Home

IGVFDS7446XPVQ

released
{
    "@context": "/terms/",
    "@id": "/measurement-sets/IGVFDS7446XPVQ/",
    "@type": [
        "MeasurementSet",
        "FileSet",
        "Item"
    ],
    "accession": "IGVFDS7446XPVQ",
    "aliases": [
        "jay-shendure:scATAC_mEBs_rep2_10XlaneA_reads"
    ],
    "assay_term": {
        "@id": "/assay-terms/OBI_0002764/",
        "assay_slims": [
            "chromatin accessibility"
        ],
        "status": "released",
        "term_name": "single-cell ATAC-seq"
    },
    "audit": {
        "NOT_COMPLIANT": [
            {
                "category": "missing read names",
                "detail": "Measurement set [IGVFDS7446XPVQ](/measurement-sets/IGVFDS7446XPVQ/) has a sequence file [IGVFFI7928KWSV](/sequence-files/IGVFFI7928KWSV/) missing `read_names`. Sequence files are expected to have read names.",
                "level": 50,
                "level_name": "NOT_COMPLIANT",
                "name": "audit_single_cell_read_names",
                "path": "/measurement-sets/IGVFDS7446XPVQ/"
            },
            {
                "category": "missing read names",
                "detail": "Measurement set [IGVFDS7446XPVQ](/measurement-sets/IGVFDS7446XPVQ/) has a sequence file [IGVFFI5441SJAB](/sequence-files/IGVFFI5441SJAB/) missing `read_names`. Sequence files are expected to have read names.",
                "level": 50,
                "level_name": "NOT_COMPLIANT",
                "name": "audit_single_cell_read_names",
                "path": "/measurement-sets/IGVFDS7446XPVQ/"
            },
            {
                "category": "missing read names",
                "detail": "Measurement set [IGVFDS7446XPVQ](/measurement-sets/IGVFDS7446XPVQ/) has a sequence file [IGVFFI9532BEXG](/sequence-files/IGVFFI9532BEXG/) missing `read_names`. Sequence files are expected to have read names.",
                "level": 50,
                "level_name": "NOT_COMPLIANT",
                "name": "audit_single_cell_read_names",
                "path": "/measurement-sets/IGVFDS7446XPVQ/"
            },
            {
                "category": "missing read names",
                "detail": "Measurement set [IGVFDS7446XPVQ](/measurement-sets/IGVFDS7446XPVQ/) has a sequence file [IGVFFI1783KKSX](/sequence-files/IGVFFI1783KKSX/) missing `read_names`. Sequence files are expected to have read names.",
                "level": 50,
                "level_name": "NOT_COMPLIANT",
                "name": "audit_single_cell_read_names",
                "path": "/measurement-sets/IGVFDS7446XPVQ/"
            },
            {
                "category": "missing strand specificity",
                "detail": "Measurement set [IGVFDS7446XPVQ](/measurement-sets/IGVFDS7446XPVQ/) is missing required `strand_specificity`. Single-cell assays are expected to specify strand specificity.",
                "level": 50,
                "level_name": "NOT_COMPLIANT",
                "name": "audit_missing_strand_specificity",
                "path": "/measurement-sets/IGVFDS7446XPVQ/"
            },
            {
                "category": "missing barcode onlist",
                "detail": "Measurement set [IGVFDS7446XPVQ](/measurement-sets/IGVFDS7446XPVQ/) has an `assay_term` of single-cell ATAC-seq but no `onlist_files` nor `onlist_methods`. Measurement sets to be processed via the single cell uniform pipeline are expected to have onlist files and onlist methods indicated.",
                "level": 50,
                "level_name": "NOT_COMPLIANT",
                "name": "audit_onlist",
                "path": "/measurement-sets/IGVFDS7446XPVQ/"
            }
        ]
    },
    "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": "2023-12-08T23:53:45.208902+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/IGVFFI8854LSLE/",
            "accession": "IGVFFI8854LSLE",
            "aliases": [
