GEOapplication/xmlftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE322nnn/GSE322813/primaryOK200GenomicsMus musculusGenome binding/occupancy profiling by high throughput sequencinghttps://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE322813GEOGSEfalseA low-input Micro-C protocol for high-resolution 3D genome mappingStandard 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.2026/03/08GSE322813GSM9559627GSM9559628GSM955962628330322813Mus musculus