. Using this method, nucleosome-free regions (NFR) identified in chicken lung overlapped half of DNase-I hypersensitive sites, coincided with active histone modifications, and specifically marked actively expressed genes. Notably, sequencing only the subnucleosomal fraction dramatically improved signal, while separation of subnucleosomal reads post-sequencing did not improve signal or peak calling. Overall, these results provide insights into the optimization of ATAC-seq and a platform for profiling open chromatin in animal tissues.


National Institute of Food and Agriculture, 2015-67015-22940


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National Center for Biotechnology Information

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  • Non-geospatial

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  • biota

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sequence analysis

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  • No

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  • Public

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It is recommended to cite the accession numbers that are assigned to data submissions, e.g. the GenBank, WGS or SRA accession numbers. If individual BioProjects need to be referenced, state that "The data have been deposited with links to BioProject accession number PRJNA605842 in the NCBI BioProject database ("

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