IGVFDS1156NHWQ

released
{
    "@context": "/terms/",
    "@id": "/auxiliary-sets/IGVFDS1156NHWQ/",
    "@type": [
        "AuxiliarySet",
        "FileSet",
        "Item"
    ],
    "accession": "IGVFDS1156NHWQ",
    "aliases": [
        "jay-shendure:dev_CRE_mEBs_oBC_repB_10Xlane1_reads"
    ],
    "audit": {
        "INTERNAL_ACTION": [
            {
                "category": "mismatched status",
                "detail": "Released in vitro system [IGVFSM8913GAXO](/in-vitro-systems/IGVFSM8913GAXO/) 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/IGVFSM8913GAXO/"
            }
        ]
    },
    "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": "2023-12-08T23:52:15.422215+00:00",
    "donors": [
        {
            "@id": "/rodent-donors/IGVFDO3898MNLZ/",
            "accession": "IGVFDO3898MNLZ",
            "aliases": [
                "jay-shendure:WD44_donor"
            ],
            "sex": "male",
            "status": "released",
            "taxa": "Mus musculus"
        }
    ],
    "file_set_type": "circularized RNA barcode detection",
    "files": [
        {
            "@id": "/sequence-files/IGVFFI5640PFLS/",
            "accession": "IGVFFI5640PFLS",
            "aliases": [
                "jay-shendure:sc_rep_devCRE_mEBs_oBC_CS1_repB_10Xlane1_I1"
            ],
            "content_type": "reads",
            "creation_timestamp": "2023-12-09T00:59:07.784513+00:00",
            "file_format": "fastq",
            "file_size": 187807387,
            "href": "/sequence-files/IGVFFI5640PFLS/@@download/IGVFFI5640PFLS.fastq.gz",
            "s3_uri": "s3://igvf-files/2023/12/09/b0273a80-80ef-4305-aaf1-42eba636d082/IGVFFI5640PFLS.fastq.gz",
            "sequencing_platform": "/platform-terms/EFO_0009173/",
            "submitted_file_name": "/net/shendure/vol8/projects/JBL/GEO_sc_rep_fastqs_nobackup/geo_submission_20221108/sc_rep_devCRE_mEBs/sc_rep_mEB_series_oBC_CS1_repB_lane1_I1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI9197GQMP/",
            "accession": "IGVFFI9197GQMP",
            "aliases": [
                "jay-shendure:sc_rep_devCRE_mEBs_oBC_CS1_repB_reseq_10Xlane1_I1"
            ],
            "content_type": "reads",
            "creation_timestamp": "2023-12-09T00:59:11.303527+00:00",
            "file_format": "fastq",
            "file_size": 306249279,
            "href": "/sequence-files/IGVFFI9197GQMP/@@download/IGVFFI9197GQMP.fastq.gz",
            "s3_uri": "s3://igvf-files/2023/12/09/16078e80-107f-4a02-9143-f57569a7618c/IGVFFI9197GQMP.fastq.gz",
            "sequencing_platform": "/platform-terms/EFO_0010963/",
            "submitted_file_name": "/net/shendure/vol8/projects/JBL/GEO_sc_rep_fastqs_nobackup/geo_submission_20221108/sc_rep_devCRE_mEBs/sc_rep_mEB_series_oBC_CS1_repB_lane1_reseq_I1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI7721URJL/",
            "accession": "IGVFFI7721URJL",
            "aliases": [
                "jay-shendure:sc_rep_devCRE_mEBs_oBC_CS1_repB_10Xlane1_R1"
            ],
            "content_type": "reads",
            "creation_timestamp": "2023-12-09T00:59:09.040415+00:00",
            "file_format": "fastq",
            "file_size": 463805765,
            "href": "/sequence-files/IGVFFI7721URJL/@@download/IGVFFI7721URJL.fastq.gz",
            "s3_uri": "s3://igvf-files/2023/12/09/90116fc0-435f-4e4b-937a-dd6d184e700c/IGVFFI7721URJL.fastq.gz",
            "sequencing_platform": "/platform-terms/EFO_0009173/",
            "submitted_file_name": "/net/shendure/vol8/projects/JBL/GEO_sc_rep_fastqs_nobackup/geo_submission_20221108/sc_rep_devCRE_mEBs/sc_rep_mEB_series_oBC_CS1_repB_lane1_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI3190GFNQ/",
            "accession": "IGVFFI3190GFNQ",
            "aliases": [
                "jay-shendure:sc_rep_devCRE_mEBs_oBC_CS1_repB_reseq_10Xlane1_R2"
            ],
            "content_type": "reads",
            "creation_timestamp": "2023-12-09T00:59:13.592732+00:00",
            "file_format": "fastq",
            "file_size": 723775319,
            "href": "/sequence-files/IGVFFI3190GFNQ/@@download/IGVFFI3190GFNQ.fastq.gz",
            "s3_uri": "s3://igvf-files/2023/12/09/d61fcc94-3c79-41c0-b7ef-74bbcc2eaf92/IGVFFI3190GFNQ.fastq.gz",
            "sequencing_platform": "/platform-terms/EFO_0010963/",
            "submitted_file_name": "/net/shendure/vol8/projects/JBL/GEO_sc_rep_fastqs_nobackup/geo_submission_20221108/sc_rep_devCRE_mEBs/sc_rep_mEB_series_oBC_CS1_repB_lane1_reseq_R2_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI7577NRWF/",
            "accession": "IGVFFI7577NRWF",
            "aliases": [
                "jay-shendure:sc_rep_devCRE_mEBs_oBC_CS1_repB_10Xlane1_R2"
            ],
            "content_type": "reads",
