IGVFDS2236AYJF

released
{
    "@context": "/terms/",
    "@id": "/measurement-sets/IGVFDS2236AYJF/",
    "@type": [
        "MeasurementSet",
        "FileSet",
        "Item"
    ],
    "accession": "IGVFDS2236AYJF",
    "aliases": [
        "jay-shendure:dev_CRE_mEBs_repA_bulk_RNA_day21_reads"
    ],
    "assay_term": {
        "@id": "/assay-terms/OBI_0002675/",
        "assay_slims": [
            "reporter"
        ],
        "status": "released",
        "term_name": "massively parallel reporter assay"
    },
    "audit": {},
    "auxiliary_sets": [
        {
            "@id": "/auxiliary-sets/IGVFDS0085UXQX/",
            "accession": "IGVFDS0085UXQX",
            "aliases": [
                "jay-shendure:dev_CRE_mEBs_repA_bulk_DNA_day21_reads"
            ],
            "file_set_type": "quantification DNA barcode sequencing",
            "status": "released"
        }
    ],
    "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"
    },
    "construct_library_sets": [
        {
            "@id": "/construct-library-sets/IGVFDS7655GRFI/",
            "accession": "IGVFDS7655GRFI",
            "file_set_type": "reporter library",
            "integrated_content_files": [
                {
                    "@id": "/tabular-files/IGVFFI8904VCYX/",
                    "accession": "IGVFFI8904VCYX",
                    "content_type": "MPRA sequence designs",
                    "status": "released",
                    "summary": "MPRA sequence designs"
                }
            ],
            "status": "released",
            "summary": "reporter library targeting accessible genome regions in many genomic loci"
        }
    ],
    "control_for": [],
    "creation_timestamp": "2023-12-08T23:53:59.285284+00:00",
    "donors": [
        {
            "@id": "/rodent-donors/IGVFDO3898MNLZ/",
            "accession": "IGVFDO3898MNLZ",
            "aliases": [
                "jay-shendure:WD44_donor"
            ],
            "sex": "male",
            "status": "released",
            "strain_background": "C57BL/6J (B6)",
            "taxa": "Mus musculus"
        }
    ],
    "externally_hosted": false,
    "file_set_type": "experimental data",
    "files": [
        {
            "@id": "/sequence-files/IGVFFI1209ULWP/",
            "accession": "IGVFFI1209ULWP",
            "aliases": [
                "jay-shendure:bulkMPRA_devCRE_mEBs_repA_day21_RNA_R2"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2023-12-09T00:55:44.106436+00:00",
            "file_format": "fastq",
            "file_size": 214960796,
            "href": "/sequence-files/IGVFFI1209ULWP/@@download/IGVFFI1209ULWP.fastq.gz",
            "s3_uri": "s3://igvf-files/2023/12/09/ed649ed9-497b-438d-a848-3d39f3a96fc4/IGVFFI1209ULWP.fastq.gz",
            "sequencing_platform": {
                "@id": "/platform-terms/EFO_0010963/",
                "status": "released",
                "term_name": "Illumina NextSeq 2000"
            },
            "status": "released",
            "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_d21_RNA_R2_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI4024EDSM/",
            "accession": "IGVFFI4024EDSM",
            "aliases": [
                "jay-shendure:bulkMPRA_devCRE_mEBs_repA_day21_RNA_R3"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2023-12-09T00:55:45.322038+00:00",
            "file_format": "fastq",
            "file_size": 249971695,
            "href": "/sequence-files/IGVFFI4024EDSM/@@download/IGVFFI4024EDSM.fastq.gz",
            "s3_uri": "s3://igvf-files/2023/12/09/ee88784c-8a87-486b-9f60-d07924acd66d/IGVFFI4024EDSM.fastq.gz",
            "sequencing_platform": {
                "@id": "/platform-terms/EFO_0010963/",
                "status": "released",
                "term_name": "Illumina NextSeq 2000"
            },
            "status": "released",
