IGVFDS5877TZTD

released
{
    "@context": "/terms/",
    "@id": "/auxiliary-sets/IGVFDS5877TZTD/",
    "@type": [
        "AuxiliarySet",
        "FileSet",
        "Item"
    ],
    "accession": "IGVFDS5877TZTD",
    "aliases": [
        "jesse-engreitz:auxiliary_sortparams_CRUDO_PILOT_CCND1-Auxin6hrs-FF1"
    ],
    "audit": {
        "NOT_COMPLIANT": [
            {
                "category": "missing file format specifications",
                "detail": "Tabular file [IGVFFI8896PYAO](/tabular-files/IGVFFI8896PYAO/) has no `file_format_specifications`. Tabular files are expected to link to a file format specifications document describing the headers of the file.",
                "level": 50,
                "level_name": "NOT_COMPLIANT",
                "name": "audit_tabular_file_no_file_format_specifications",
                "path": "/tabular-files/IGVFFI8896PYAO/"
            }
        ]
    },
    "award": {
        "@id": "/awards/HG011972/",
        "component": "functional characterization",
        "contact_pi": {
            "@id": "/users/6c75dbfa-635e-4a7a-8ec8-9e51e9c380a4/",
            "title": "Jesse Engreitz"
        },
        "title": "Stanford Center for Connecting DNA Variants to Function and Phenotype"
    },
    "control_for": [],
    "creation_timestamp": "2024-07-02T23:41:50.886675+00:00",
    "donors": [
        {
            "@id": "/human-donors/IGVFDO0384OZRW/",
            "accession": "IGVFDO0384OZRW",
            "aliases": [
                "igvf:donor_of_HCT116"
            ],
            "sex": "male",
            "status": "released",
            "taxa": "Homo sapiens"
        }
    ],
    "file_set_type": "cell sorting",
    "files": [
        {
            "@id": "/tabular-files/IGVFFI8896PYAO/",
            "accession": "IGVFFI8896PYAO",
            "aliases": [
                "jesse-engreitz:auxiliary_sortparams_file_CRUDO_PILOT_CCND1-Auxin6hrs-FF1"
            ],
            "content_type": "sample sort parameters",
            "controlled_access": false,
            "creation_timestamp": "2024-07-03T00:35:13.629110+00:00",
            "file_format": "tsv",
            "file_size": 242,
            "href": "/tabular-files/IGVFFI8896PYAO/@@download/IGVFFI8896PYAO.tsv.gz",
            "s3_uri": "s3://igvf-files/2024/07/03/0f85abff-cf62-4f32-b817-f88fe9e4317c/IGVFFI8896PYAO.tsv.gz",
            "status": "released",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/sortparams/210301B002_2.tsv.gz",
            "upload_status": "validated"
        }
    ],
    "input_for": [
        "/analysis-sets/IGVFDS2982SJGW/"
    ],
    "lab": {
        "@id": "/labs/jesse-engreitz/",
        "title": "Jesse Engreitz, Stanford"
    },
    "measurement_sets": [
        {
            "@id": "/measurement-sets/IGVFDS0964GIQS/",
            "accession": "IGVFDS0964GIQS",
            "aliases": [
                "jesse-engreitz:measurement_CRUDO_PILOT_CCND1-Auxin6hrs-FF1-BinA-PCR1_S1",
                "jesse-engreitz:measurement_CRUDO_PILOT_CCND1-Auxin6hrs-FF1-BinA-PCR2_S97",
                "jesse-engreitz:measurement_CRUDO_PILOT_CCND1-Auxin6hrs-FF1-BinA-PCR3_S193",
                "jesse-engreitz:measurement_CRUDO_PILOT_CCND1-Auxin6hrs-FF1-BinA-PCR4_S289"
            ],
            "preferred_assay_title": "CRISPR FlowFISH screen",
            "status": "released"
        },
        {
            "@id": "/measurement-sets/IGVFDS5146ALYO/",
            "accession": "IGVFDS5146ALYO",
            "aliases": [
                "jesse-engreitz:measurement_CRUDO_PILOT_CCND1-Auxin6hrs-FF1-BinD-PCR1_S4",
                "jesse-engreitz:measurement_CRUDO_PILOT_CCND1-Auxin6hrs-FF1-BinD-PCR2_S100",
