IGVFDS5464XLTY

released
{
    "@context": "/terms/",
    "@id": "/auxiliary-sets/IGVFDS5464XLTY/",
    "@type": [
        "AuxiliarySet",
        "FileSet",
        "Item"
    ],
    "accession": "IGVFDS5464XLTY",
    "aliases": [
        "jesse-engreitz:auxiliary_sortparams_CRUDO_CCND1_Auxin0hrs-FF1"
    ],
    "audit": {
        "NOT_COMPLIANT": [
            {
                "category": "missing file format specifications",
                "detail": "Tabular file [IGVFFI0860RTJY](/tabular-files/IGVFFI0860RTJY/) 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/IGVFFI0860RTJY/"
            }
        ]
    },
    "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": "2024-07-02T23:41:51.460413+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/IGVFFI0860RTJY/",
            "accession": "IGVFFI0860RTJY",
            "aliases": [
                "jesse-engreitz:auxiliary_sortparams_file_CRUDO_CCND1_Auxin0hrs-FF1"
            ],
            "content_type": "sample sort parameters",
            "controlled_access": false,
            "creation_timestamp": "2024-07-03T00:35:16.184339+00:00",
            "file_format": "tsv",
            "file_size": 466,
            "href": "/tabular-files/IGVFFI0860RTJY/@@download/IGVFFI0860RTJY.tsv.gz",
            "s3_uri": "s3://igvf-files/2024/07/03/19d639d6-09e3-4dae-8f8d-5800ca2ffbd6/IGVFFI0860RTJY.tsv.gz",
            "status": "released",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/sortparams/220307B014_2.tsv.gz",
            "upload_status": "validated"
        }
    ],
    "input_for": [
        "/analysis-sets/IGVFDS1569RNPD/"
    ],
    "lab": {
        "@id": "/labs/jesse-engreitz/",
        "title": "Jesse Engreitz, Stanford"
    },
    "measurement_sets": [
        {
            "@id": "/measurement-sets/IGVFDS2241NBBY/",
            "accession": "IGVFDS2241NBBY",
            "aliases": [
                "jesse-engreitz:measurement_CRUDO_CCND1_Auxin0hrs-FF1-BinF-PCR1-Rep1_S222",
                "jesse-engreitz:measurement_CRUDO_CCND1_Auxin0hrs-FF1-BinF-PCR2-Rep1_S228",
                "jesse-engreitz:measurement_CRUDO_CCND1_Auxin0hrs-FF1-BinF-PCR3-Rep1_S264",
                "jesse-engreitz:measurement_CRUDO_CCND1_Auxin0hrs-FF1-BinF-PCR4-Rep1_S270"
            ],
            "preferred_assay_title": "CRISPR FlowFISH screen",
            "status": "released"
        },
        {
            "@id": "/measurement-sets/IGVFDS0528ZIOC/",
            "accession": "IGVFDS0528ZIOC",
            "aliases": [
                "jesse-engreitz:measurement_CRUDO_CCND1_Auxin0hrs-FF1-BinC-PCR1-Rep1_S219",
                "jesse-engreitz:measurement_CRUDO_CCND1_Auxin0hrs-FF1-BinC-PCR2-Rep1_S225",
                "jesse-engreitz:measurement_CRUDO_CCND1_Auxin0hrs-FF1-BinC-PCR3-Rep1_S261",
                "jesse-engreitz:measurement_CRUDO_CCND1_Auxin0hrs-FF1-BinC-PCR4-Rep1_S267"
            ],
            "preferred_assay_title": "CRISPR FlowFISH screen",
            "status": "released"
        },
        {
            "@id": "/measurement-sets/IGVFDS0483TWVD/",
            "accession": "IGVFDS0483TWVD",
            "aliases": [
                "jesse-engreitz:measurement_CRUDO_CCND1_Auxin0hrs-FF1-BinE-PCR1-Rep1_S221",
                "jesse-engreitz:measurement_CRUDO_CCND1_Auxin0hrs-FF1-BinE-PCR2-Rep1_S227",
                "jesse-engreitz:measurement_CRUDO_CCND1_Auxin0hrs-FF1-BinE-PCR3-Rep1_S263",
                "jesse-engreitz:measurement_CRUDO_CCND1_Auxin0hrs-FF1-BinE-PCR4-Rep1_S269"
            ],
            "preferred_assay_title": "CRISPR FlowFISH screen",
            "status": "released"
        },
        {
            "@id": "/measurement-sets/IGVFDS6376TFTJ/",
            "accession": "IGVFDS6376TFTJ",
            "aliases": [
