IGVFDS6449NYRM

released
{
    "@context": "/terms/",
    "@id": "/auxiliary-sets/IGVFDS6449NYRM/",
    "@type": [
        "AuxiliarySet",
        "FileSet",
        "Item"
    ],
    "accession": "IGVFDS6449NYRM",
    "aliases": [
        "jesse-engreitz:auxiliary_CRUDO_FAM3C_Auxin0hrs-FF1-BinB-PCR1-Rep1_S110",
        "jesse-engreitz:auxiliary_CRUDO_FAM3C_Auxin0hrs-FF1-BinB-PCR2-Rep1_S116",
        "jesse-engreitz:auxiliary_CRUDO_FAM3C_Auxin0hrs-FF1-BinB-PCR3-Rep1_S164",
        "jesse-engreitz:auxiliary_CRUDO_FAM3C_Auxin0hrs-FF1-BinB-PCR4-Rep1_S170"
    ],
    "audit": {
        "INTERNAL_ACTION": [
            {
                "category": "missing sequencing kit",
                "detail": "Auxiliary set [IGVFDS6449NYRM](/auxiliary-sets/IGVFDS6449NYRM/) has sequence file(s) [IGVFFI5340ERRF](/sequence-files/IGVFFI5340ERRF/), [IGVFFI3781TWXY](/sequence-files/IGVFFI3781TWXY/), [IGVFFI7194FCZO](/sequence-files/IGVFFI7194FCZO/), [IGVFFI5756XBGF](/sequence-files/IGVFFI5756XBGF/) which lack specification of a `sequencing_kit`. Sequence files should specify a sequencing kit.",
                "level": 30,
                "level_name": "INTERNAL_ACTION",
                "name": "audit_inconsistent_sequencing_kit",
                "path": "/auxiliary-sets/IGVFDS6449NYRM/"
            }
        ]
    },
    "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": "2024-05-14T16:23:50.611222+00:00",
    "donors": [
        {
            "@id": "/human-donors/IGVFDO0384OZRW/",
            "accession": "IGVFDO0384OZRW",
            "aliases": [
                "igvf:donor_of_HCT116"
            ],
            "sex": "male",
            "status": "released",
            "taxa": "Homo sapiens"
        }
    ],
    "file_set_type": "gRNA sequencing",
    "files": [
        {
            "@id": "/sequence-files/IGVFFI5340ERRF/",
            "accession": "IGVFFI5340ERRF",
            "aliases": [
                "jesse-engreitz:auxiliary_file_CRUDO_FAM3C_Auxin0hrs-FF1-BinB-PCR1-Rep1_S110"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-06-01T01:50:53.033706+00:00",
            "file_format": "fastq",
            "file_size": 29645689,
            "href": "/sequence-files/IGVFFI5340ERRF/@@download/IGVFFI5340ERRF.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/06/01/b2be5530-e578-4e63-aa88-2a3336957ba3/IGVFFI5340ERRF.fastq.gz",
            "sequencing_platform": "/platform-terms/EFO_0008565/",
            "status": "released",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220308B014_CCND1_SSFA2_FAM3C/fastq_trim/FAM3C-Auxin0hrs-FF1-BinB-PCR1-Rep1_S110_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/configuration-files/IGVFFI8839AZBX/",
            "accession": "IGVFFI8839AZBX",
            "aliases": [
                "jesse-engreitz:seqspecfile_CRUDO_FAM3C_Auxin0hrs-FF1-BinB-PCR1-Rep1_S110"
            ],
            "content_type": "seqspec",
            "creation_timestamp": "2024-06-11T20:41:51.907765+00:00",
            "file_format": "yaml",
            "file_size": 913,
            "href": "/configuration-files/IGVFFI8839AZBX/@@download/IGVFFI8839AZBX.yaml.gz",
            "s3_uri": "s3://igvf-files/2024/06/11/c4bb3e42-d746-4b1a-9dd4-8fb2b84c8773/IGVFFI8839AZBX.yaml.gz",
            "status": "released",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.FAM3C_Auxin0hrs-FF1-BinB-PCR1-Rep1_S110.yaml",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI3781TWXY/",
            "accession": "IGVFFI3781TWXY",
            "aliases": [