                "jesse-engreitz:measurement_CRUDO_PILOT_CCND1-Auxin6hrs-FF1-BinD-PCR3_S196",
                "jesse-engreitz:measurement_CRUDO_PILOT_CCND1-Auxin6hrs-FF1-BinD-PCR4_S292"
            ],
            "preferred_assay_title": "CRISPR FlowFISH screen",
            "status": "released"
        },
        {
            "@id": "/measurement-sets/IGVFDS2079MGOR/",
            "accession": "IGVFDS2079MGOR",
            "aliases": [
                "jesse-engreitz:measurement_CRUDO_PILOT_CCND1-Auxin6hrs-FF1-BinF-PCR1_S6",
                "jesse-engreitz:measurement_CRUDO_PILOT_CCND1-Auxin6hrs-FF1-BinF-PCR2_S102",
                "jesse-engreitz:measurement_CRUDO_PILOT_CCND1-Auxin6hrs-FF1-BinF-PCR3_S198",
                "jesse-engreitz:measurement_CRUDO_PILOT_CCND1-Auxin6hrs-FF1-BinF-PCR4_S294"
            ],
            "preferred_assay_title": "CRISPR FlowFISH screen",
            "status": "released"
        },
        {
            "@id": "/measurement-sets/IGVFDS8571HTVZ/",
            "accession": "IGVFDS8571HTVZ",
            "aliases": [
                "jesse-engreitz:measurement_CRUDO_PILOT_CCND1-Auxin6hrs-FF1-BinC-PCR1_S3",
                "jesse-engreitz:measurement_CRUDO_PILOT_CCND1-Auxin6hrs-FF1-BinC-PCR2_S99",
                "jesse-engreitz:measurement_CRUDO_PILOT_CCND1-Auxin6hrs-FF1-BinC-PCR3_S195",
                "jesse-engreitz:measurement_CRUDO_PILOT_CCND1-Auxin6hrs-FF1-BinC-PCR4_S291"
            ],
            "preferred_assay_title": "CRISPR FlowFISH screen",
            "status": "released"
        },
        {
            "@id": "/measurement-sets/IGVFDS9594DNWM/",
            "accession": "IGVFDS9594DNWM",
            "aliases": [
                "jesse-engreitz:measurement_CRUDO_PILOT_CCND1-Auxin6hrs-FF1-BinB-PCR1_S2",
                "jesse-engreitz:measurement_CRUDO_PILOT_CCND1-Auxin6hrs-FF1-BinB-PCR2_S98",
                "jesse-engreitz:measurement_CRUDO_PILOT_CCND1-Auxin6hrs-FF1-BinB-PCR3_S194",
                "jesse-engreitz:measurement_CRUDO_PILOT_CCND1-Auxin6hrs-FF1-BinB-PCR4_S290"
            ],
            "preferred_assay_title": "CRISPR FlowFISH screen",
            "status": "released"
        },
        {
            "@id": "/measurement-sets/IGVFDS3802XLBV/",
            "accession": "IGVFDS3802XLBV",
            "aliases": [
                "jesse-engreitz:measurement_CRUDO_PILOT_CCND1-Auxin6hrs-FF1-BinE-PCR1_S5",
                "jesse-engreitz:measurement_CRUDO_PILOT_CCND1-Auxin6hrs-FF1-BinE-PCR2_S101",
                "jesse-engreitz:measurement_CRUDO_PILOT_CCND1-Auxin6hrs-FF1-BinE-PCR3_S197",
                "jesse-engreitz:measurement_CRUDO_PILOT_CCND1-Auxin6hrs-FF1-BinE-PCR4_S293"
            ],
            "preferred_assay_title": "CRISPR FlowFISH screen",
            "status": "released"
        }
    ],
    "release_timestamp": "2024-07-10T20:29:37.529300+00:00",
    "samples": [
        {
            "@id": "/in-vitro-systems/IGVFSM0561OELB/",
            "@type": [
                "InVitroSystem",
                "Biosample",
                "Sample",
                "Item"
            ],
            "accession": "IGVFSM0561OELB",
            "aliases": [
                "jesse-engreitz:in-vitro-system_CRUDO_PILOT_CCND1-Auxin6hrs-FF1-BinA-PCR1_S1",
                "jesse-engreitz:in-vitro-system_CRUDO_PILOT_CCND1-Auxin6hrs-FF1-BinA-PCR2_S97",
                "jesse-engreitz:in-vitro-system_CRUDO_PILOT_CCND1-Auxin6hrs-FF1-BinA-PCR3_S193",
                "jesse-engreitz:in-vitro-system_CRUDO_PILOT_CCND1-Auxin6hrs-FF1-BinA-PCR4_S289"
            ],
            "classifications": [
                "cell line"
            ],
            "construct_library_sets": [
                "/construct-library-sets/IGVFDS0392OWNZ/"