                "jay-shendure:scATAC_mEBs_rep2_day21_10XlaneA_I1"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2023-12-09T00:57:45.160358+00:00",
            "file_format": "fastq",
            "file_size": 701885955,
            "href": "/sequence-files/IGVFFI8854LSLE/@@download/IGVFFI8854LSLE.fastq.gz",
            "s3_uri": "s3://igvf-files/2023/12/09/2a229a45-faa1-40ee-9bfe-a42cc2f7478d/IGVFFI8854LSLE.fastq.gz",
            "sequencing_platform": {
                "@id": "/platform-terms/EFO_0009173/",
                "status": "released",
                "term_name": "Illumina NextSeq 500"
            },
            "status": "released",
            "submitted_file_name": "/net/shendure/vol8/projects/JBL/GEO_scATAC_EB_correction_nobackup/scATAC_mEBs/scATAC_mEBs_d21_crispri_rep2_lane_a_I1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI7928KWSV/",
            "accession": "IGVFFI7928KWSV",
            "aliases": [
                "jay-shendure:scATAC_mEBs_rep2_day21_10XlaneA_reseq_R2"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2023-12-09T00:57:51.481507+00:00",
            "file_format": "fastq",
            "file_size": 3343112538,
            "href": "/sequence-files/IGVFFI7928KWSV/@@download/IGVFFI7928KWSV.fastq.gz",
            "s3_uri": "s3://igvf-files/2023/12/09/71d76129-661b-43f5-aca0-c553aa4b1194/IGVFFI7928KWSV.fastq.gz",
            "sequencing_platform": {
                "@id": "/platform-terms/EFO_0009173/",
                "status": "released",
                "term_name": "Illumina NextSeq 500"
            },
            "status": "released",
            "submitted_file_name": "/net/shendure/vol8/projects/JBL/GEO_scATAC_EB_correction_nobackup/scATAC_mEBs/scATAC_mEBs_d21_crispri_rep2_lane_a_reseq_R2_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI5441SJAB/",
            "accession": "IGVFFI5441SJAB",
            "aliases": [
                "jay-shendure:scATAC_mEBs_rep2_day21_10XlaneA_R1"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2023-12-09T00:57:46.284709+00:00",
            "file_format": "fastq",
            "file_size": 3206801276,
            "href": "/sequence-files/IGVFFI5441SJAB/@@download/IGVFFI5441SJAB.fastq.gz",
            "s3_uri": "s3://igvf-files/2023/12/09/4a853a76-d586-4793-a3ba-12d2806de7cf/IGVFFI5441SJAB.fastq.gz",
            "sequencing_platform": {
                "@id": "/platform-terms/EFO_0009173/",
                "status": "released",
                "term_name": "Illumina NextSeq 500"
            },
            "status": "released",
            "submitted_file_name": "/net/shendure/vol8/projects/JBL/GEO_scATAC_EB_correction_nobackup/scATAC_mEBs/scATAC_mEBs_d21_crispri_rep2_lane_a_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI9532BEXG/",
            "accession": "IGVFFI9532BEXG",
            "aliases": [
                "jay-shendure:scATAC_mEBs_rep2_day21_10XlaneA_R2"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2023-12-09T00:57:47.406070+00:00",
            "file_format": "fastq",
            "file_size": 3274841779,
            "href": "/sequence-files/IGVFFI9532BEXG/@@download/IGVFFI9532BEXG.fastq.gz",
            "s3_uri": "s3://igvf-files/2023/12/09/c9c27fcb-543d-4e60-816e-251a7070ffdb/IGVFFI9532BEXG.fastq.gz",
            "sequencing_platform": {
                "@id": "/platform-terms/EFO_0009173/",
                "status": "released",
                "term_name": "Illumina NextSeq 500"
            },
            "status": "released",
            "submitted_file_name": "/net/shendure/vol8/projects/JBL/GEO_scATAC_EB_correction_nobackup/scATAC_mEBs/scATAC_mEBs_d21_crispri_rep2_lane_a_R2_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI1783KKSX/",
            "accession": "IGVFFI1783KKSX",
            "aliases": [
                "jay-shendure:scATAC_mEBs_rep2_day21_10XlaneA_reseq_R1"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2023-12-09T00:57:49.716837+00:00",
