EXPERIMENT_TITLE: snHiChew sequencing of hek293t ctcfkd cells
STUDY_DESCRIPTOR_STUDY_ABSTRACT: We present HiChew (High efficient chromatin conformation capture with post-enrichment), a novel method for analyzing three-dimensional chromatin organization in single cells and low-input samples. HiChew combines efficient sticky-end ligation with post-PCR enrichment using methylation-based selection, addressing key limitations of existing chromatin conformation capture methods. The method achieves significantly higher valid pair ratios (approximately 50%) compared to unenriched methods (8%) while maintaining high capture sensitivity. For single-cell applications, snHiChew demonstrates superior performance with 45-50% valid pair ratios and the ability to generate up to 7.3 million unique valid contacts per cell. This enhanced efficiency enables high-resolution mapping of chromatin interactions at 5-10 kb resolution with 70-80% bin coverage. We validate HiChew's accuracy through comparative analyses with conventional Hi-C data, showing high correlations in compartment scores, topologically associating domains (TADs), and loop detection. The method's scalability and cost-effectiveness make it particularly suitable for large-scale single-cell chromatin conformation studies. HiChew represents a significant advancement in chromatin architecture analysis, offering improved efficiency without compromising data quality or sensitivity.
SAMPLE_TITLE: hek293t CTCF knockdown
SAMPLE_SAMPLE_ATTRIBUTES_SAMPLE_ATTRIBUTE: [{"TAG": "isolate", "VALUE": "Monoisolate"}, {"TAG": "age", "VALUE": "adult"}, {"TAG": "biomaterial_provider", "VALUE": "abclonal"}, {"TAG": "collection_date", "VALUE": "2023-12-16"}, {"TAG": "geo_loc_name", "VALUE": "USA"}, {"TAG": "sex", "VALUE": "female"}, {"TAG": "tissue", "VALUE": "kidney"}, {"TAG": "BioSampleModel", "VALUE": "Human"}]
Pool_Member_@attributes_sample_title: hek293t CTCF knockdown
RUN_SET_RUN_Pool_Member_@attributes_sample_title: hek293t CTCF knockdown
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