            ],
            "modifications": [
                {
                    "@id": "/degron-modifications/95081d1b-08b4-49ed-b324-e53fc43d8456/",
                    "modality": "degradation",
                    "status": "released"
                },
                {
                    "@id": "/crispr-modifications/8543fa06-1720-4e7d-8e8f-7e24c1b1cf79/",
                    "modality": "interference",
                    "status": "released"
                }
            ],
            "sample_terms": [
                {
                    "@id": "/sample-terms/EFO_0002824/",
                    "@type": [
                        "SampleTerm",
                        "OntologyTerm",
                        "Item"
                    ],
                    "aliases": [
                        "igvf:HCT116"
                    ],
                    "status": "released",
                    "summary": "HCT116",
                    "term_name": "HCT116"
                }
            ],
            "status": "released",
            "summary": "HCT116 cell line, male, Homo sapiens (sorting details: FACS bin A for 0-10% expression of CCND1) treated with 1 μM 5-Phenyl-1H-indole-3-acetic acid for 6 hours, modified with AID system targeting RAD21, CRISPRi Sp-dCas9-KOX1-KRAB, transfected with a guide library",
            "taxa": "Homo sapiens",
            "treatments": [
                {
                    "@id": "/treatments/d35868d1-c45b-49ae-8ff3-a9c0c22551c2/",
                    "status": "released",
                    "treatment_term_name": "5-Phenyl-1H-indole-3-acetic acid"
                }
            ]
        },
        {
            "@id": "/in-vitro-systems/IGVFSM8104CCIE/",
            "@type": [
                "InVitroSystem",
                "Biosample",
                "Sample",
                "Item"
            ],
            "accession": "IGVFSM8104CCIE",
            "aliases": [
                "jesse-engreitz:in-vitro-system_CRUDO_PILOT_CCND1-Auxin6hrs-FF1-BinB-PCR1_S2",
                "jesse-engreitz:in-vitro-system_CRUDO_PILOT_CCND1-Auxin6hrs-FF1-BinB-PCR2_S98",
                "jesse-engreitz:in-vitro-system_CRUDO_PILOT_CCND1-Auxin6hrs-FF1-BinB-PCR3_S194",
                "jesse-engreitz:in-vitro-system_CRUDO_PILOT_CCND1-Auxin6hrs-FF1-BinB-PCR4_S290"
            ],
            "classifications": [
                "cell line"
            ],
            "construct_library_sets": [
                "/construct-library-sets/IGVFDS0392OWNZ/"
            ],
            "modifications": [
                {
                    "@id": "/degron-modifications/95081d1b-08b4-49ed-b324-e53fc43d8456/",
                    "modality": "degradation",
                    "status": "released"
                },
                {
                    "@id": "/crispr-modifications/8543fa06-1720-4e7d-8e8f-7e24c1b1cf79/",
                    "modality": "interference",
                    "status": "released"
                }
            ],
            "sample_terms": [
                {
                    "@id": "/sample-terms/EFO_0002824/",
                    "@type": [
                        "SampleTerm",
                        "OntologyTerm",
                        "Item"
                    ],
                    "aliases": [
                        "igvf:HCT116"
                    ],
                    "status": "released",
                    "summary": "HCT116",
                    "term_name": "HCT116"
                }
            ],
            "status": "released",
            "summary": "HCT116 cell line, male, Homo sapiens (sorting details: FACS bin B for 10-20% expression of CCND1) treated with 1 μM 5-Phenyl-1H-indole-3-acetic acid for 6 hours, modified with AID system targeting RAD21, CRISPRi Sp-dCas9-KOX1-KRAB, transfected with a guide library",