                "jesse-engreitz:measurement_CRUDO_CCND1_Auxin0hrs-FF1-BinA-PCR1-Rep1_S217",
                "jesse-engreitz:measurement_CRUDO_CCND1_Auxin0hrs-FF1-BinA-PCR2-Rep1_S223",
                "jesse-engreitz:measurement_CRUDO_CCND1_Auxin0hrs-FF1-BinA-PCR3-Rep1_S259",
                "jesse-engreitz:measurement_CRUDO_CCND1_Auxin0hrs-FF1-BinA-PCR4-Rep1_S265"
            ],
            "preferred_assay_title": "CRISPR FlowFISH screen",
            "status": "released"
        },
        {
            "@id": "/measurement-sets/IGVFDS6001NZOV/",
            "accession": "IGVFDS6001NZOV",
            "aliases": [
                "jesse-engreitz:measurement_CRUDO_CCND1_Auxin0hrs-FF1-BinD-PCR1-Rep1_S220",
                "jesse-engreitz:measurement_CRUDO_CCND1_Auxin0hrs-FF1-BinD-PCR2-Rep1_S226",
                "jesse-engreitz:measurement_CRUDO_CCND1_Auxin0hrs-FF1-BinD-PCR3-Rep1_S262",
                "jesse-engreitz:measurement_CRUDO_CCND1_Auxin0hrs-FF1-BinD-PCR4-Rep1_S268"
            ],
            "preferred_assay_title": "CRISPR FlowFISH screen",
            "status": "released"
        },
        {
            "@id": "/measurement-sets/IGVFDS7173YRIO/",
            "accession": "IGVFDS7173YRIO",
            "aliases": [
                "jesse-engreitz:measurement_CRUDO_CCND1_Auxin0hrs-FF1-BinB-PCR1-Rep1_S218",
                "jesse-engreitz:measurement_CRUDO_CCND1_Auxin0hrs-FF1-BinB-PCR2-Rep1_S224",
                "jesse-engreitz:measurement_CRUDO_CCND1_Auxin0hrs-FF1-BinB-PCR3-Rep1_S260",
                "jesse-engreitz:measurement_CRUDO_CCND1_Auxin0hrs-FF1-BinB-PCR4-Rep1_S266"
            ],
            "preferred_assay_title": "CRISPR FlowFISH screen",
            "status": "released"
        }
    ],
    "release_timestamp": "2024-07-10T20:27:01.893189+00:00",
    "samples": [
        {
            "@id": "/in-vitro-systems/IGVFSM9315IOJD/",
            "@type": [
                "InVitroSystem",
                "Biosample",
                "Sample",
                "Item"
            ],
            "accession": "IGVFSM9315IOJD",
            "aliases": [
                "jesse-engreitz:in-vitro-system_CRUDO_CCND1_Auxin0hrs-FF1-BinA-PCR1-Rep1_S217",
                "jesse-engreitz:in-vitro-system_CRUDO_CCND1_Auxin0hrs-FF1-BinA-PCR2-Rep1_S223",
                "jesse-engreitz:in-vitro-system_CRUDO_CCND1_Auxin0hrs-FF1-BinA-PCR3-Rep1_S259",
                "jesse-engreitz:in-vitro-system_CRUDO_CCND1_Auxin0hrs-FF1-BinA-PCR4-Rep1_S265"
            ],
            "classifications": [
                "cell line"
            ],
            "construct_library_sets": [
                "/construct-library-sets/IGVFDS6351FGNG/"
            ],
            "modifications": [
                {
                    "@id": "/crispr-modifications/8543fa06-1720-4e7d-8e8f-7e24c1b1cf79/",
                    "modality": "interference",
                    "status": "released"
                },
                {
                    "@id": "/degron-modifications/2e8d10cc-fc98-44d5-a7d9-e2892e16c98a/",
                    "modality": "degradation",
                    "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) modified with CRISPRi Sp-dCas9-KOX1-KRAB, inactive AID system targeting RAD21, transfected with a guide library",
            "taxa": "Homo sapiens"
        },
        {
            "@id": "/in-vitro-systems/IGVFSM4779RXHT/",
            "@type": [
                "InVitroSystem",
                "Biosample",
                "Sample",
                "Item"
            ],
            "accession": "IGVFSM4779RXHT",
            "aliases": [
                "jesse-engreitz:in-vitro-system_CRUDO_CCND1_Auxin0hrs-FF1-BinB-PCR1-Rep1_S218",
                "jesse-engreitz:in-vitro-system_CRUDO_CCND1_Auxin0hrs-FF1-BinB-PCR2-Rep1_S224",
