IGVFDS8386FNRJ

released
{
    "@context": "/terms/",
    "@id": "/auxiliary-sets/IGVFDS8386FNRJ/",
    "@type": [
        "AuxiliarySet",
        "FileSet",
        "Item"
    ],
    "accession": "IGVFDS8386FNRJ",
    "aliases": [
        "jay-shendure:CRISPRa_singlecell_iPSC-derived-neurons_VPH_10Xlane1_CS1"
    ],
    "audit": {
        "NOT_COMPLIANT": [
            {
                "category": "missing sequence specification",
                "detail": "Auxiliary set [IGVFDS8386FNRJ](/auxiliary-sets/IGVFDS8386FNRJ/) has sequence file(s): [IGVFFI3534JLPF](/sequence-files/IGVFFI3534JLPF/), [IGVFFI4980GVVC](/sequence-files/IGVFFI4980GVVC/), [IGVFFI9263MTNB](/sequence-files/IGVFFI9263MTNB/), [IGVFFI3537WAMV](/sequence-files/IGVFFI3537WAMV/), [IGVFFI6258TUAO](/sequence-files/IGVFFI6258TUAO/), [IGVFFI6689DLGE](/sequence-files/IGVFFI6689DLGE/), [IGVFFI0070OAUF](/sequence-files/IGVFFI0070OAUF/), [IGVFFI2908NAIM](/sequence-files/IGVFFI2908NAIM/) which do not have any `seqspecs`. Sequence files in a file set are expected to link to a sequence specification file.",
                "level": 50,
                "level_name": "NOT_COMPLIANT",
                "name": "audit_missing_seqspec",
                "path": "/auxiliary-sets/IGVFDS8386FNRJ/"
            }
        ]
    },
    "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": "2023-12-08T23:52:05.762124+00:00",
    "donors": [
        {
            "@id": "/human-donors/IGVFDO1756PPKO/",
            "accession": "IGVFDO1756PPKO",
            "aliases": [
                "igvf:donor_of_WTC11"
            ],
            "sex": "male",
            "status": "released",
            "taxa": "Homo sapiens"
        }
    ],
    "file_set_type": "gRNA sequencing",
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                "jay-shendure:CRISPRa_singlecell_iPSCneuron_VPH_sequence_CS1_10Xlane1_seqlane1_I1"
            ],
            "content_type": "reads",
            "creation_timestamp": "2023-12-09T00:50:53.650937+00:00",
            "file_format": "fastq",
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            "sequencing_platform": "/platform-terms/EFO_0010963/",
            "submitted_file_name": "/net/shendure/vol10/www/content/members/CRISPRa_QTL_website/public/data/neuron_data/sequencing_data/cellranger_mkfastq_output/outs/fastq_path/AAAMCTVHV/CS1_1/CS1_1_S5_L001_I1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI4980GVVC/",
            "accession": "IGVFFI4980GVVC",
            "aliases": [
                "jay-shendure:CRISPRa_singlecell_iPSCneuron_VPH_sequence_CS1_10Xlane1_seqlane1_R2"
            ],
            "content_type": "reads",
            "creation_timestamp": "2023-12-09T00:50:57.034977+00:00",
            "file_format": "fastq",
            "file_size": 1173968840,
            "href": "/sequence-files/IGVFFI4980GVVC/@@download/IGVFFI4980GVVC.fastq.gz",
            "s3_uri": "s3://igvf-files/2023/12/09/a0eaee33-5e89-4ba3-b8ba-a3ca0867279b/IGVFFI4980GVVC.fastq.gz",
            "sequencing_platform": "/platform-terms/EFO_0010963/",
            "submitted_file_name": "/net/shendure/vol10/www/content/members/CRISPRa_QTL_website/public/data/neuron_data/sequencing_data/cellranger_mkfastq_output/outs/fastq_path/AAAMCTVHV/CS1_1/CS1_1_S5_L001_R2_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI9263MTNB/",
            "accession": "IGVFFI9263MTNB",
            "aliases": [
                "jay-shendure:CRISPRa_singlecell_iPSCneuron_VPH_sequence_CS1_10Xlane1_seqlane2_R1"
            ],
            "content_type": "reads",
            "creation_timestamp": "2023-12-09T00:51:00.492108+00:00",
            "file_format": "fastq",
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            "s3_uri": "s3://igvf-files/2023/12/09/277e7654-02d5-4c34-8c8f-40fac1c898f6/IGVFFI9263MTNB.fastq.gz",