            "taxa": "Homo sapiens",
            "treatments": [
                {
                    "@id": "/treatments/d35868d1-c45b-49ae-8ff3-a9c0c22551c2/",
                    "status": "released",
                    "treatment_term_name": "5-Phenyl-1H-indole-3-acetic acid"
                }
            ]
        },
        {
            "@id": "/in-vitro-systems/IGVFSM6480FETB/",
            "@type": [
                "InVitroSystem",
                "Biosample",
                "Sample",
                "Item"
            ],
            "accession": "IGVFSM6480FETB",
            "aliases": [
                "jesse-engreitz:in-vitro-system_CRUDO_PILOT_CCND1-Auxin6hrs-FF1-BinC-PCR1_S3",
                "jesse-engreitz:in-vitro-system_CRUDO_PILOT_CCND1-Auxin6hrs-FF1-BinC-PCR2_S99",
                "jesse-engreitz:in-vitro-system_CRUDO_PILOT_CCND1-Auxin6hrs-FF1-BinC-PCR3_S195",
                "jesse-engreitz:in-vitro-system_CRUDO_PILOT_CCND1-Auxin6hrs-FF1-BinC-PCR4_S291"
            ],
            "classifications": [
                "cell line"
            ],
            "construct_library_sets": [
                "/construct-library-sets/IGVFDS0392OWNZ/"
            ],
            "modifications": [
                {
                    "@id": "/degron-modifications/95081d1b-08b4-49ed-b324-e53fc43d8456/",
                    "modality": "degradation",
                    "status": "released"
                },
                {
                    "@id": "/crispr-modifications/8543fa06-1720-4e7d-8e8f-7e24c1b1cf79/",
                    "modality": "interference",
                    "status": "released"
                }
            ],
            "sample_terms": [
                {
                    "@id": "/sample-terms/EFO_0002824/",
                    "@type": [
                        "SampleTerm",
                        "OntologyTerm",
                        "Item"
                    ],
                    "aliases": [
                        "igvf:HCT116"
                    ],
                    "status": "released",
                    "summary": "HCT116",
                    "term_name": "HCT116"
                }
            ],
            "status": "released",
            "summary": "HCT116 cell line, male, Homo sapiens (sorting details: FACS bin C for 35-45% expression of CCND1) treated with 1 μM 5-Phenyl-1H-indole-3-acetic acid for 6 hours, modified with AID system targeting RAD21, CRISPRi Sp-dCas9-KOX1-KRAB, transfected with a guide library",
            "taxa": "Homo sapiens",
            "treatments": [
                {
                    "@id": "/treatments/d35868d1-c45b-49ae-8ff3-a9c0c22551c2/",
                    "status": "released",
                    "treatment_term_name": "5-Phenyl-1H-indole-3-acetic acid"
                }
            ]
        },
        {
            "@id": "/in-vitro-systems/IGVFSM7735WAOD/",
            "@type": [
                "InVitroSystem",
                "Biosample",
                "Sample",
                "Item"
            ],
            "accession": "IGVFSM7735WAOD",
            "aliases": [
                "jesse-engreitz:in-vitro-system_CRUDO_PILOT_CCND1-Auxin6hrs-FF1-BinD-PCR1_S4",
                "jesse-engreitz:in-vitro-system_CRUDO_PILOT_CCND1-Auxin6hrs-FF1-BinD-PCR2_S100",
                "jesse-engreitz:in-vitro-system_CRUDO_PILOT_CCND1-Auxin6hrs-FF1-BinD-PCR3_S196",
                "jesse-engreitz:in-vitro-system_CRUDO_PILOT_CCND1-Auxin6hrs-FF1-BinD-PCR4_S292"
            ],
            "classifications": [
                "cell line"