                "jesse-engreitz:in-vitro-system_CRUDO_CCND1_Auxin0hrs-FF1-BinB-PCR3-Rep1_S260",
                "jesse-engreitz:in-vitro-system_CRUDO_CCND1_Auxin0hrs-FF1-BinB-PCR4-Rep1_S266"
            ],
            "classifications": [
                "cell line"
            ],
            "construct_library_sets": [
                "/construct-library-sets/IGVFDS6351FGNG/"
            ],
            "modifications": [
                {
                    "@id": "/crispr-modifications/8543fa06-1720-4e7d-8e8f-7e24c1b1cf79/",
                    "modality": "interference",
                    "status": "released"
                },
                {
                    "@id": "/degron-modifications/2e8d10cc-fc98-44d5-a7d9-e2892e16c98a/",
                    "modality": "degradation",
                    "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) modified with CRISPRi Sp-dCas9-KOX1-KRAB, inactive AID system targeting RAD21, transfected with a guide library",
            "taxa": "Homo sapiens"
        },
        {
            "@id": "/in-vitro-systems/IGVFSM2913DQHN/",
            "@type": [
                "InVitroSystem",
                "Biosample",
                "Sample",
                "Item"
            ],
            "accession": "IGVFSM2913DQHN",
            "aliases": [
                "jesse-engreitz:in-vitro-system_CRUDO_CCND1_Auxin0hrs-FF1-BinC-PCR1-Rep1_S219",
                "jesse-engreitz:in-vitro-system_CRUDO_CCND1_Auxin0hrs-FF1-BinC-PCR2-Rep1_S225",
                "jesse-engreitz:in-vitro-system_CRUDO_CCND1_Auxin0hrs-FF1-BinC-PCR3-Rep1_S261",
                "jesse-engreitz:in-vitro-system_CRUDO_CCND1_Auxin0hrs-FF1-BinC-PCR4-Rep1_S267"
            ],
            "classifications": [
                "cell line"
            ],
            "construct_library_sets": [
                "/construct-library-sets/IGVFDS6351FGNG/"
            ],
            "modifications": [
                {
                    "@id": "/crispr-modifications/8543fa06-1720-4e7d-8e8f-7e24c1b1cf79/",
                    "modality": "interference",
                    "status": "released"
                },
                {
                    "@id": "/degron-modifications/2e8d10cc-fc98-44d5-a7d9-e2892e16c98a/",
                    "modality": "degradation",
                    "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) modified with CRISPRi Sp-dCas9-KOX1-KRAB, inactive AID system targeting RAD21, transfected with a guide library",
            "taxa": "Homo sapiens"
        },
        {
            "@id": "/in-vitro-systems/IGVFSM6400EVKX/",
            "@type": [
                "InVitroSystem",
                "Biosample",
                "Sample",
                "Item"
            ],
            "accession": "IGVFSM6400EVKX",
            "aliases": [
                "jesse-engreitz:in-vitro-system_CRUDO_CCND1_Auxin0hrs-FF1-BinD-PCR1-Rep1_S220",
                "jesse-engreitz:in-vitro-system_CRUDO_CCND1_Auxin0hrs-FF1-BinD-PCR2-Rep1_S226",
                "jesse-engreitz:in-vitro-system_CRUDO_CCND1_Auxin0hrs-FF1-BinD-PCR3-Rep1_S262",
                "jesse-engreitz:in-vitro-system_CRUDO_CCND1_Auxin0hrs-FF1-BinD-PCR4-Rep1_S268"
            ],
            "classifications": [
                "cell line"
            ],
            "construct_library_sets": [
                "/construct-library-sets/IGVFDS6351FGNG/"
            ],
            "modifications": [
                {
                    "@id": "/crispr-modifications/8543fa06-1720-4e7d-8e8f-7e24c1b1cf79/",
                    "modality": "interference",
                    "status": "released"
                },
                {
                    "@id": "/degron-modifications/2e8d10cc-fc98-44d5-a7d9-e2892e16c98a/",
                    "modality": "degradation",
