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Archival chromatin sequencing in formalin-fixed mouse specimens

GSE256158 Mus musculus Expression profiling by high throughput sequencing 6 samples Submitted 2024/03/01 Platform GPL24247
Summary
Formalin induces inter- and intra-molecular crosslinks within exposed cells. This cross-linking can be exploited to characterise chromatin state as in the FAIRE (Formaldehyde-Assisted Isolation of Regulatory Elements) and MNase (micrococcal nuclease) assays. Here, we optimised the FAIRE and MNase assays for application upon heavily-fixed tissues as is typically found in historical formalin-preserved museum specimens. We demonstrate these assays in formalin-fixed mouse specimens and compare the chromatin signatures to specimen-matched fresh tissues. We found that heavy formalin fixation modulates rather than eliminates signatures of differential chromatin accessibility and that these chromatin profiles are reproducible, tissue-specific and sex-specific in vertebrate specimens.
Published in
Century-old chromatin architecture revealed in formalin-fixed vertebrates
Hahn EE, Stiller J, Alexander MR et al. · Nature communications 2024 · PMID 39075073 · doi:10.1038/s41467-024-50668-4
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Also filed as BioProject PRJNA1078348 and SRA study SRP490600. Searching any of these in the dataset finder brings you back here.

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