            ],
            "construct_library_sets": [
                "/construct-library-sets/IGVFDS0392OWNZ/"
            ],
            "modifications": [
                {
                    "@id": "/degron-modifications/95081d1b-08b4-49ed-b324-e53fc43d8456/",
                    "modality": "degradation",
                    "status": "released"
                },
                {
                    "@id": "/crispr-modifications/8543fa06-1720-4e7d-8e8f-7e24c1b1cf79/",
                    "modality": "interference",
                    "status": "released"
                }
            ],
            "sample_terms": [
                {
                    "@id": "/sample-terms/EFO_0002824/",
                    "@type": [
                        "SampleTerm",
                        "OntologyTerm",
                        "Item"
                    ],
                    "aliases": [
                        "igvf:HCT116"
                    ],
                    "status": "released",
                    "summary": "HCT116",
                    "term_name": "HCT116"
                }
            ],
            "status": "released",
            "summary": "HCT116 cell line, male, Homo sapiens (sorting details: FACS bin D for 55-65% expression of CCND1) treated with 1 μM 5-Phenyl-1H-indole-3-acetic acid for 6 hours, modified with AID system targeting RAD21, CRISPRi Sp-dCas9-KOX1-KRAB, transfected with a guide library",
            "taxa": "Homo sapiens",
            "treatments": [
                {
                    "@id": "/treatments/d35868d1-c45b-49ae-8ff3-a9c0c22551c2/",
                    "status": "released",
                    "treatment_term_name": "5-Phenyl-1H-indole-3-acetic acid"
                }
            ]
        },
        {
            "@id": "/in-vitro-systems/IGVFSM9116DXLY/",
            "@type": [
                "InVitroSystem",
                "Biosample",
                "Sample",
                "Item"
            ],
            "accession": "IGVFSM9116DXLY",
            "aliases": [
                "jesse-engreitz:in-vitro-system_CRUDO_PILOT_CCND1-Auxin6hrs-FF1-BinE-PCR1_S5",
                "jesse-engreitz:in-vitro-system_CRUDO_PILOT_CCND1-Auxin6hrs-FF1-BinE-PCR2_S101",
                "jesse-engreitz:in-vitro-system_CRUDO_PILOT_CCND1-Auxin6hrs-FF1-BinE-PCR3_S197",
                "jesse-engreitz:in-vitro-system_CRUDO_PILOT_CCND1-Auxin6hrs-FF1-BinE-PCR4_S293"
            ],
            "classifications": [
                "cell line"
            ],
            "construct_library_sets": [
                "/construct-library-sets/IGVFDS0392OWNZ/"
            ],
            "modifications": [
                {
                    "@id": "/degron-modifications/95081d1b-08b4-49ed-b324-e53fc43d8456/",
                    "modality": "degradation",
                    "status": "released"
                },
                {
                    "@id": "/crispr-modifications/8543fa06-1720-4e7d-8e8f-7e24c1b1cf79/",
                    "modality": "interference",
                    "status": "released"
                }
            ],
            "sample_terms": [
                {
                    "@id": "/sample-terms/EFO_0002824/",
                    "@type": [
                        "SampleTerm",
                        "OntologyTerm",
                        "Item"
                    ],
                    "aliases": [
                        "igvf:HCT116"
                    ],
                    "status": "released",
                    "summary": "HCT116",
                    "term_name": "HCT116"
                }
            ],
            "status": "released",