            "sequencing_platform": "/platform-terms/EFO_0010963/",
            "submitted_file_name": "/net/shendure/vol10/www/content/members/CRISPRa_QTL_website/public/data/neuron_data/sequencing_data/cellranger_mkfastq_output/outs/fastq_path/AAAMCTVHV/CS1_1/CS1_1_S5_L002_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI3537WAMV/",
            "accession": "IGVFFI3537WAMV",
            "aliases": [
                "jay-shendure:CRISPRa_singlecell_iPSCneuron_VPH_sequence_CS1_10Xlane1_seqlane2_I2"
            ],
            "content_type": "reads",
            "creation_timestamp": "2023-12-09T00:50:59.208018+00:00",
            "file_format": "fastq",
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            "href": "/sequence-files/IGVFFI3537WAMV/@@download/IGVFFI3537WAMV.fastq.gz",
            "s3_uri": "s3://igvf-files/2023/12/09/3aeb5043-316b-4fff-a61a-5df49e97ed1c/IGVFFI3537WAMV.fastq.gz",
            "sequencing_platform": "/platform-terms/EFO_0010963/",
            "submitted_file_name": "/net/shendure/vol10/www/content/members/CRISPRa_QTL_website/public/data/neuron_data/sequencing_data/cellranger_mkfastq_output/outs/fastq_path/AAAMCTVHV/CS1_1/CS1_1_S5_L002_I2_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI6258TUAO/",
            "accession": "IGVFFI6258TUAO",
            "aliases": [
                "jay-shendure:CRISPRa_singlecell_iPSCneuron_VPH_sequence_CS1_10Xlane1_seqlane1_I2"
            ],
            "content_type": "reads",
            "creation_timestamp": "2023-12-09T00:50:54.735024+00:00",
            "file_format": "fastq",
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            "sequencing_platform": "/platform-terms/EFO_0010963/",
            "submitted_file_name": "/net/shendure/vol10/www/content/members/CRISPRa_QTL_website/public/data/neuron_data/sequencing_data/cellranger_mkfastq_output/outs/fastq_path/AAAMCTVHV/CS1_1/CS1_1_S5_L001_I2_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI6689DLGE/",
            "accession": "IGVFFI6689DLGE",
            "aliases": [
                "jay-shendure:CRISPRa_singlecell_iPSCneuron_VPH_sequence_CS1_10Xlane1_seqlane1_R1"
            ],
            "content_type": "reads",
            "creation_timestamp": "2023-12-09T00:50:55.949835+00:00",
            "file_format": "fastq",
            "file_size": 1044468908,
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            "s3_uri": "s3://igvf-files/2023/12/09/260c6f0b-67f9-4cb8-96f6-807582406b69/IGVFFI6689DLGE.fastq.gz",
            "sequencing_platform": "/platform-terms/EFO_0010963/",
            "submitted_file_name": "/net/shendure/vol10/www/content/members/CRISPRa_QTL_website/public/data/neuron_data/sequencing_data/cellranger_mkfastq_output/outs/fastq_path/AAAMCTVHV/CS1_1/CS1_1_S5_L001_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI0070OAUF/",
            "accession": "IGVFFI0070OAUF",
            "aliases": [
                "jay-shendure:CRISPRa_singlecell_iPSCneuron_VPH_sequence_CS1_10Xlane1_seqlane2_I1"
            ],
            "content_type": "reads",
            "creation_timestamp": "2023-12-09T00:50:58.127910+00:00",
            "file_format": "fastq",
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            "sequencing_platform": "/platform-terms/EFO_0010963/",
            "submitted_file_name": "/net/shendure/vol10/www/content/members/CRISPRa_QTL_website/public/data/neuron_data/sequencing_data/cellranger_mkfastq_output/outs/fastq_path/AAAMCTVHV/CS1_1/CS1_1_S5_L002_I1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI2908NAIM/",
            "accession": "IGVFFI2908NAIM",
            "aliases": [
                "jay-shendure:CRISPRa_singlecell_iPSCneuron_VPH_sequence_CS1_10Xlane1_seqlane2_R2"
            ],
