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They should be largely similar to those available in the Processed Files tab, which were generated with the previous version of the standard pipeline.  One potential difference of note is that the version of cooler used to generate the mcool file has a bug fix to prevent a pixel duplication issue which is observed in some files generated by the previous version of the pipeline.  Another notable difference is that a filter is applied to remove reads with MAPQ scores below 30 prior to mcool file generation."}], "crosslinking_temperature": 25.0, "@id": "/experiments-hi-c/4DNEXNCQS8V9/", "@type": ["ExperimentHiC", "Experiment", "Item"], "uuid": "a33dd5ef-7512-4427-b6d6-cc6ca28ffa96", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "display_title": "in situ Hi-C on cerebral cortex with MboI - 4DNEXNCQS8V9", "external_references": [{"ref": "GEO:GSM2434090", "uri": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM2434090"}], "experiment_sets": [{"accession": "4DNESUQT299T", "@id": "/experiment-set-replicates/4DNESUQT299T/", "experimentset_type": "replicate", "@type": ["ExperimentSetReplicate", "ExperimentSet", "Item"], "status": "released", "uuid": "7dfac163-ccb5-4277-a773-097c2d0a5f74", "display_title": "4DNESUQT299T", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "produced_in_pub": {"display_title": "Du Z et al. (2017) PMID:28703188", "@id": "/publications/7b570ea3-1ca6-4076-83a3-666d35819cf1/", "status": "current", "uuid": "7b570ea3-1ca6-4076-83a3-666d35819cf1", "journal": "Nature", "abstract": "In mammals, chromatin organization undergoes drastic reprogramming after fertilization. However, the three-dimensional structure of chromatin and its reprogramming in preimplantation development remain poorly understood. Here, by developing a low-input Hi-C (genome-wide chromosome conformation capture) approach, we examined the reprogramming of chromatin organization during early development in mice. We found that oocytes in metaphase II show homogeneous chromatin folding that lacks detectable topologically associating domains (TADs)  and chromatin compartments. Strikingly, chromatin shows greatly diminished higher-order structure after fertilization. Unexpectedly, the subsequent establishment of chromatin organization is a prolonged process that extends through preimplantation development, as characterized by slow consolidation of TADs and segregation of chromatin compartments. The two sets of parental chromosomes are spatially separated from each other and display distinct compartmentalization in zygotes. Such allele separation and allelic compartmentalization can be found as late as the 8-cell stage. Finally, we show that chromatin compaction in preimplantation embryos can partially proceed in the absence of zygotic transcription and is a multi-level hierarchical process. Taken together, our data suggest that chromatin may exist in a markedly relaxed state after fertilization, followed by progressive maturation of higher-order chromatin architecture during early development.", "short_attribution": "Du Z et al. (2017)", "ID": "PMID:28703188", "date_published": "2017-07-12", "authors": ["Du Z", "Zheng H", "Huang B", "Ma R", "Wu J", "Zhang X", "He J", "Xiang Y", "Wang Q", "Li Y", "Ma J", "Zhang X", "Zhang K", "Wang Y", "Zhang MQ", "Gao J", "Dixon JR", "Wang X", "Zeng J", "Xie W"], "title": "Allelic reprogramming of 3D chromatin architecture during early mammalian development.", "@type": ["Publication", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "publications_of_exp": [{"uuid": "7b570ea3-1ca6-4076-83a3-666d35819cf1", "@id": "/publications/7b570ea3-1ca6-4076-83a3-666d35819cf1/", "ID": "PMID:28703188", "display_title": "Du Z et al. (2017) PMID:28703188", "journal": "Nature", "@type": ["Publication", "Item"], "short_attribution": "Du Z et al. (2017)", "date_published": "2017-07-12", "title": "Allelic reprogramming of 3D chromatin architecture during early mammalian development.", "abstract": "In mammals, chromatin organization undergoes drastic reprogramming after fertilization. However, the three-dimensional structure of chromatin and its reprogramming in preimplantation development remain poorly understood. Here, by developing a low-input Hi-C (genome-wide chromosome conformation capture) approach, we examined the reprogramming of chromatin organization during early development in mice. We found that oocytes in metaphase II show homogeneous chromatin folding that lacks detectable topologically associating domains (TADs)  and chromatin compartments. Strikingly, chromatin shows greatly diminished higher-order structure after fertilization. Unexpectedly, the subsequent establishment of chromatin organization is a prolonged process that extends through preimplantation development, as characterized by slow consolidation of TADs and segregation of chromatin compartments. The two sets of parental chromosomes are spatially separated from each other and display distinct compartmentalization in zygotes. Such allele separation and allelic compartmentalization can be found as late as the 8-cell stage. Finally, we show that chromatin compaction in preimplantation embryos can partially proceed in the absence of zygotic transcription and is a multi-level hierarchical process. Taken together, our data suggest that chromatin may exist in a markedly relaxed state after fertilization, followed by progressive maturation of higher-order chromatin architecture during early development.", "authors": ["Du Z", "Zheng H", "Huang B", "Ma R", "Wu J", "Zhang X", "He J", "Xiang Y", "Wang Q", "Li Y", "Ma J", "Zhang X", "Zhang K", "Wang Y", "Zhang MQ", "Gao J", "Dixon JR", "Wang X", "Zeng J", "Xie W"], "status": "current", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "experiment_categorizer": {"field": "Enzyme", "value": "MboI", "combined": "Enzyme: MboI"}, "experiment_summary": "in situ Hi-C on cerebral cortex with MboI", "@context": "/terms/", "aggregated-items": {"badges": []}, "validation-errors": []}