IGVFDS1064LHGI

released
{
    "@context": "/terms/",
    "@id": "/auxiliary-sets/IGVFDS1064LHGI/",
    "@type": [
        "AuxiliarySet",
        "FileSet",
        "Item"
    ],
    "accession": "IGVFDS1064LHGI",
    "aliases": [
        "jay-shendure:dev_CRE_mEBs_repA_bulk_DNA_day14_reads"
    ],
    "audit": {
        "INTERNAL_ACTION": [
            {
                "category": "mismatched status",
                "detail": "Released in vitro system [IGVFSM5739JCXR](/in-vitro-systems/IGVFSM5739JCXR/) has in progress subobject construct library set [IGVFDS7655GRFI](/construct-library-sets/IGVFDS7655GRFI/).",
                "level": 30,
                "level_name": "INTERNAL_ACTION",
                "name": "audit_item_status",
                "path": "/in-vitro-systems/IGVFSM5739JCXR/"
            }
        ],
        "NOT_COMPLIANT": [
            {
                "category": "missing sequence specification",
                "detail": "Auxiliary set [IGVFDS1064LHGI](/auxiliary-sets/IGVFDS1064LHGI/) has sequence file(s): [IGVFFI6463QEVA](/sequence-files/IGVFFI6463QEVA/), [IGVFFI4166WVRQ](/sequence-files/IGVFFI4166WVRQ/), [IGVFFI2968UQFI](/sequence-files/IGVFFI2968UQFI/) which do not have any `seqspecs`. Sequence files in a file set are expected to link to a sequence specification file.",
                "level": 50,
                "level_name": "NOT_COMPLIANT",
                "name": "audit_missing_seqspec",
                "path": "/auxiliary-sets/IGVFDS1064LHGI/"
            }
        ]
    },
    "award": {
        "@id": "/awards/HG011966/",
        "component": "functional characterization",
        "contact_pi": {
            "@id": "/users/eb543cda-67b7-493c-84eb-187d0dac13ba/",
            "title": "Jay Shendure"
        },
        "title": "Massively parallel characterization of variants and elements impacting transcriptional regulation in dynamic cellular systems"
    },
    "control_for": [],
    "creation_timestamp": "2023-12-08T23:52:24.501305+00:00",
    "donors": [
        {
            "@id": "/rodent-donors/IGVFDO3898MNLZ/",
            "accession": "IGVFDO3898MNLZ",
            "aliases": [
                "jay-shendure:WD44_donor"
            ],
            "sex": "male",
            "status": "released",
            "taxa": "Mus musculus"
        }
    ],
    "file_set_type": "quantification DNA barcode sequencing",
    "files": [
        {
            "@id": "/sequence-files/IGVFFI6463QEVA/",
            "accession": "IGVFFI6463QEVA",
            "aliases": [
                "jay-shendure:bulkMPRA_devCRE_mEBs_repA_day14_DNA_R3"
            ],
            "content_type": "reads",
            "creation_timestamp": "2023-12-09T00:55:02.931922+00:00",
            "file_format": "fastq",
            "file_size": 365727602,
            "href": "/sequence-files/IGVFFI6463QEVA/@@download/IGVFFI6463QEVA.fastq.gz",
            "s3_uri": "s3://igvf-files/2023/12/09/2c750e4d-137d-4726-b4db-b4f829e83af8/IGVFFI6463QEVA.fastq.gz",
            "sequencing_platform": "/platform-terms/EFO_0010963/",
            "submitted_file_name": "/net/shendure/vol8/projects/JBL/GEO_sc_rep_fastqs_nobackup/geo_submission_20221108/bulkMPRA_devCRE_mEBs/bulk_MPRA_mEB_series_mBC_repA_d14_DNA_R3_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI4166WVRQ/",
            "accession": "IGVFFI4166WVRQ",
            "aliases": [
                "jay-shendure:bulkMPRA_devCRE_mEBs_repA_day14_DNA_R2"
            ],
            "content_type": "reads",
            "creation_timestamp": "2023-12-09T00:55:01.271175+00:00",
            "file_format": "fastq",
            "file_size": 289912481,
            "href": "/sequence-files/IGVFFI4166WVRQ/@@download/IGVFFI4166WVRQ.fastq.gz",
            "s3_uri": "s3://igvf-files/2023/12/09/556968b9-f33f-4298-becb-b3ecefca0d32/IGVFFI4166WVRQ.fastq.gz",
            "sequencing_platform": "/platform-terms/EFO_0010963/",
