{"lab": {"@id": "/labs/4dn-dcic-lab/", "display_title": "4DN DCIC, HMS", "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "@type": ["Lab", "Item"], "status": "current", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "award": {"uuid": "b0b9c607-f8b4-4f02-93f4-9895b461334b", "@id": "/awards/1U01CA200059-01/", "display_title": "4D NUCLEOME NETWORK DATA COORDINATION AND INTEGRATION CENTER - PHASE I", "@type": ["Award", "Item"], "status": "current", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "title": "DNA SPRITE", "status": "released", "other_tags": ["DNA-DNA", "Multi-contact", "3D"], "date_created": "2019-03-28T18:07:16.767643+00:00", "submitted_by": {"error": "no view permissions"}, "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2019-07-22T15:26:48.895872+00:00"}, "raw_file_types": "Reads (fastq) provided by lab", "reference_pubs": [{"journal": "Cell", "display_title": "Quinodoz SA et al. (2018) doi:10.1016/j.cell.2018.05.024", "@type": ["Publication", "Item"], "status": "current", "@id": "/publications/4ab311b1-a442-46b4-ae4f-16c57521f52e/", "short_attribution": "Quinodoz SA et al. (2018)", "authors": ["Quinodoz SA", "Ollikainen N", "Tabak B", "Palla A", "Schmidt JM", "Detmar E", "Lai MM", "Shishkin AA", "Bhat P", "Takei Y", "Trinh V", "Aznauryan E", "Russell P", "Cheng C", "Jovanovic M", "Chow A", "Cai L", "McDonel P", "Garber M", "Guttman M"], "date_published": "2018-06-07", "uuid": "4ab311b1-a442-46b4-ae4f-16c57521f52e", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "schema_version": "1", "static_content": [{"content": {"error": "no view permissions"}, "location": "tab:overview"}, {"content": {"content": "A 4DN Data Processing pipeline is not yet available for SPRITE. \nPreliminary processed files for SPRITE experiments are \navailable in the Supplementary Files tab of the Experiment Set\n and were generated by analysis pipelines of the attributed \nlab.\n\n<br><br> \n\n<style> \n    table, th, td { \n        border: 1px solid #ddd; \n        font-size: 100%; \n        padding: 20px; \n    } \n</style> \n<table style=\"width:100%\"> \n    <thead> \n        <tr> \n            <th style=\"text-align:left; padding:15px; width:128px\">File Type</th>\n            <th style=\"text-align:left; padding:15px\">File Format</th>\n            <th style=\"text-align:left; padding:15px\">Description</th> \n        </tr> \n    </thead> \n    <tr> \n        <td style=\"padding:20px\">Clusters</td>\n        <td style=\"padding:20px\">.clusters.gz</td>\n        <td style=\"padding:20px\">SPRITE clusters are contained in gzipped tab-delimited files, where the first column is the combination of barcodes for reads in the cluster, and the subsequent columns are the start of the mapping location of each read in the cluster. Lines have variable numbers of columns. Generally the clusters from individual replicate experiments will be merged into a single clusters file for the experiment set. Code for the analysis of SPRITE clusters is available <a href=\"https://github.com/GuttmanLab/sprite-pipeline/wiki\">here</a>.</td> \n    </tr>\n    <tr>\n        <td style=\"padding:20px\">Contact Matrix</td>\n        <td style=\"padding:20px\"><a href=\"https://cooler.readthedocs.io/en/latest/datamodel.html\">.mcool</a></td> \n        <td style=\"padding:20px\">SPRITE clusters can be converted to pairwise contact matrices in .mcool format. For each cluster, all possible combinations of pairs are generated, generally with a downweighted count of 2/n, where n is the number of reads in the cluster. The pairs are then streamed into Cooler to generate a .cool file, after which a multi-resolution .mcool is generated. These can be visualized on the portal with <a href=\"https://higlass.io\">HiGlass</a>.</td> \n    </tr>\n</table>", "@type": ["StaticSection", "UserContent", "Item"], "award": {"status": "current", "@type": ["Award", "Item"], "uuid": "b0b9c607-f8b4-4f02-93f4-9895b461334b", "display_title": "4D NUCLEOME NETWORK DATA COORDINATION AND INTEGRATION CENTER - PHASE I", "@id": "/awards/1U01CA200059-01/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "options": {"filetype": "html", "collapsible": false, "default_open": true}, "filetype": "html", "display_title": "sprite-processed-files", "name": "sprite-processed-files", "uuid": "b83cd860-e33f-4d17-97c2-c023e0e81fe4", "@id": "/static-sections/b83cd860-e33f-4d17-97c2-c023e0e81fe4/", "lab": {"status": "current", "@type": ["Lab", "Item"], "@id": "/labs/4dn-dcic-lab/", "display_title": "4DN DCIC, HMS", "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "userid.986b362f-4eb6-4a9c-8173-3ab267307e3a"]}}, "location": "tab:processed_files"}], "controlled_term": {"term_url": "http://www.ebi.ac.uk/efo/EFO_0009985", "@id": "/ontology-terms/EFO:0009985/", "preferred_name": "DNA SPRITE", "status": "released", "term_id": "EFO:0009985", "term_name": "DNA SPRITE", "display_title": "DNA SPRITE", "uuid": "26f863c2-76a1-40b2-a7d5-8647f9050c5a", "@type": ["OntologyTerm", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "experiment_name": "dna-sprite", "valid_item_types": ["ExperimentSeq"], "experiment_category": "Sequencing", "assay_classification": "Ligation-free 3C", "assay_subclass_short": "Ligation-free 3C", "assay_subclassification": "DNA-DNA Multi-way Interactions", "@id": "/experiment-types/dna-sprite/", "@type": ["ExperimentType", "Item"], "uuid": "4004ae76-2f5c-42b6-9f72-488f60963f04", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "display_title": "DNA SPRITE", "external_references": [], "@context": "/terms/", "aggregated-items": {}, "validation-errors": []}