            "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_d21_RNA_R3_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI1666ZOWK/",
            "accession": "IGVFFI1666ZOWK",
            "aliases": [
                "jay-shendure:bulkMPRA_devCRE_mEBs_repA_day21_RNA_R1"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2023-12-09T00:55:43.019236+00:00",
            "file_format": "fastq",
            "file_size": 247265949,
            "href": "/sequence-files/IGVFFI1666ZOWK/@@download/IGVFFI1666ZOWK.fastq.gz",
            "s3_uri": "s3://igvf-files/2023/12/09/facb136d-808a-43c8-8f52-8ed801ee7569/IGVFFI1666ZOWK.fastq.gz",
            "sequencing_platform": {
                "@id": "/platform-terms/EFO_0010963/",
                "status": "released",
                "term_name": "Illumina NextSeq 2000"
            },
            "status": "released",
            "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_d21_RNA_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/configuration-files/IGVFFI5103ARWG/",
            "accession": "IGVFFI5103ARWG",
            "aliases": [
                "jay-shendure:seqspec_of_dev_CRE_mEBs_repA_bulk_RNA_day21_reads"
            ],
            "content_type": "seqspec",
            "creation_timestamp": "2025-04-03T22:50:11.633927+00:00",
            "file_format": "yaml",
            "file_size": 1148,
            "href": "/configuration-files/IGVFFI5103ARWG/@@download/IGVFFI5103ARWG.yaml.gz",
            "s3_uri": "s3://igvf-files/2025/04/03/3ed4c615-87b8-43c8-862a-1ef407c05f00/IGVFFI5103ARWG.yaml.gz",
            "status": "in progress",
            "submitted_file_name": "/net/shendure/vol1/home/martin91/IGVF/forupload/seqspecs/scQers-bulkMPRA/scQers_IGVFDS2236AYJF_seqspec_v3.yaml.gz",
            "upload_status": "validated"
        }
    ],
    "input_for": [
        "/analysis-sets/IGVFDS2622CKLA/"
    ],
    "lab": {
        "@id": "/labs/jay-shendure/",
        "title": "Jay Shendure, UW"
    },
    "notes": "The readout b59a5259-3a53-482b-a7a5-6f401bdad220 was removed from this measurement set.",
    "preferred_assay_title": "MPRA",
    "protocols": [
        "https://www.protocols.io/file/n92rb7r27.pdf"
    ],
    "publications": [
        {
            "@id": "/publications/398edd7f-1ebb-40a0-a04b-450a2565667c/",
            "publication_identifiers": [
                "doi:10.1038/s41592-024-02260-3",
                "PMID:38724692"
            ],
            "status": "released"
        }
    ],
    "release_timestamp": "2024-06-27T00:41:12.197486+00:00",
    "samples": [
        {
            "@id": "/in-vitro-systems/IGVFSM3027MUYF/",
            "@type": [
                "InVitroSystem",
                "Biosample",
                "Sample",
                "Item"
            ],
            "accession": "IGVFSM3027MUYF",
            "aliases": [
                "jay-shendure:dev_CRE_mEBs_repA_bulk_day21"
            ],
            "classifications": [
                "differentiated cell specimen"
            ],
            "institutional_certificates": [],
            "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": "Mus musculus WD44 (male) mouse embryonic stem differentiated cell specimen induced to embryoid body for 21 days transfected with a reporter library",
            "targeted_sample_term": {
                "@id": "/sample-terms/UBERON_0014374/",
                "status": "released",
                "term_name": "embryoid body"
            },
            "taxa": "Mus musculus"
        }
    ],
    "schema_version": "26",
    "status": "released",
    "submitted_by": {
        "@id": "/users/73f58e9f-8f5d-4fee-a7cd-dd63c0167e4b/",
        "title": "Beth Martin"
    },
    "submitted_files_timestamp": "2023-12-09T00:55:38.202732+00:00",
    "summary": "MPRA integrating a reporter library targeting accessible genome regions in many genomic loci",
    "uuid": "11333ba3-8324-46a9-ab82-f0bc06076309"
}