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A low-input Micro-C protocol for high-resolution 3D genome mapping

GSE322813 Mus musculus Genome binding/occupancy profiling by high throughput sequencing 3 samples Submitted 2026/03/08 Platform GPL28330
Summary
Standard Micro-C protocols typically require millions of cells, which limits their application to rare cell populations. Here, we present an optimized low-input Micro-C workflow that requires only 100,000 cells. By comparing 30 G of sequencing data from 100,000 cells with that from 5 million G1E-ER4 cells, we demonstrate that all key architectural features—compartments, TADs, and chromatin loops—are reliably detected. Applying this method to investigate acute CTCF degradation, we observed the loss of loops and TAD boundaries in CTCF-degraded samples, consistent with previous reports. Our optimized protocol enables nucleosome-resolution 3D genome mapping for sample-limited studies.
Published in
A low-input Micro-C protocol for high-resolution 3D genome mapping
Shan F, Pei C, Xia S et al. · Biology methods & protocols 2026 · PMID 42112493 · doi:10.1093/biomethods/bpag019
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Also filed as BioProject PRJNA1431898 and SRA study SRP680848. Searching any of these in the dataset finder brings you back here.

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