                "jesse-engreitz:auxiliary_file_CRUDO_FAM3C_Auxin0hrs-FF1-BinB-PCR2-Rep1_S116"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-06-01T01:51:13.343746+00:00",
            "file_format": "fastq",
            "file_size": 17142969,
            "href": "/sequence-files/IGVFFI3781TWXY/@@download/IGVFFI3781TWXY.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/06/01/63935fca-4d4d-47c0-a3b7-4428efb9fc41/IGVFFI3781TWXY.fastq.gz",
            "sequencing_platform": "/platform-terms/EFO_0008565/",
            "status": "released",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220308B014_CCND1_SSFA2_FAM3C/fastq_trim/FAM3C-Auxin0hrs-FF1-BinB-PCR2-Rep1_S116_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI7194FCZO/",
            "accession": "IGVFFI7194FCZO",
            "aliases": [
                "jesse-engreitz:auxiliary_file_CRUDO_FAM3C_Auxin0hrs-FF1-BinB-PCR3-Rep1_S164"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-06-01T01:51:31.659015+00:00",
            "file_format": "fastq",
            "file_size": 33809110,
            "href": "/sequence-files/IGVFFI7194FCZO/@@download/IGVFFI7194FCZO.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/06/01/8b4e27a1-caf4-4d02-b66a-1c7e5db9772f/IGVFFI7194FCZO.fastq.gz",
            "sequencing_platform": "/platform-terms/EFO_0008565/",
            "status": "released",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220308B014_CCND1_SSFA2_FAM3C/fastq_trim/FAM3C-Auxin0hrs-FF1-BinB-PCR3-Rep1_S164_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI5756XBGF/",
            "accession": "IGVFFI5756XBGF",
            "aliases": [
                "jesse-engreitz:auxiliary_file_CRUDO_FAM3C_Auxin0hrs-FF1-BinB-PCR4-Rep1_S170"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-06-01T01:51:51.214330+00:00",
            "file_format": "fastq",
            "file_size": 25935699,
            "href": "/sequence-files/IGVFFI5756XBGF/@@download/IGVFFI5756XBGF.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/06/01/17415866-bf69-449f-8b96-ad863438e9c1/IGVFFI5756XBGF.fastq.gz",
            "sequencing_platform": "/platform-terms/EFO_0008565/",
            "status": "released",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220308B014_CCND1_SSFA2_FAM3C/fastq_trim/FAM3C-Auxin0hrs-FF1-BinB-PCR4-Rep1_S170_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/configuration-files/IGVFFI3497STEU/",
            "accession": "IGVFFI3497STEU",
            "aliases": [
                "jesse-engreitz:seqspecfile_CRUDO_FAM3C_Auxin0hrs-FF1-BinB-PCR4-Rep1_S170"
            ],
            "content_type": "seqspec",
            "creation_timestamp": "2024-06-11T20:42:35.238532+00:00",
            "file_format": "yaml",
            "file_size": 914,
            "href": "/configuration-files/IGVFFI3497STEU/@@download/IGVFFI3497STEU.yaml.gz",
            "s3_uri": "s3://igvf-files/2024/06/11/331ed763-685b-45ff-9c1f-922f1f7f5a5c/IGVFFI3497STEU.yaml.gz",
            "status": "released",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.FAM3C_Auxin0hrs-FF1-BinB-PCR4-Rep1_S170.yaml",
            "upload_status": "validated"
        },
        {
            "@id": "/configuration-files/IGVFFI6612QXQL/",
            "accession": "IGVFFI6612QXQL",
            "aliases": [
                "jesse-engreitz:seqspecfile_CRUDO_FAM3C_Auxin0hrs-FF1-BinB-PCR2-Rep1_S116"
            ],
            "content_type": "seqspec",
            "creation_timestamp": "2024-06-11T20:42:07.386375+00:00",