            "submitted_file_name": "/net/shendure/vol8/projects/JBL/GEO_sc_rep_fastqs_nobackup/geo_submission_20221108/bulkMPRA_devCRE_mEBs/bulk_MPRA_mEB_series_mBC_repA_d14_DNA_R2_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI2968UQFI/",
            "accession": "IGVFFI2968UQFI",
            "aliases": [
                "jay-shendure:bulkMPRA_devCRE_mEBs_repA_day14_DNA_R1"
            ],
            "content_type": "reads",
            "creation_timestamp": "2023-12-09T00:54:59.852208+00:00",
            "file_format": "fastq",
            "file_size": 362626874,
            "href": "/sequence-files/IGVFFI2968UQFI/@@download/IGVFFI2968UQFI.fastq.gz",
            "s3_uri": "s3://igvf-files/2023/12/09/5110e0bb-cdab-4a14-8859-4872d1fc4582/IGVFFI2968UQFI.fastq.gz",
            "sequencing_platform": "/platform-terms/EFO_0010963/",
            "submitted_file_name": "/net/shendure/vol8/projects/JBL/GEO_sc_rep_fastqs_nobackup/geo_submission_20221108/bulkMPRA_devCRE_mEBs/bulk_MPRA_mEB_series_mBC_repA_d14_DNA_R1_001.fastq.gz",
            "upload_status": "validated"
        }
    ],
    "input_file_set_for": [
        "/analysis-sets/IGVFDS2622CKLA/"
    ],
    "lab": {
        "@id": "/labs/jay-shendure/",
        "title": "Jay Shendure, UW"
    },
    "measurement_sets": [
        {
            "@id": "/measurement-sets/IGVFDS9566FDYZ/",
            "accession": "IGVFDS9566FDYZ",
            "aliases": [
                "jay-shendure:dev_CRE_mEBs_repA_bulk_RNA_day14_reads"
            ],
            "preferred_assay_title": "MPRA"
        }
    ],
    "publications": [
        {
            "@id": "/publications/398edd7f-1ebb-40a0-a04b-450a2565667c/",
            "publication_identifiers": [
                "doi:10.1038/s41592-024-02260-3",
                "PMID:38724692"
            ]
        }
    ],
    "release_timestamp": "2024-06-27T00:41:18.025099+00:00",
    "samples": [
        {
            "@id": "/in-vitro-systems/IGVFSM5739JCXR/",
            "@type": [
                "InVitroSystem",
                "Biosample",
                "Sample",
                "Item"
            ],
            "accession": "IGVFSM5739JCXR",
            "aliases": [
                "jay-shendure:dev_CRE_mEBs_repA_bulk_day14"
            ],
            "cell_fate_change_treatments": [
                "/treatments/9acc7857-c9dd-4b4a-a78b-fdf10c8ae679/"
            ],
            "classifications": [
                "differentiated cell specimen"
            ],
            "construct_library_sets": [
                "/construct-library-sets/IGVFDS7655GRFI/"
            ],
            "sample_terms": [
                {
                    "@id": "/sample-terms/EFO_0004038/",
                    "@type": [
                        "SampleTerm",
                        "OntologyTerm",
                        "Item"
                    ],
                    "status": "released",
                    "summary": "mouse embryonic stem cell",
                    "term_name": "mouse embryonic stem cell"
                }
            ],
            "status": "released",
            "summary": "mouse embryonic stem differentiated cell specimen induced to embryoid body for 14 days, male, Mus musculus WD44 modified with a reporter library",
            "targeted_sample_term": {
                "@id": "/sample-terms/UBERON_0014374/",
                "term_name": "embryoid body"
            },
            "taxa": "Mus musculus"
        }
    ],
    "schema_version": "11",
    "status": "released",
    "submitted_by": {
        "@id": "/users/73f58e9f-8f5d-4fee-a7cd-dd63c0167e4b/",
        "title": "Beth Martin"
    },
    "submitted_files_timestamp": "2023-12-09T00:54:59.852208+00:00",
    "summary": "quantification DNA barcode sequencing for MPRA integrating a reporter library targeting accessible genome regions in many genomic loci",
    "uuid": "8156407f-6acd-4280-90b4-f32c403fca67"
}