            "file_format": "fastq",
            "file_size": 3267406738,
            "href": "/sequence-files/IGVFFI1783KKSX/@@download/IGVFFI1783KKSX.fastq.gz",
            "s3_uri": "s3://igvf-files/2023/12/09/b09aa956-b6b4-4370-9ba6-f8327fde7529/IGVFFI1783KKSX.fastq.gz",
            "sequencing_platform": {
                "@id": "/platform-terms/EFO_0009173/",
                "status": "released",
                "term_name": "Illumina NextSeq 500"
            },
            "status": "released",
            "submitted_file_name": "/net/shendure/vol8/projects/JBL/GEO_scATAC_EB_correction_nobackup/scATAC_mEBs/scATAC_mEBs_d21_crispri_rep2_lane_a_reseq_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI2924IWFH/",
            "accession": "IGVFFI2924IWFH",
            "aliases": [
                "jay-shendure:scATAC_mEBs_rep2_day21_10XlaneA_reseq_I1"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2023-12-09T00:57:48.592810+00:00",
            "file_format": "fastq",
            "file_size": 715974909,
            "href": "/sequence-files/IGVFFI2924IWFH/@@download/IGVFFI2924IWFH.fastq.gz",
            "s3_uri": "s3://igvf-files/2023/12/09/913ba1fa-cc8c-4829-a17d-0643b22e16b2/IGVFFI2924IWFH.fastq.gz",
            "sequencing_platform": {
                "@id": "/platform-terms/EFO_0009173/",
                "status": "released",
                "term_name": "Illumina NextSeq 500"
            },
            "status": "released",
            "submitted_file_name": "/net/shendure/vol8/projects/JBL/GEO_scATAC_EB_correction_nobackup/scATAC_mEBs/scATAC_mEBs_d21_crispri_rep2_lane_a_reseq_I1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI9392NJAO/",
            "accession": "IGVFFI9392NJAO",
            "aliases": [
                "jay-shendure:scATAC_mEBs_rep2_day21_10XlaneA_I2"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-05-09T16:52:21.904091+00:00",
            "file_format": "fastq",
            "file_size": 1643283451,
            "href": "/sequence-files/IGVFFI9392NJAO/@@download/IGVFFI9392NJAO.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/05/09/55c3e494-7ab9-4c1a-857c-579076de7b62/IGVFFI9392NJAO.fastq.gz",
            "sequencing_platform": {
                "@id": "/platform-terms/EFO_0009173/",
                "status": "released",
                "term_name": "Illumina NextSeq 500"
            },
            "status": "released",
            "submitted_file_name": "/net/shendure/vol8/projects/JBL/GEO_scATAC_EB_correction_nobackup/scATAC_mEBs/scATAC_mEBs_d21_crispri_rep2_lane_a_I2_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI4921RBMQ/",
            "accession": "IGVFFI4921RBMQ",
            "aliases": [
                "jay-shendure:scATAC_mEBs_rep2_day21_10XlaneA_reseq_I2"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-05-09T16:52:24.600373+00:00",
            "file_format": "fastq",
            "file_size": 1676807154,
            "href": "/sequence-files/IGVFFI4921RBMQ/@@download/IGVFFI4921RBMQ.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/05/09/39b46c83-70f8-40ac-99ab-4cc76ab967f6/IGVFFI4921RBMQ.fastq.gz",
            "sequencing_platform": {
                "@id": "/platform-terms/EFO_0009173/",
                "status": "released",
                "term_name": "Illumina NextSeq 500"
            },
            "status": "released",
            "submitted_file_name": "/net/shendure/vol8/projects/JBL/GEO_scATAC_EB_correction_nobackup/scATAC_mEBs/scATAC_mEBs_d21_crispri_rep2_lane_a_reseq_I2_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/configuration-files/IGVFFI0177NTVE/",
            "accession": "IGVFFI0177NTVE",
            "aliases": [
                "jay-shendure:seqspec_of_set_IGVFDS7446XPVQ-1"
            ],
            "content_type": "seqspec",
            "creation_timestamp": "2024-05-09T23:23:25.148319+00:00",