            "file_format": "yaml",
            "file_size": 915,
            "href": "/configuration-files/IGVFFI6612QXQL/@@download/IGVFFI6612QXQL.yaml.gz",
            "s3_uri": "s3://igvf-files/2024/06/11/f110eaf1-dfaf-4174-9b83-e2e5ce637ccd/IGVFFI6612QXQL.yaml.gz",
            "status": "released",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.FAM3C_Auxin0hrs-FF1-BinB-PCR2-Rep1_S116.yaml",
            "upload_status": "validated"
        },
        {
            "@id": "/configuration-files/IGVFFI2959DQXK/",
            "accession": "IGVFFI2959DQXK",
            "aliases": [
                "jesse-engreitz:seqspecfile_CRUDO_FAM3C_Auxin0hrs-FF1-BinB-PCR3-Rep1_S164"
            ],
            "content_type": "seqspec",
            "creation_timestamp": "2024-06-11T20:42:22.189814+00:00",
            "file_format": "yaml",
            "file_size": 914,
            "href": "/configuration-files/IGVFFI2959DQXK/@@download/IGVFFI2959DQXK.yaml.gz",
            "s3_uri": "s3://igvf-files/2024/06/11/3a95b09e-8aa1-4892-8d8b-08aa1f2fb77d/IGVFFI2959DQXK.yaml.gz",
            "status": "released",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.FAM3C_Auxin0hrs-FF1-BinB-PCR3-Rep1_S164.yaml",
            "upload_status": "validated"
        }
    ],
    "input_for": [
        "/analysis-sets/IGVFDS5239VQTN/"
    ],
    "lab": {
        "@id": "/labs/jesse-engreitz/",
        "title": "Jesse Engreitz, Stanford"
    },
    "measurement_sets": [
        {
            "@id": "/measurement-sets/IGVFDS6704KMTH/",
            "accession": "IGVFDS6704KMTH",
            "aliases": [
                "jesse-engreitz:measurement_CRUDO_FAM3C_Auxin0hrs-FF1-BinB-PCR1-Rep1_S110",
                "jesse-engreitz:measurement_CRUDO_FAM3C_Auxin0hrs-FF1-BinB-PCR2-Rep1_S116",
                "jesse-engreitz:measurement_CRUDO_FAM3C_Auxin0hrs-FF1-BinB-PCR3-Rep1_S164",
                "jesse-engreitz:measurement_CRUDO_FAM3C_Auxin0hrs-FF1-BinB-PCR4-Rep1_S170"
            ],
            "preferred_assay_title": "CRISPR FlowFISH screen",
            "status": "released"
        }
    ],
    "release_timestamp": "2024-07-10T20:10:45.555140+00:00",
    "samples": [
        {
            "@id": "/in-vitro-systems/IGVFSM0069TVXJ/",
            "@type": [
                "InVitroSystem",
                "Biosample",
                "Sample",
                "Item"
            ],
            "accession": "IGVFSM0069TVXJ",
            "aliases": [
                "jesse-engreitz:in-vitro-system_CRUDO_FAM3C_Auxin0hrs-FF1-BinB-PCR1-Rep1_S110",
                "jesse-engreitz:in-vitro-system_CRUDO_FAM3C_Auxin0hrs-FF1-BinB-PCR2-Rep1_S116",
                "jesse-engreitz:in-vitro-system_CRUDO_FAM3C_Auxin0hrs-FF1-BinB-PCR3-Rep1_S164",
                "jesse-engreitz:in-vitro-system_CRUDO_FAM3C_Auxin0hrs-FF1-BinB-PCR4-Rep1_S170"
            ],
            "classifications": [
                "cell line"
            ],
            "construct_library_sets": [
                "/construct-library-sets/IGVFDS1891GTLU/"
            ],
            "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 FAM3C) 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/3bd6f74c-8cf3-4c35-a94d-0c7c11654815/",
        "title": "Chongyon Park"
    },
    "submitted_files_timestamp": "2024-06-01T01:50:53.033706+00:00",
    "summary": "gRNA sequencing for mixed CRISPR FlowFISH screen integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
    "uuid": "60782528-957f-4783-b0ce-6cf44a347685"
}