IGVFDS5248DHZT

released
{
    "@context": "/terms/",
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    "@type": [
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        "FileSet",
        "Item"
    ],
    "accession": "IGVFDS5248DHZT",
    "aliases": [
        "jay-shendure:dev_CRE_mEBs_GEx_repA_10Xlane1_reads"
    ],
    "assay_term": {
        "@id": "/assay-terms/OBI_0002675/",
        "term_name": "massively parallel reporter assay"
    },
    "audit": {
        "INTERNAL_ACTION": [
            {
                "category": "mismatched status",
                "detail": "Released in vitro system [IGVFSM4494VUEQ](/in-vitro-systems/IGVFSM4494VUEQ/) 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/IGVFSM4494VUEQ/"
            }
        ]
    },
    "auxiliary_sets": [
        {
            "@id": "/auxiliary-sets/IGVFDS5801KSAS/",
            "accession": "IGVFDS5801KSAS",
            "aliases": [
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            ],
            "file_set_type": "quantification DNA barcode sequencing"
        },
        {
            "@id": "/auxiliary-sets/IGVFDS7792HFAY/",
            "accession": "IGVFDS7792HFAY",
            "aliases": [
                "jay-shendure:dev_CRE_mEBs_oBC_repA_10Xlane1_reads"
            ],
            "file_set_type": "circularized RNA barcode detection"
        }
    ],
    "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": "2023-12-08T23:53:46.743065+00:00",
    "donors": [
        {
            "@id": "/rodent-donors/IGVFDO3898MNLZ/",
            "accession": "IGVFDO3898MNLZ",
            "aliases": [
                "jay-shendure:WD44_donor"
            ],
            "sex": "male",
            "status": "released",
            "taxa": "Mus musculus"
        }
    ],
    "file_set_type": "experimental data",
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            "creation_timestamp": "2023-12-09T00:58:07.059552+00:00",
            "file_format": "fastq",
            "file_size": 395407505,
            "href": "/sequence-files/IGVFFI8739CFNW/@@download/IGVFFI8739CFNW.fastq.gz",
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            "sequencing_platform": {
                "@id": "/platform-terms/EFO_0009173/",
                "term_name": "Illumina NextSeq 500"
            },
            "submitted_file_name": "/net/shendure/vol8/projects/JBL/GEO_sc_rep_fastqs_nobackup/geo_submission_20221108/sc_rep_devCRE_mEBs/sc_rep_mEB_series_GEx_repA_lane1_I1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI5772LMXH/",
            "accession": "IGVFFI5772LMXH",
            "aliases": [
                "jay-shendure:sc_rep_devCRE_mEBs_GEx_repA_10Xlane1_R1"
            ],
            "content_type": "reads",
            "creation_timestamp": "2023-12-09T00:58:08.214125+00:00",
            "file_format": "fastq",
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            "sequencing_platform": {
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                "term_name": "Illumina NextSeq 500"
            },
            "submitted_file_name": "/net/shendure/vol8/projects/JBL/GEO_sc_rep_fastqs_nobackup/geo_submission_20221108/sc_rep_devCRE_mEBs/sc_rep_mEB_series_GEx_repA_lane1_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI9161RRDV/",
            "accession": "IGVFFI9161RRDV",
            "aliases": [
                "jay-shendure:sc_rep_devCRE_mEBs_GEx_repA_10Xlane1_R2"
            ],
            "content_type": "reads",
            "creation_timestamp": "2023-12-09T00:58:09.308750+00:00",
            "file_format": "fastq",
            "file_size": 1860772006,
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            "sequencing_platform": {
                "@id": "/platform-terms/EFO_0009173/",
                "term_name": "Illumina NextSeq 500"
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            "submitted_file_name": "/net/shendure/vol8/projects/JBL/GEO_sc_rep_fastqs_nobackup/geo_submission_20221108/sc_rep_devCRE_mEBs/sc_rep_mEB_series_GEx_repA_lane1_R2_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/configuration-files/IGVFFI1829MGSH/",
            "accession": "IGVFFI1829MGSH",
            "aliases": [
                "jay-shendure:seqspec_of_set_IGVFDS5248DHZT"
            ],
            "content_type": "seqspec",
            "creation_timestamp": "2024-08-22T22:51:06.744269+00:00",
            "file_format": "yaml",
            "file_size": 829,
            "href": "/configuration-files/IGVFFI1829MGSH/@@download/IGVFFI1829MGSH.yaml.gz",
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            "submitted_file_name": "/net/shendure/vol1/home/martin91/IGVF/forupload/seqspecs/scQers/scQers_IGVFDS5248DHZT_seqspec.yaml.gz",
            "upload_status": "validated"
        }
    ],
    "input_file_set_for": [
        "/analysis-sets/IGVFDS2774OLAH/"
    ],
    "lab": {
        "@id": "/labs/jay-shendure/",
        "title": "Jay Shendure, UW"
    },
    "notes": "The readout 86015c12-b9a6-43ba-9601-5d75aab4d39c was removed from this measurement set.",
    "preferred_assay_title": "MPRA (scQer)",
    "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"
            ]
        }
    ],
    "release_timestamp": "2024-06-27T00:41:46.650330+00:00",
    "samples": [
        {
            "@id": "/in-vitro-systems/IGVFSM4494VUEQ/",
            "@type": [
                "InVitroSystem",
                "Biosample",
                "Sample",
                "Item"
            ],
            "accession": "IGVFSM4494VUEQ",
            "aliases": [
                "jay-shendure:dev_CRE_mEBs_repA_10Xlane1"
            ],
            "cell_fate_change_treatments": [
                {
                    "@id": "/treatments/9acc7857-c9dd-4b4a-a78b-fdf10c8ae679/",
                    "purpose": "differentiation",
                    "summary": "Depletion of Leukemia inhibitory factor",
                    "treatment_type": "protein"
                }
            ],
            "classifications": [
                "differentiated cell specimen"
            ],
            "construct_library_sets": [
                {
                    "@id": "/construct-library-sets/IGVFDS7655GRFI/",
                    "accession": "IGVFDS7655GRFI",
                    "file_set_type": "reporter library",
                    "summary": "Reporter library targeting accessible genome regions in many genomic loci"
                }
            ],
            "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 21 days (cellular sub pool: 10Xlane1), 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": "21",
    "status": "released",
    "submitted_by": {
        "@id": "/users/73f58e9f-8f5d-4fee-a7cd-dd63c0167e4b/",
        "title": "Beth Martin"
    },
    "submitted_files_timestamp": "2023-12-09T00:58:07.059552+00:00",
    "summary": "MPRA (scQer) integrating a reporter library targeting accessible genome regions in many genomic loci",
    "uuid": "575ddf6b-2fad-4b0d-8ee7-88f64faf0a05"
}