EXPERIMENT_TITLE: GSM7158146: MCF10DCIS,P6,cHiC; Homo sapiens; Hi-C
EXPERIMENT_DESIGN_LIBRARY_DESCRIPTOR_LIBRARY_CONSTRUCTION_PROTOC: Hi-C was performed as previously described (Belton et al., 2012) and capture probes were designed in collaboration with Agilent. The capture procedure was performed as per the manufacturer's instructions. Cells were fixed with 1% methanol free formaldehyde for 10′ at room temperature, treated with glycine on ice for 15 minutes, PBS rinsed, and snap frozen in liquid nitrogen. HINDIII restriction digested products were blunt ligated after incorporation of biotinylated dCTP. The DNA was sonicated and crosslinks were reversed. Beads were used to pull down biotinylated di-tags. Sheered ends were repaired, A-tailed, and barcoded adapters were ligated. High ligation efficiency was determined by nhel restriction digestion (blunt end formation creates a nheI site). The Belton et al., 2012 protocol was modified to increase the ligation step to 10 hours with a second spike-in of t4 ligase at hour 4. We found a dramatic increase in ligation efficiency using these conditions.
STUDY_DESCRIPTOR_STUDY_ABSTRACT: Cell cycle controlled mechanistic remodeling of chromatin architecture at HLBs as non-membranous phase-separated nuclear domains represents a novel dimension to regulation of cell proliferation. Therefore, we sought to resolve a gap in our understanding of how 3D higher-order genomic organization supports the activation of multiple clustered histone genes. Our findings are consistent model that the HINFP/NPAT complex controls the formation and dynamic remodeling of higher-order genomic organization of histone gene clusters at HLBs in early to late G1 phase to support production of histone mRNAs in S phase. that the two principal histone gene regulators HINFP and NPAT are located at anchor-points for chromatin loops reflecting their obligatory functions in remodeling the spatiotemporal genomic organization at HLBs during the G1 phase to accommodate histone gene expression in S phase. Overall design: cHiC in the MCF10DCIS cell, 2 biological replicates enriched for the histone locus body on chr6.
SAMPLE_TITLE: MCF10DCIS,P6,cHiC
SAMPLE_SAMPLE_ATTRIBUTES_SAMPLE_ATTRIBUTE: [{"TAG": "source_name", "VALUE": "MCF10DCIS"}, {"TAG": "cell line", "VALUE": "MCF10DCIS"}, {"TAG": "replicate", "VALUE": "rep2"}, {"TAG": "geo_loc_name", "VALUE": "missing"}, {"TAG": "collection_date", "VALUE": "missing"}]
Pool_Member_@attributes_sample_title: MCF10DCIS,P6,cHiC
RUN_SET_RUN_Pool_Member_@attributes_sample_title: MCF10DCIS,P6,cHiC
RUN_SET_RUN_SRAFiles_SRAFile: [{"Alternatives": [null, null, null], "@attributes": {"cluster": "public", "filename": "SRR24118582.lite", "url": "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos4/sra-pub-zq-3/SRR024/24118/SRR24118582/SRR24118582.lite.1", "size": "3236587940", "date": "2023-05-06 23:11:47", "md5": "0951d78ef7406eea29f3896f9558df7d", "version": "1", "semantic_name": "SRA Lite", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "SRR24118582", "url": "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR24118582/SRR24118582", "size": "6040716060", "date": "2023-04-10 14:32:13", "md5": "fd529a7238a393bfd1bbfbd2ec2d14eb", "version": "1", "semantic_name": "SRA Normalized", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "MCF10DCIS_P6_cHiC_R2.fastq.gz", "size": "4348952680", "date": "2023-04-10 14:31:25", "md5": "bceed7cfa50d542e5eb45ab90c65d669", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "MCF10DCIS_P6_cHiC_R1.fastq.gz", "size": "4277754933", "date": "2023-04-10 14:31:14", "md5": "dfe966f0f8f74b806641e541abec8b94", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}]