EXPERIMENT_TITLE: GSM2844408: RaeI shCTRL HiC; Homo sapiens; Human gammaherpesvirus 4; Hi-C
EXPERIMENT_DESIGN_LIBRARY_DESCRIPTOR_LIBRARY_CONSTRUCTION_PROTOC: In situ Hi-C was performed with 5 million cells per experiment and restriction enzyme MboI as described (Rao et al., 2014) with slight modifications. After end-repair and washes, Dynabeads (Thermo Fisher Scientific) with bound DNA were resuspended in 10 mM Tris, 0.1 mM EDTA pH 8.0 and transferred to new tubes. Sequencing libraries were created from bound DNA using the Ovation Ultralow Library System V2 kit (NuGEN) with one modification. After adapter ligation, because DNA is still attached to the beads, water instead of SPRI beads was added to the reaction. DNA bound to the beads was purified with a magnet, washed, and the beads were resuspended in 10 mM Tris, 0.1 mM EDTA pH 8.0. After library amplification, SPRI beads were added as directed to purify the amplified DNA.
STUDY_DESCRIPTOR_STUDY_ABSTRACT: Using chromatin conformation capture methods, we learned that the latent episome of the human Epstein-Barr virus (EBV) displays preferential chromosome association that correlates with gene density. The episome avoids gene-rich chromosomes and favors gene-poor chromosomes. Kaposi's sarcoma-associated herpesvirus behaves similarly, but human papillomavirus does not, suggesting limited evolutionary conservation of this strategy. Moreover, the strongest contacts we detected between the human genome and EBV episome localized to OriP, the latent origin of replication. This genetic element, and the EBNA1 protein that binds there, are sufficient to reconstitute chromosome association preferences of the entire episome. Upon reactivation from latency, however, these preferences are lost. Detailed mapping of changes in interchromosomal contacts reveal that the episome moves away from repressive heterochromatin and toward activating euchromatin. Our work adds three-dimensional relocalization to the molecular events that occur during the genetic switch from EBV latency to reactivation. The involvement of only a myriad of interchromosomal contacts also argues for a possible role of this type of long-range association in gene regulation. Overall design: Hi-C examination of host-viral genome interactions during reactivation and latency
SAMPLE_TITLE: RaeI shCTRL HiC
SAMPLE_SAMPLE_ATTRIBUTES_SAMPLE_ATTRIBUTE: [{"TAG": "source_name", "VALUE": "RaeI cells"}, {"TAG": "cell type", "VALUE": "RaeI"}, {"TAG": "transfection", "VALUE": "shCTRL"}]
Pool_Member_@attributes_sample_title: RaeI shCTRL HiC
RUN_SET_RUN_Pool_Member_@attributes_sample_title: RaeI shCTRL HiC
RUN_SET_RUN_SRAFiles_SRAFile: [{"Alternatives": null, "@attributes": {"cluster": "public", "filename": "SRR6266207", "url": "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR6266207/SRR6266207", "size": "860529666", "date": "2017-11-07 16:59:23", "md5": "6d3801e80af08eae49a8eb65a5f34ded", "version": "1", "semantic_name": "SRA Normalized", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": [null, null, null], "@attributes": {"cluster": "public", "filename": "SRR6266207.sralite", "url": "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-11/SRR006/266/SRR6266207/SRR6266207.sralite.1", "size": "515669602", "date": "2020-06-14 00:44:46", "md5": "98d874ccf363ff18833cb8323b58f9a3", "version": "1", "semantic_name": "SRA Lite", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "SM225_S8_L003_R2_001.fastq.gz", "size": "786127871", "date": "2020-03-16 05:15:36", "md5": "b869ec866187152c3ade48e428813367", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "SM225_S8_L003_R1_001.fastq.gz", "size": "700830811", "date": "2020-03-16 06:27:03", "md5": "8a6ba7e1a3544732acc21eaaf418f597", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}]