IGVFFI3571ZWPJ

released
validated
{
    "@context": "/terms/",
    "@id": "/sequence-files/IGVFFI3571ZWPJ/",
    "@type": [
        "SequenceFile",
        "File",
        "Item"
    ],
    "accession": "IGVFFI3571ZWPJ",
    "aliases": [
        "ansuman-satpathy:igvf_exp4_atac_10x2_NGS2_i1"
    ],
    "assay_titles": [
        "10x multiome with MULTI-seq"
    ],
    "audit": {},
    "award": {
        "@id": "/awards/HG012076/",
        "component": "mapping"
    },
    "content_md5sum": "c361843effd51bc22bce4f5977958e1e",
    "content_type": "reads",
    "controlled_access": false,
    "creation_timestamp": "2024-07-22T00:29:30.768959+00:00",
    "externally_hosted": false,
    "file_format": "fastq",
    "file_set": {
        "@id": "/measurement-sets/IGVFDS6995DUBD/",
        "@type": [
            "MeasurementSet",
            "FileSet",
            "Item"
        ],
        "accession": "IGVFDS6995DUBD",
        "assay_term": {
            "@id": "/assay-terms/OBI_0002762/",
            "term_name": "single-nucleus ATAC-seq"
        },
        "file_set_type": "experimental data",
        "samples": [
            {
                "@id": "/multiplexed-samples/IGVFSM7068ZFMY/",
                "@type": [
                    "MultiplexedSample",
                    "Sample",
                    "Item"
                ],
                "accession": "IGVFSM7068ZFMY",
                "classifications": [
                    "cell line",
                    "multiplexed sample"
                ],
                "disease_terms": [],
                "modifications": [],
                "sample_terms": [
                    {
                        "@id": "/sample-terms/EFO_0009747/",
                        "status": "released",
                        "term_name": "GM25256 (WTC-11)"
                    }
                ],
                "status": "released",
                "summary": "multiplexed sample: Homo sapiens (male) GM25256 (WTC-11) cell line treated with 50 ng/mL interleukin 4 for 1 day; Homo sapiens (male) GM25256 (WTC-11) cell line treated with 100 ng/mL macrophage colony-stimulating factor 1 for 7 days; ... and 13 more samples",
                "taxa": "Homo sapiens",
                "treatments": [
                    {
                        "@id": "/treatments/2987f643-86dc-4113-af7e-d4b5d162b5c8/",
                        "purpose": "differentiation",
                        "status": "in progress",
                        "summary": "Treatment of 0.025 ng/mL acetylated low density lipoprotein for 1 day",
                        "treatment_term_name": "acetylated low density lipoprotein"
                    },
                    {
                        "@id": "/treatments/729630f8-aa05-47f5-9cba-ee7a264da593/",
                        "purpose": "differentiation",
                        "status": "in progress",
                        "summary": "Treatment of 50 ng/mL interleukin 4 for 1 day",
                        "treatment_term_name": "interleukin 4"
                    },
                    {
                        "@id": "/treatments/ae8065d2-85f3-498e-b4f2-01a38756d48e/",
                        "purpose": "differentiation",
                        "status": "in progress",
                        "summary": "Treatment of 20 ng/mL interferon gamma for 1 day",
                        "treatment_term_name": "interferon gamma"
                    },
                    {
                        "@id": "/treatments/bec71d5e-97ef-489a-acb7-5336691b6c39/",
                        "purpose": "differentiation",
                        "status": "in progress",
                        "summary": "Treatment of 100 ng/mL macrophage colony-stimulating factor 1 for 7 days",
                        "treatment_term_name": "macrophage colony-stimulating factor 1"
                    }
                ]
            }
        ],
        "status": "released",
        "summary": "single-nucleus ATAC-seq (10x multiome with MULTI-seq)"
    },
    "file_size": 4094963424,
    "flowcell_id": "222YV7LT3",
    "gene_list_for": [],
    "href": "/sequence-files/IGVFFI3571ZWPJ/@@download/IGVFFI3571ZWPJ.fastq.gz",
    "illumina_read_type": "I1",
    "input_file_for": [
        "/tabular-files/IGVFFI7268PNWE/"
    ],
    "integrated_in": [],
    "lab": {
        "@id": "/labs/ansuman-satpathy/",
        "title": "Ansuman Satpathy, Stanford"
    },
    "lane": 4,
    "loci_list_for": [],
    "maximum_read_length": 8,
    "md5sum": "358c9779be3b2b7f7eef5664ff59395b",
    "mean_read_length": 8,
    "minimum_read_length": 8,
    "quality_metrics": [],
    "read_count": 649875768,
    "release_timestamp": "2025-03-07T01:11:31.264586+00:00",
    "s3_uri": "s3://igvf-files/2024/07/22/f339da85-c65a-466f-8fe1-6c75cb7cd593/IGVFFI3571ZWPJ.fastq.gz",
    "schema_version": "15",
    "seqspecs": [
        "/configuration-files/IGVFFI1276MPAQ/"
    ],
    "sequencing_kit": "NovaSeq X Series 10B Reagent Kit",
    "sequencing_platform": {
        "@id": "/platform-terms/EFO_0022840/",
        "status": "released",
        "term_name": "Illumina NovaSeq X"
    },
    "sequencing_run": 1,
    "status": "released",
    "submitted_by": {
        "@id": "/users/353655bc-31a1-4cd9-bac3-c7d34faf722f/",
        "title": "Christopher Mcginnis"
    },
    "submitted_file_name": "/oak/stanford/projects/igvf/Projects/230522_IGVF4_McGinnis/ATAC/FASTQ/_ATAC_2_S6_L004_I1_001.fastq.gz",
    "summary": "I1 reads from sequencing run 1",
    "upload_status": "validated",
    "uuid": "f339da85-c65a-466f-8fe1-6c75cb7cd593"
}