            "file_format": "yaml",
            "file_size": 849,
            "href": "/configuration-files/IGVFFI0177NTVE/@@download/IGVFFI0177NTVE.yaml.gz",
            "s3_uri": "s3://igvf-files/2024/05/09/e8e7f4bb-ce54-467a-aebd-e6a1b4bbd6fb/IGVFFI0177NTVE.yaml.gz",
            "status": "released",
            "submitted_file_name": "/net/shendure/vol1/home/martin91/IGVF/forupload/seqspecs/10XATAC-IGVFDS7446XPVQ-1.yaml.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/configuration-files/IGVFFI4458PPBH/",
            "accession": "IGVFFI4458PPBH",
            "aliases": [
                "jay-shendure:seqspec_of_set_IGVFDS7446XPVQ-2"
            ],
            "content_type": "seqspec",
            "creation_timestamp": "2024-05-09T23:23:26.996475+00:00",
            "file_format": "yaml",
            "file_size": 851,
            "href": "/configuration-files/IGVFFI4458PPBH/@@download/IGVFFI4458PPBH.yaml.gz",
            "s3_uri": "s3://igvf-files/2024/05/09/0fb692be-64de-4142-ae6a-164e99f5fa81/IGVFFI4458PPBH.yaml.gz",
            "status": "released",
            "submitted_file_name": "/net/shendure/vol1/home/martin91/IGVF/forupload/seqspecs/10XATAC-IGVFDS7446XPVQ-2.yaml.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/configuration-files/IGVFFI0917IUPZ/",
            "accession": "IGVFFI0917IUPZ",
            "aliases": [
                "jay-shendure:seqspec2_of_set_IGVFDS7446XPVQ-1"
            ],
            "content_type": "seqspec",
            "creation_timestamp": "2025-03-24T19:38:26.777522+00:00",
            "file_format": "yaml",
            "file_size": 1221,
            "href": "/configuration-files/IGVFFI0917IUPZ/@@download/IGVFFI0917IUPZ.yaml.gz",
            "s3_uri": "s3://igvf-files/2025/03/24/466e31d1-4272-408e-8282-1f1cf528b85d/IGVFFI0917IUPZ.yaml.gz",
            "status": "in progress",
            "submitted_file_name": "/net/shendure/vol1/home/martin91/IGVF/forupload/seqspecs/10XATAC/10XATAC_IGVFDS7446XPVQ-1_seqspec_v3.yaml.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/configuration-files/IGVFFI6062EMVH/",
            "accession": "IGVFFI6062EMVH",
            "aliases": [
                "jay-shendure:seqspec2_of_set_IGVFDS7446XPVQ-2"
            ],
            "content_type": "seqspec",
            "creation_timestamp": "2025-03-24T19:38:28.133939+00:00",
            "file_format": "yaml",
            "file_size": 1221,
            "href": "/configuration-files/IGVFFI6062EMVH/@@download/IGVFFI6062EMVH.yaml.gz",
            "s3_uri": "s3://igvf-files/2025/03/24/c5b4b5d6-4f31-4ddd-a239-01c364a7a4db/IGVFFI6062EMVH.yaml.gz",
            "status": "in progress",
            "submitted_file_name": "/net/shendure/vol1/home/martin91/IGVF/forupload/seqspecs/10XATAC/10XATAC_IGVFDS7446XPVQ-2_seqspec_v3.yaml.gz",
            "upload_status": "validated"
        }
    ],
    "input_for": [
        "/analysis-sets/IGVFDS7801YPEU/"
    ],
    "lab": {
        "@id": "/labs/jay-shendure/",
        "title": "Jay Shendure, UW"
    },
    "preferred_assay_title": "scATAC-seq",
    "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": "2024-07-09T20:16:42.608841+00:00",
    "samples": [
        {
            "@id": "/in-vitro-systems/IGVFSM7126ZMPT/",
            "@type": [
                "InVitroSystem",
                "Biosample",
                "Sample",
                "Item"
            ],
            "accession": "IGVFSM7126ZMPT",
            "aliases": [
                "jay-shendure:scATAC_mEBs_rep2_10XlaneA"
            ],
            "cellular_sub_pool": "10XlaneA",
            "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 (cellular sub pool: 10XlaneA)",
            "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": "2023-12-09T00:57:45.160358+00:00",
    "summary": "scATAC-seq",
    "uuid": "3920fe84-26e0-4ccc-a2d5-4bd496e849ed"
}