                    "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) modified with CRISPRi Sp-dCas9-KOX1-KRAB, inactive AID system targeting RAD21, transfected with a guide library",
            "taxa": "Homo sapiens"
        },
        {
            "@id": "/in-vitro-systems/IGVFSM7928IVYJ/",
            "@type": [
                "InVitroSystem",
                "Biosample",
                "Sample",
                "Item"
            ],
            "accession": "IGVFSM7928IVYJ",
            "aliases": [
                "jesse-engreitz:in-vitro-system_CRUDO_CCND1_Auxin0hrs-FF1-BinE-PCR1-Rep1_S221",
                "jesse-engreitz:in-vitro-system_CRUDO_CCND1_Auxin0hrs-FF1-BinE-PCR2-Rep1_S227",
                "jesse-engreitz:in-vitro-system_CRUDO_CCND1_Auxin0hrs-FF1-BinE-PCR3-Rep1_S263",
                "jesse-engreitz:in-vitro-system_CRUDO_CCND1_Auxin0hrs-FF1-BinE-PCR4-Rep1_S269"
            ],
            "classifications": [
                "cell line"
            ],
            "construct_library_sets": [
                "/construct-library-sets/IGVFDS6351FGNG/"
            ],
            "modifications": [
                {
                    "@id": "/crispr-modifications/8543fa06-1720-4e7d-8e8f-7e24c1b1cf79/",
                    "modality": "interference",
                    "status": "released"
                },
                {
                    "@id": "/degron-modifications/2e8d10cc-fc98-44d5-a7d9-e2892e16c98a/",
                    "modality": "degradation",
                    "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) modified with CRISPRi Sp-dCas9-KOX1-KRAB, inactive AID system targeting RAD21, transfected with a guide library",
            "taxa": "Homo sapiens"
        },
        {
            "@id": "/in-vitro-systems/IGVFSM4218VHTT/",
            "@type": [
                "InVitroSystem",
                "Biosample",
                "Sample",
                "Item"
            ],
            "accession": "IGVFSM4218VHTT",
            "aliases": [
                "jesse-engreitz:in-vitro-system_CRUDO_CCND1_Auxin0hrs-FF1-BinF-PCR1-Rep1_S222",
                "jesse-engreitz:in-vitro-system_CRUDO_CCND1_Auxin0hrs-FF1-BinF-PCR2-Rep1_S228",
                "jesse-engreitz:in-vitro-system_CRUDO_CCND1_Auxin0hrs-FF1-BinF-PCR3-Rep1_S264",
                "jesse-engreitz:in-vitro-system_CRUDO_CCND1_Auxin0hrs-FF1-BinF-PCR4-Rep1_S270"
            ],
            "classifications": [
                "cell line"
            ],
            "construct_library_sets": [
                "/construct-library-sets/IGVFDS6351FGNG/"
            ],
            "modifications": [
                {
                    "@id": "/crispr-modifications/8543fa06-1720-4e7d-8e8f-7e24c1b1cf79/",
                    "modality": "interference",
                    "status": "released"
                },
                {
                    "@id": "/degron-modifications/2e8d10cc-fc98-44d5-a7d9-e2892e16c98a/",
                    "modality": "degradation",
                    "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) modified with CRISPRi Sp-dCas9-KOX1-KRAB, inactive AID system targeting RAD21, transfected with a guide library",
            "taxa": "Homo sapiens"
        }
    ],
    "schema_version": "12",
    "status": "released",
    "submitted_by": {
        "@id": "/users/100f06c6-83a7-4b4d-9dfd-053a1829773b/",
        "title": "Benjamin Doughty"
    },
    "submitted_files_timestamp": "2024-07-03T00:35:16.184339+00:00",
    "summary": "cell sorting for mixed CRISPR FlowFISH screen integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci, mixed CRISPR FlowFISH screen integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci, ... and 4 more measurement sets",
    "uuid": "b25df0e5-97ec-49b4-b316-46408b924fa2"
}