IGVFDS1635IQIT

released
{
    "@context": "/terms/",
    "@id": "/auxiliary-sets/IGVFDS1635IQIT/",
    "@type": [
        "AuxiliarySet",
        "FileSet",
        "Item"
    ],
    "accession": "IGVFDS1635IQIT",
    "aliases": [
        "jesse-engreitz:auxiliary_CRUDO_KITLG-Auxin0hrs-FF1-BinB-PCR1_S2",
        "jesse-engreitz:auxiliary_CRUDO_KITLG-Auxin0hrs-FF1-BinB-PCR2_S8",
        "jesse-engreitz:auxiliary_CRUDO_KITLG-Auxin0hrs-FF1-BinB-PCR3_S98",
        "jesse-engreitz:auxiliary_CRUDO_KITLG-Auxin0hrs-FF1-BinB-PCR4_S104"
    ],
    "audit": {
        "INTERNAL_ACTION": [
            {
                "category": "missing sequencing kit",
                "detail": "Auxiliary set [IGVFDS1635IQIT](/auxiliary-sets/IGVFDS1635IQIT/) has sequence file(s) [IGVFFI0357RECW](/sequence-files/IGVFFI0357RECW/), [IGVFFI0079YAMM](/sequence-files/IGVFFI0079YAMM/), [IGVFFI7682PLQL](/sequence-files/IGVFFI7682PLQL/), [IGVFFI2660UTOF](/sequence-files/IGVFFI2660UTOF/) 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/IGVFDS1635IQIT/"
            }
        ]
    },
    "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": "2024-05-16T17:41:02.269582+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/IGVFFI0357RECW/",
            "accession": "IGVFFI0357RECW",
            "aliases": [
                "jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin0hrs-FF1-BinB-PCR1_S2"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-06-01T02:10:14.444737+00:00",
            "file_format": "fastq",
            "file_size": 17777080,
            "href": "/sequence-files/IGVFFI0357RECW/@@download/IGVFFI0357RECW.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/06/01/d6ba4e2b-9d9d-46d5-abd2-fbf5ae98274c/IGVFFI0357RECW.fastq.gz",
            "sequencing_platform": "/platform-terms/EFO_0008565/",
            "status": "released",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220104B013_Cohesin_KITLG/fastq_trim/Auxin0hrs-FF1-BinB-PCR1_S2_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/configuration-files/IGVFFI6958FQNG/",
            "accession": "IGVFFI6958FQNG",
            "aliases": [
                "jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin0hrs-FF1-BinB-PCR1_S2"
            ],
            "content_type": "seqspec",
            "creation_timestamp": "2024-06-11T22:05:42.644512+00:00",
            "file_format": "yaml",
            "file_size": 900,
            "href": "/configuration-files/IGVFFI6958FQNG/@@download/IGVFFI6958FQNG.yaml.gz",
            "s3_uri": "s3://igvf-files/2024/06/11/9ffcc9c7-bcb3-429a-96b5-1c0b91fc3d22/IGVFFI6958FQNG.yaml.gz",
            "status": "released",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin0hrs-FF1-BinB-PCR1_S2.yaml",
            "upload_status": "validated"
        },
        {
            "@id": "/configuration-files/IGVFFI3962TRBT/",
            "accession": "IGVFFI3962TRBT",
            "aliases": [
                "jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin0hrs-FF1-BinB-PCR2_S8"
            ],
            "content_type": "seqspec",
            "creation_timestamp": "2024-06-11T22:05:56.882382+00:00",
            "file_format": "yaml",
            "file_size": 900,
            "href": "/configuration-files/IGVFFI3962TRBT/@@download/IGVFFI3962TRBT.yaml.gz",
            "s3_uri": "s3://igvf-files/2024/06/11/4b2aa2a9-fc18-40cf-8d5d-5abf28eccf8f/IGVFFI3962TRBT.yaml.gz",
            "status": "released",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin0hrs-FF1-BinB-PCR2_S8.yaml",
            "upload_status": "validated"
        },
        {
            "@id": "/configuration-files/IGVFFI8059ZOIT/",
            "accession": "IGVFFI8059ZOIT",
            "aliases": [
                "jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin0hrs-FF1-BinB-PCR4_S104"
            ],
            "content_type": "seqspec",
            "creation_timestamp": "2024-06-11T22:06:23.697671+00:00",
            "file_format": "yaml",
            "file_size": 902,
            "href": "/configuration-files/IGVFFI8059ZOIT/@@download/IGVFFI8059ZOIT.yaml.gz",
            "s3_uri": "s3://igvf-files/2024/06/11/e99a5bd6-3a30-4e37-b249-9134d0cedd17/IGVFFI8059ZOIT.yaml.gz",
            "status": "released",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin0hrs-FF1-BinB-PCR4_S104.yaml",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI0079YAMM/",
            "accession": "IGVFFI0079YAMM",
            "aliases": [
                "jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin0hrs-FF1-BinB-PCR3_S98"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-06-01T02:10:55.160854+00:00",
            "file_format": "fastq",
            "file_size": 40391210,
            "href": "/sequence-files/IGVFFI0079YAMM/@@download/IGVFFI0079YAMM.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/06/01/c37dea70-4c22-471e-8ef0-97af0e2f5a4e/IGVFFI0079YAMM.fastq.gz",