            "content_type": "reads",
            "creation_timestamp": "2023-12-09T00:51:01.550881+00:00",
            "file_format": "fastq",
            "file_size": 1089164603,
            "href": "/sequence-files/IGVFFI2908NAIM/@@download/IGVFFI2908NAIM.fastq.gz",
            "s3_uri": "s3://igvf-files/2023/12/09/ff8f27d2-547e-4bcf-922b-3174afb4815e/IGVFFI2908NAIM.fastq.gz",
            "sequencing_platform": "/platform-terms/EFO_0010963/",
            "submitted_file_name": "/net/shendure/vol10/www/content/members/CRISPRa_QTL_website/public/data/neuron_data/sequencing_data/cellranger_mkfastq_output/outs/fastq_path/AAAMCTVHV/CS1_1/CS1_1_S5_L002_R2_001.fastq.gz",
            "upload_status": "validated"
        }
    ],
    "input_file_set_for": [
        "/analysis-sets/IGVFDS4021XJLW/"
    ],
    "lab": {
        "@id": "/labs/jay-shendure/",
        "title": "Jay Shendure, UW"
    },
    "measurement_sets": [
        {
            "@id": "/measurement-sets/IGVFDS9384BVGM/",
            "accession": "IGVFDS9384BVGM",
            "aliases": [
                "jay-shendure:CRISPRa_singlecell_iPSC-derived-neurons_VPH_10Xlane1_exprs"
            ],
            "preferred_assay_title": "scCRISPR screen"
        }
    ],
    "publications": [
        {
            "@id": "/publications/20fcbdbb-5a47-41c6-b80b-e6dd0e8a8d3e/",
            "publication_identifiers": [
                "doi:10.1101/2023.03.28.534017"
            ]
        }
    ],
    "release_timestamp": "2024-08-13T20:47:21.563052+00:00",
    "samples": [
        {
            "@id": "/in-vitro-systems/IGVFSM7750SNNY/",
            "@type": [
                "InVitroSystem",
                "Biosample",
                "Sample",
                "Item"
            ],
            "accession": "IGVFSM7750SNNY",
            "aliases": [
                "jay-shendure:CRISPRa_VPH_NGN2_WTC11_neurons_10Xlane1"
            ],
            "cell_fate_change_treatments": [
                "/treatments/13a2bfe2-9124-4254-b0fe-8c221077201f/"
            ],
            "classifications": [
                "differentiated cell specimen"
            ],
            "construct_library_sets": [
                "/construct-library-sets/IGVFDS7581DNXF/"
            ],
            "modifications": [
                "/crispr-modifications/426a4099-35d9-4c65-8851-5e788a3d4e70/"
            ],
            "sample_terms": [
                {
                    "@id": "/sample-terms/EFO_0009747/",
                    "@type": [
                        "SampleTerm",
                        "OntologyTerm",
                        "Item"
                    ],
                    "aliases": [
                        "igvf:WTC11"
                    ],
                    "status": "released",
                    "summary": "GM25256 (WTC-11)",
                    "term_name": "GM25256 (WTC-11)"
                }
            ],
            "status": "released",
            "summary": "GM25256 (WTC-11) differentiated cell specimen induced to neuron for 19 days (cellular sub pool: 10Xlane1), male, Homo sapiens modified with a guide library",
            "targeted_sample_term": {
                "@id": "/sample-terms/CL_0000540/",
                "term_name": "neuron"
            },
            "taxa": "Homo sapiens"
        }
    ],
    "schema_version": "11",
    "status": "released",
    "submitted_by": {
        "@id": "/users/73f58e9f-8f5d-4fee-a7cd-dd63c0167e4b/",
        "title": "Beth Martin"
    },
    "submitted_files_timestamp": "2023-12-09T00:50:53.650937+00:00",
    "summary": "gRNA sequencing for scCRISPR activation screen integrating a guide (sgRNA) library targeting TF binding sites, candidate cis-regulatory elements in many genomic loci",
    "uuid": "ba54d793-6bd3-4793-b689-f1798ad3d759"
}