            "creation_timestamp": "2023-12-09T00:59:10.273137+00:00",
            "file_format": "fastq",
            "file_size": 651111535,
            "href": "/sequence-files/IGVFFI7577NRWF/@@download/IGVFFI7577NRWF.fastq.gz",
            "s3_uri": "s3://igvf-files/2023/12/09/60823bcd-c7b1-42da-b904-28abaa99797a/IGVFFI7577NRWF.fastq.gz",
            "sequencing_platform": "/platform-terms/EFO_0009173/",
            "submitted_file_name": "/net/shendure/vol8/projects/JBL/GEO_sc_rep_fastqs_nobackup/geo_submission_20221108/sc_rep_devCRE_mEBs/sc_rep_mEB_series_oBC_CS1_repB_lane1_R2_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI5061UUQA/",
            "accession": "IGVFFI5061UUQA",
            "aliases": [
                "jay-shendure:sc_rep_devCRE_mEBs_oBC_CS1_repB_reseq_10Xlane1_R1"
            ],
            "content_type": "reads",
            "creation_timestamp": "2023-12-09T00:59:12.491592+00:00",
            "file_format": "fastq",
            "file_size": 932932385,
            "href": "/sequence-files/IGVFFI5061UUQA/@@download/IGVFFI5061UUQA.fastq.gz",
            "s3_uri": "s3://igvf-files/2023/12/09/87fcc5bd-1337-4f29-af1d-836ded395cca/IGVFFI5061UUQA.fastq.gz",
            "sequencing_platform": "/platform-terms/EFO_0010963/",
            "submitted_file_name": "/net/shendure/vol8/projects/JBL/GEO_sc_rep_fastqs_nobackup/geo_submission_20221108/sc_rep_devCRE_mEBs/sc_rep_mEB_series_oBC_CS1_repB_lane1_reseq_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/configuration-files/IGVFFI9532SVZB/",
            "accession": "IGVFFI9532SVZB",
            "aliases": [
                "jay-shendure:seqspec_of_set_IGVFDS1156NHWQ-reseq"
            ],
            "content_type": "seqspec",
            "creation_timestamp": "2024-08-22T22:51:34.627421+00:00",
            "file_format": "yaml",
            "file_size": 887,
            "href": "/configuration-files/IGVFFI9532SVZB/@@download/IGVFFI9532SVZB.yaml.gz",
            "s3_uri": "s3://igvf-files/2024/08/22/53adb440-1c5e-4c73-89e0-2e887c3e7243/IGVFFI9532SVZB.yaml.gz",
            "submitted_file_name": "/net/shendure/vol1/home/martin91/IGVF/forupload/seqspecs/scQers/scQers_IGVFDS1156NHWQ_reseq_seqspec.yaml.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/configuration-files/IGVFFI4325OITW/",
            "accession": "IGVFFI4325OITW",
            "aliases": [
                "jay-shendure:seqspec_of_set_IGVFDS1156NHWQ"
            ],
            "content_type": "seqspec",
            "creation_timestamp": "2024-08-22T22:51:32.150285+00:00",
            "file_format": "yaml",
            "file_size": 884,
            "href": "/configuration-files/IGVFFI4325OITW/@@download/IGVFFI4325OITW.yaml.gz",
            "s3_uri": "s3://igvf-files/2024/08/22/e336865e-acad-469f-b7ef-194160b3320a/IGVFFI4325OITW.yaml.gz",
            "submitted_file_name": "/net/shendure/vol1/home/martin91/IGVF/forupload/seqspecs/scQers/scQers_IGVFDS1156NHWQ_seqspec.yaml.gz",
            "upload_status": "validated"
        }
    ],
    "input_file_set_for": [
        "/analysis-sets/IGVFDS2774OLAH/"
    ],
    "lab": {
        "@id": "/labs/jay-shendure/",
        "title": "Jay Shendure, UW"
    },
    "measurement_sets": [
        {
            "@id": "/measurement-sets/IGVFDS0228POXF/",
            "accession": "IGVFDS0228POXF",
            "aliases": [
                "jay-shendure:dev_CRE_mEBs_GEx_repB_10Xlane1_reads"
            ],
            "preferred_assay_title": "MPRA (scQer)"
        }
    ],
    "publications": [
        {
            "@id": "/publications/398edd7f-1ebb-40a0-a04b-450a2565667c/",
            "publication_identifiers": [
                "doi:10.1038/s41592-024-02260-3",
                "PMID:38724692"
            ]
        }
    ],
    "release_timestamp": "2024-06-27T00:41:46.317583+00:00",
    "samples": [
        {
            "@id": "/in-vitro-systems/IGVFSM8913GAXO/",
            "@type": [
                "InVitroSystem",
                "Biosample",
                "Sample",
                "Item"
            ],
            "accession": "IGVFSM8913GAXO",
            "aliases": [
                "jay-shendure:dev_CRE_mEBs_repB_10Xlane1"
            ],
            "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 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": "11",
    "status": "released",
    "submitted_by": {
        "@id": "/users/73f58e9f-8f5d-4fee-a7cd-dd63c0167e4b/",
        "title": "Beth Martin"
    },
    "submitted_files_timestamp": "2023-12-09T00:59:07.784513+00:00",
    "summary": "circularized RNA barcode detection for MPRA (scQer) integrating a reporter library targeting accessible genome regions in many genomic loci",
    "uuid": "878d1268-2155-4997-89cc-13354d03b31e"
}