            "summary": "HCT116 cell line, male, Homo sapiens (sorting details: FACS bin E for 80-90% expression of CCND1) treated with 1 μM 5-Phenyl-1H-indole-3-acetic acid for 6 hours, modified with AID system targeting RAD21, CRISPRi Sp-dCas9-KOX1-KRAB, transfected with a guide library",
            "taxa": "Homo sapiens",
            "treatments": [
                {
                    "@id": "/treatments/d35868d1-c45b-49ae-8ff3-a9c0c22551c2/",
                    "status": "released",
                    "treatment_term_name": "5-Phenyl-1H-indole-3-acetic acid"
                }
            ]
        },
        {
            "@id": "/in-vitro-systems/IGVFSM0904FNLS/",
            "@type": [
                "InVitroSystem",
                "Biosample",
                "Sample",
                "Item"
            ],
            "accession": "IGVFSM0904FNLS",
            "aliases": [
                "jesse-engreitz:in-vitro-system_CRUDO_PILOT_CCND1-Auxin6hrs-FF1-BinF-PCR1_S6",
                "jesse-engreitz:in-vitro-system_CRUDO_PILOT_CCND1-Auxin6hrs-FF1-BinF-PCR2_S102",
                "jesse-engreitz:in-vitro-system_CRUDO_PILOT_CCND1-Auxin6hrs-FF1-BinF-PCR3_S198",
                "jesse-engreitz:in-vitro-system_CRUDO_PILOT_CCND1-Auxin6hrs-FF1-BinF-PCR4_S294"
            ],
            "classifications": [
                "cell line"
            ],
            "construct_library_sets": [
                "/construct-library-sets/IGVFDS0392OWNZ/"
            ],
            "modifications": [
                {
                    "@id": "/degron-modifications/95081d1b-08b4-49ed-b324-e53fc43d8456/",
                    "modality": "degradation",
                    "status": "released"
                },
                {
                    "@id": "/crispr-modifications/8543fa06-1720-4e7d-8e8f-7e24c1b1cf79/",
                    "modality": "interference",
                    "status": "released"
                }
            ],
            "sample_terms": [
                {
                    "@id": "/sample-terms/EFO_0002824/",
                    "@type": [
                        "SampleTerm",
                        "OntologyTerm",
                        "Item"
                    ],
                    "aliases": [
                        "igvf:HCT116"
                    ],
                    "status": "released",
                    "summary": "HCT116",
                    "term_name": "HCT116"
                }
            ],
            "status": "released",
            "summary": "HCT116 cell line, male, Homo sapiens (sorting details: FACS bin F for 80-100% expression of CCND1) treated with 1 μM 5-Phenyl-1H-indole-3-acetic acid for 6 hours, modified with AID system targeting RAD21, CRISPRi Sp-dCas9-KOX1-KRAB, transfected with a guide library",
            "taxa": "Homo sapiens",
            "treatments": [
                {
                    "@id": "/treatments/d35868d1-c45b-49ae-8ff3-a9c0c22551c2/",
                    "status": "released",
                    "treatment_term_name": "5-Phenyl-1H-indole-3-acetic acid"
                }
            ]
        }
    ],
    "schema_version": "12",
    "status": "released",
    "submitted_by": {
        "@id": "/users/100f06c6-83a7-4b4d-9dfd-053a1829773b/",
        "title": "Benjamin Doughty"
    },
    "submitted_files_timestamp": "2024-07-03T00:35:13.629110+00:00",
    "summary": "cell sorting for mixed CRISPR FlowFISH screen integrating a guide (sgRNA) library targeting accessible genome regions in 36 genomic loci, mixed CRISPR FlowFISH screen integrating a guide (sgRNA) library targeting accessible genome regions in 36 genomic loci, ... and 4 more measurement sets",
    "uuid": "32cb7a0d-e0ea-4917-a9eb-50956f0799d6"
}