IGVFDS2532AVSC

released
{
    "@context": "/terms/",
    "@id": "/auxiliary-sets/IGVFDS2532AVSC/",
    "@type": [
        "AuxiliarySet",
        "FileSet",
        "Item"
    ],
    "accession": "IGVFDS2532AVSC",
    "aliases": [
        "jay-shendure:CRISPRa_singlecell_iPSC-derived-neurons_VPH_10Xlane3_CS1"
    ],
    "audit": {
        "NOT_COMPLIANT": [
            {
                "category": "missing sequence specification",
                "detail": "Auxiliary set [IGVFDS2532AVSC](/auxiliary-sets/IGVFDS2532AVSC/) has sequence file(s): [IGVFFI5740EZRO](/sequence-files/IGVFFI5740EZRO/), [IGVFFI5101XXFL](/sequence-files/IGVFFI5101XXFL/), [IGVFFI2904WAAT](/sequence-files/IGVFFI2904WAAT/), [IGVFFI7440JFKZ](/sequence-files/IGVFFI7440JFKZ/), [IGVFFI3911GHFM](/sequence-files/IGVFFI3911GHFM/), [IGVFFI4073XXVS](/sequence-files/IGVFFI4073XXVS/), [IGVFFI8818WFVA](/sequence-files/IGVFFI8818WFVA/), [IGVFFI3761PGKJ](/sequence-files/IGVFFI3761PGKJ/) 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/IGVFDS2532AVSC/"
            }
        ]
    },
    "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": "2023-12-08T23:52:07.294289+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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            ],
            "content_type": "reads",
            "creation_timestamp": "2023-12-09T00:51:13.101456+00:00",
            "file_format": "fastq",
            "file_size": 324594933,
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            "s3_uri": "s3://igvf-files/2023/12/09/2ed80854-f0f2-4150-83f1-401911932c59/IGVFFI5740EZRO.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_3/CS1_3_S7_L001_I1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI5101XXFL/",
            "accession": "IGVFFI5101XXFL",
            "aliases": [
                "jay-shendure:CRISPRa_singlecell_iPSCneuron_VPH_sequence_CS1_10Xlane3_seqlane1_I2"
            ],
            "content_type": "reads",
            "creation_timestamp": "2023-12-09T00:51:14.179268+00:00",
            "file_format": "fastq",
            "file_size": 355771100,
            "href": "/sequence-files/IGVFFI5101XXFL/@@download/IGVFFI5101XXFL.fastq.gz",
            "s3_uri": "s3://igvf-files/2023/12/09/331186b7-353d-4d0c-b2a9-3889114ff0e0/IGVFFI5101XXFL.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_3/CS1_3_S7_L001_I2_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI2904WAAT/",
            "accession": "IGVFFI2904WAAT",
            "aliases": [
                "jay-shendure:CRISPRa_singlecell_iPSCneuron_VPH_sequence_CS1_10Xlane3_seqlane1_R2"
            ],
            "content_type": "reads",
            "creation_timestamp": "2023-12-09T00:51:16.521027+00:00",
            "file_format": "fastq",
            "file_size": 1408130266,
            "href": "/sequence-files/IGVFFI2904WAAT/@@download/IGVFFI2904WAAT.fastq.gz",
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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_3/CS1_3_S7_L001_R2_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI7440JFKZ/",
            "accession": "IGVFFI7440JFKZ",
            "aliases": [
                "jay-shendure:CRISPRa_singlecell_iPSCneuron_VPH_sequence_CS1_10Xlane3_seqlane2_I1"
            ],
            "content_type": "reads",
            "creation_timestamp": "2023-12-09T00:51:17.541296+00:00",
            "file_format": "fastq",
            "file_size": 290436430,
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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_3/CS1_3_S7_L002_I1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI3911GHFM/",
            "accession": "IGVFFI3911GHFM",
            "aliases": [
                "jay-shendure:CRISPRa_singlecell_iPSCneuron_VPH_sequence_CS1_10Xlane3_seqlane1_R1"
            ],
            "content_type": "reads",
            "creation_timestamp": "2023-12-09T00:51:15.316015+00:00",
            "file_format": "fastq",
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            "s3_uri": "s3://igvf-files/2023/12/09/33eca167-e12c-4b0d-8d55-ca6923f27c11/IGVFFI3911GHFM.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_3/CS1_3_S7_L001_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI4073XXVS/",
            "accession": "IGVFFI4073XXVS",
            "aliases": [
                "jay-shendure:CRISPRa_singlecell_iPSCneuron_VPH_sequence_CS1_10Xlane3_seqlane2_R1"
            ],
            "content_type": "reads",
            "creation_timestamp": "2023-12-09T00:51:19.833843+00:00",
            "file_format": "fastq",
            "file_size": 1022000865,
            "href": "/sequence-files/IGVFFI4073XXVS/@@download/IGVFFI4073XXVS.fastq.gz",
            "s3_uri": "s3://igvf-files/2023/12/09/b3d52aa8-0c29-4283-a73b-c01eab2d1ee1/IGVFFI4073XXVS.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_3/CS1_3_S7_L002_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI8818WFVA/",
            "accession": "IGVFFI8818WFVA",
            "aliases": [
                "jay-shendure:CRISPRa_singlecell_iPSCneuron_VPH_sequence_CS1_10Xlane3_seqlane2_R2"
            ],
            "content_type": "reads",
            "creation_timestamp": "2023-12-09T00:51:20.981173+00:00",
            "file_format": "fastq",
            "file_size": 1290293278,
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            "s3_uri": "s3://igvf-files/2023/12/09/3b111af3-b042-45b6-b441-b9379ab0cad6/IGVFFI8818WFVA.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_3/CS1_3_S7_L002_R2_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI3761PGKJ/",
            "accession": "IGVFFI3761PGKJ",
            "aliases": [
                "jay-shendure:CRISPRa_singlecell_iPSCneuron_VPH_sequence_CS1_10Xlane3_seqlane2_I2"
            ],
            "content_type": "reads",
            "creation_timestamp": "2023-12-09T00:51:18.782469+00:00",
            "file_format": "fastq",
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            "href": "/sequence-files/IGVFFI3761PGKJ/@@download/IGVFFI3761PGKJ.fastq.gz",
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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_3/CS1_3_S7_L002_I2_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/IGVFDS2385QENN/",
            "accession": "IGVFDS2385QENN",
            "aliases": [
                "jay-shendure:CRISPRa_singlecell_iPSC-derived-neurons_VPH_10Xlane3_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": "2024-08-13T20:47:22.719369+00:00",
    "samples": [
        {
            "@id": "/in-vitro-systems/IGVFSM8317ZTFV/",
            "@type": [
                "InVitroSystem",
                "Biosample",
                "Sample",
                "Item"
            ],
            "accession": "IGVFSM8317ZTFV",
            "aliases": [
                "jay-shendure:CRISPRa_VPH_NGN2_WTC11_neurons_10Xlane3"
            ],
            "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: 10Xlane3), 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": "2023-12-09T00:51:13.101456+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": "d6a27c6b-d621-4087-8026-03e8c25dc7b3"
}