IGVFFI7951DAQB

{
    "@context": "/terms/",
    "@id": "/sequence-files/IGVFFI7951DAQB/",
    "@type": [
        "SequenceFile",
        "File",
        "Item"
    ],
    "accession": "IGVFFI7951DAQB",
    "aliases": [
        "ansuman-satpathy:igvf_exp10_rna_10x2_NGS1_r2"
    ],
    "assay_titles": [
        "10x multiome with MULTI-seq"
    ],
    "audit": {},
    "award": {
        "@id": "/awards/HG012076/",
        "component": "mapping"
    },
    "content_md5sum": "fa79a2d289c269155d4ad3887c579340",
    "content_type": "reads",
    "controlled_access": false,
    "creation_timestamp": "2024-07-22T17:05:30.473484+00:00",
    "externally_hosted": false,
    "file_format": "fastq",
    "file_set": {
        "@id": "/measurement-sets/IGVFDS9139TBCB/",
        "accession": "IGVFDS9139TBCB",
        "file_set_type": "experimental data",
        "samples": [
            {
                "@id": "/multiplexed-samples/IGVFSM0539NUPM/",
                "accession": "IGVFSM0539NUPM",
                "classifications": [
                    "cell line",
                    "multiplexed sample"
                ],
                "disease_terms": [],
                "modifications": [
                    {
                        "@id": "/crispr-modifications/b4bc725a-8eeb-4180-9789-bece3516c0c1/",
                        "modality": "interference",
                        "status": "released",
                        "summary": "CRISPRi Sp-dCas9-KOX1-KRAB"
                    }
                ],
                "sample_terms": [
                    {
                        "@id": "/sample-terms/EFO_0001253/",
                        "status": "released",
                        "term_name": "THP-1"
                    },
                    {
                        "@id": "/sample-terms/EFO_0002067/",
                        "status": "released",
                        "term_name": "K562"
                    },
                    {
                        "@id": "/sample-terms/EFO_0002796/",
                        "status": "released",
                        "term_name": "Jurkat"
                    },
                    {
                        "@id": "/sample-terms/NTR_0000753/",
                        "status": "released",
                        "term_name": "TeloHAEC"
                    }
                ],
                "status": "released",
                "summary": "multiplexed sample: Jurkat cell line, male, Homo sapiens treated with 100 ng/mL phorbol 13-acetate 12-myristate for 4 hours, 5 μg/mL T-cell surface glycoprotein CD3 gamma chain for 4 hours; K562 cell line, female, Homo sapiens modified with CRISPRi Sp-dCas9-KOX1-KRAB; ... and 8 more samples",
                "taxa": "Homo sapiens",
                "treatments": [
                    {
                        "@id": "/treatments/42b3c61d-38de-4bd2-bb39-33c125a417cb/",
                        "purpose": "stimulation",
                        "status": "released",
                        "summary": "Treatment of 100 ng/mL phorbol 13-acetate 12-myristate for 4 hours",
                        "treatment_term_name": "phorbol 13-acetate 12-myristate"
                    },
                    {
                        "@id": "/treatments/df02c0d4-f796-4f77-bfbc-388cdbfcc615/",
                        "purpose": "stimulation",
                        "status": "released",
                        "summary": "Treatment of 5 μg/mL T-cell surface glycoprotein CD3 gamma chain for 4 hours",
                        "treatment_term_name": "T-cell surface glycoprotein CD3 gamma chain"
                    }
                ]
            }
        ],
        "status": "released",
        "summary": "interference single-nucleus RNA sequencing assay (10x multiome with MULTI-seq)"
    },
    "file_size": 21867079155,
    "flowcell_id": "223JHYLT3",
    "gene_list_for": [],
    "href": "/sequence-files/IGVFFI7951DAQB/@@download/IGVFFI7951DAQB.fastq.gz",
    "illumina_read_type": "R2",
    "input_file_for": [
        "/matrix-files/IGVFFI5029LHBH/"
    ],
    "integrated_in": [],
    "lab": {
        "@id": "/labs/ansuman-satpathy/",
        "title": "Ansuman Satpathy, Stanford"
    },
    "lane": 4,
    "loci_list_for": [],
    "maximum_read_length": 90,
    "md5sum": "4e05b91f9660e1c50f79729068b8a87d",
    "mean_read_length": 90,
    "minimum_read_length": 90,
    "quality_metrics": [],
    "read_count": 517392579,
    "read_names": [
        "Read 2"
    ],
    "release_timestamp": "2025-03-07T01:13:59.521020+00:00",
    "s3_uri": "s3://igvf-files/2024/07/22/22bcada2-b201-4ecb-89c1-e8f0c95450ec/IGVFFI7951DAQB.fastq.gz",
    "schema_version": "15",
    "seqspecs": [
        "/configuration-files/IGVFFI2433YUEJ/"
    ],
    "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/230707_IGVF10_McGinnis/GEX/FASTQ/GEX_2_CMAS_IGVF10_R_S10_L004_R2_001.fastq.gz",
    "summary": "R2 reads from sequencing run 1",
    "upload_status": "validated",
    "uuid": "22bcada2-b201-4ecb-89c1-e8f0c95450ec"
}