            "sequencing_platform": "/platform-terms/EFO_0008565/",
            "status": "released",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220104B013_Cohesin_KITLG/fastq_trim/Auxin0hrs-FF1-BinB-PCR3_S98_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI7682PLQL/",
            "accession": "IGVFFI7682PLQL",
            "aliases": [
                "jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin0hrs-FF1-BinB-PCR4_S104"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-06-01T02:11:13.396167+00:00",
            "file_format": "fastq",
            "file_size": 23961767,
            "href": "/sequence-files/IGVFFI7682PLQL/@@download/IGVFFI7682PLQL.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/06/01/331fdc20-281c-4047-9495-aae48f0a4a43/IGVFFI7682PLQL.fastq.gz",
            "sequencing_platform": "/platform-terms/EFO_0008565/",
            "status": "released",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220104B013_Cohesin_KITLG/fastq_trim/Auxin0hrs-FF1-BinB-PCR4_S104_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI2660UTOF/",
            "accession": "IGVFFI2660UTOF",
            "aliases": [
                "jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin0hrs-FF1-BinB-PCR2_S8"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-06-01T02:10:33.277352+00:00",
            "file_format": "fastq",
            "file_size": 12033624,
            "href": "/sequence-files/IGVFFI2660UTOF/@@download/IGVFFI2660UTOF.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/06/01/9e67465c-0499-4e06-8669-943c21a7644b/IGVFFI2660UTOF.fastq.gz",
            "sequencing_platform": "/platform-terms/EFO_0008565/",
            "status": "released",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220104B013_Cohesin_KITLG/fastq_trim/Auxin0hrs-FF1-BinB-PCR2_S8_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/configuration-files/IGVFFI6721VKWR/",
            "accession": "IGVFFI6721VKWR",
            "aliases": [
                "jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin0hrs-FF1-BinB-PCR3_S98"
            ],
            "content_type": "seqspec",
            "creation_timestamp": "2024-06-11T22:06:10.471658+00:00",
            "file_format": "yaml",
            "file_size": 902,
            "href": "/configuration-files/IGVFFI6721VKWR/@@download/IGVFFI6721VKWR.yaml.gz",
            "s3_uri": "s3://igvf-files/2024/06/11/712800c8-4045-4c16-949c-b8ae61f947cf/IGVFFI6721VKWR.yaml.gz",
            "status": "released",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin0hrs-FF1-BinB-PCR3_S98.yaml",
            "upload_status": "validated"
        }
    ],
    "input_for": [
        "/analysis-sets/IGVFDS6482AXWW/"
    ],
    "lab": {
        "@id": "/labs/jesse-engreitz/",
        "title": "Jesse Engreitz, Stanford"
    },
    "measurement_sets": [
        {
            "@id": "/measurement-sets/IGVFDS1679JOIX/",
            "accession": "IGVFDS1679JOIX",
            "aliases": [
                "jesse-engreitz:measurement_CRUDO_KITLG-Auxin0hrs-FF1-BinB-PCR1_S2",
                "jesse-engreitz:measurement_CRUDO_KITLG-Auxin0hrs-FF1-BinB-PCR2_S8",
                "jesse-engreitz:measurement_CRUDO_KITLG-Auxin0hrs-FF1-BinB-PCR3_S98",
                "jesse-engreitz:measurement_CRUDO_KITLG-Auxin0hrs-FF1-BinB-PCR4_S104"
            ],
            "preferred_assay_title": "CRISPR FlowFISH screen",
            "status": "released"
        }
    ],
    "release_timestamp": "2024-07-10T20:13:38.706593+00:00",
    "samples": [
        {
            "@id": "/in-vitro-systems/IGVFSM4469TBGW/",
            "@type": [
                "InVitroSystem",
                "Biosample",
                "Sample",
                "Item"
            ],
            "accession": "IGVFSM4469TBGW",
            "aliases": [
                "jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin0hrs-FF1-BinB-PCR1_S2",
                "jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin0hrs-FF1-BinB-PCR2_S8",
                "jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin0hrs-FF1-BinB-PCR3_S98",
                "jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin0hrs-FF1-BinB-PCR4_S104"
            ],
            "classifications": [
                "cell line"
            ],
            "construct_library_sets": [
                "/construct-library-sets/IGVFDS7846UISG/"
            ],
            "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 KITLG) 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": "2024-06-01T02:10:14.444737+00:00",
    "summary": "gRNA sequencing for mixed CRISPR FlowFISH screen integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
    "uuid": "d40ee258-469a-4fd8-82ae-05563be7388b"
}