EXPERIMENT_TITLE: snHiChew of gm12878 400 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: snHiChew of hek293t and gm12878
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: snHiChew of hek293t and gm12878
RUN_SET_RUN_Pool_Member_@attributes_sample_title: snHiChew of hek293t and gm12878
RUN_SET_RUN_SRAFiles_SRAFile: [{"Alternatives": [null, null, null], "@attributes": {"cluster": "public", "filename": "SRR31657843.lite", "url": "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos7/sra-pub-zq-41/SRR031/31657/SRR31657843/SRR31657843.lite.1", "size": "15043985571", "date": "2024-12-13 01:32:11", "md5": "97ccd85df956d58affb5cb3473dc0629", "version": "1", "semantic_name": "SRA Lite", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "SRR31657843", "url": "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR31657843/SRR31657843", "size": "19603104335", "date": "2024-12-12 19:55:54", "md5": "c801c7be9057f3fc1b7711aec3c1eb99", "version": "1", "semantic_name": "SRA Normalized", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "snHiChew_gm12878_R2.fq.gz", "size": "14590254624", "date": "2024-12-12 19:51:58", "md5": "555196cefe7b05673b0fd52fbd124318", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "snHiChew_gm12878_R1.fq.gz", "size": "12516220694", "date": "2024-12-12 19:52:31", "md5": "fa93540877a493212f86efcd713d49a6", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}]