IGVFDS9078ZWQH

released
{
    "@context": "/terms/",
    "@id": "/analysis-sets/IGVFDS9078ZWQH/",
    "@type": [
        "AnalysisSet",
        "FileSet",
        "Item"
    ],
    "accession": "IGVFDS9078ZWQH",
    "aliases": [
        "jay-shendure:analysis_set_CRISPRa_K562"
    ],
    "assay_titles": [
        "scCRISPR screen"
    ],
    "audit": {
        "WARNING": [
            {
                "category": "missing analysis step version",
                "detail": "Analysis set [IGVFDS9078ZWQH](/analysis-sets/IGVFDS9078ZWQH/) links to file(s) [IGVFFI5652WMRK](/tabular-files/IGVFFI5652WMRK/), [IGVFFI4612KEHH](/tabular-files/IGVFFI4612KEHH/) that are missing `analysis_step_version`. Analysis set files are expected to specify analysis step version.",
                "level": 40,
                "level_name": "WARNING",
                "name": "audit_analysis_set_files_missing_analysis_step_version",
                "path": "/analysis-sets/IGVFDS9078ZWQH/"
            },
            {
                "category": "missing derived from",
                "detail": "Analysis set [IGVFDS9078ZWQH](/analysis-sets/IGVFDS9078ZWQH/) links to file(s) [IGVFFI5652WMRK](/tabular-files/IGVFFI5652WMRK/), [IGVFFI4612KEHH](/tabular-files/IGVFFI4612KEHH/) that have no `derived_from`. Files in an analysis set are expected to be derived from other files.",
                "level": 40,
                "level_name": "WARNING",
                "name": "audit_input_file_sets_derived_from",
                "path": "/analysis-sets/IGVFDS9078ZWQH/"
            }
        ]
    },
    "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": "2023-12-12T23:07:33.755844+00:00",
    "donors": [
        {
            "@id": "/human-donors/IGVFDO9208RPQQ/",
            "accession": "IGVFDO9208RPQQ",
            "aliases": [
                "igvf:donor_of_K562"
            ],
            "sex": "female",
            "status": "released",
            "taxa": "Homo sapiens"
        }
    ],
    "file_set_type": "principal analysis",
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            "aliases": [
                "jay-shendure:analysis_set_CRISPRa_K562_matrix"
            ],
            "content_type": "sparse gene count matrix",
            "creation_timestamp": "2023-12-13T00:09:56.255569+00:00",
            "file_format": "tar",
            "file_size": 537616943,
            "href": "/matrix-files/IGVFFI5731ZKRJ/@@download/IGVFFI5731ZKRJ.tar.gz",
            "s3_uri": "s3://igvf-files/2023/12/13/f6f37514-eaf7-4b5d-97b9-e00a37f3ac1d/IGVFFI5731ZKRJ.tar.gz",
            "submitted_file_name": "/net/shendure/vol10/projects/IGVFtemp/Shendure_K562_CRISPRa_matrix.tar.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/tabular-files/IGVFFI5652WMRK/",
            "accession": "IGVFFI5652WMRK",
            "aliases": [
                "jay-shendure:tabularfile_S4_Chardon-McDiarmid"
            ],
            "content_type": "differential gene expression quantifications",
            "creation_timestamp": "2024-10-14T18:38:59.978827+00:00",
            "file_format": "csv",
            "file_size": 6873,
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            "submitted_file_name": "/net/shendure/vol1/home/martin91/IGVF/forupload/CRISPRa/41467_2024_52490_MOESM7_ESM.csv.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/tabular-files/IGVFFI4612KEHH/",
            "accession": "IGVFFI4612KEHH",
            "aliases": [
                "jay-shendure:tabularfile_S11_Chardon-McDiarmid"
            ],
            "content_type": "differential gene expression quantifications",
            "creation_timestamp": "2024-10-14T18:39:03.562166+00:00",
            "file_format": "csv",
            "file_size": 3314,
            "href": "/tabular-files/IGVFFI4612KEHH/@@download/IGVFFI4612KEHH.csv.gz",
            "s3_uri": "s3://igvf-files/2024/10/14/12aa9f23-4832-4e9e-9cc2-9d94f4545063/IGVFFI4612KEHH.csv.gz",
            "submitted_file_name": "/net/shendure/vol1/home/martin91/IGVF/forupload/CRISPRa/41467_2024_52490_MOESM14_ESM.csv.gz",
            "upload_status": "validated"
        }
    ],
    "functional_assay_mechanisms": [],
    "input_file_sets": [
        {
            "@id": "/measurement-sets/IGVFDS4863BMGZ/",
            "accession": "IGVFDS4863BMGZ",
            "aliases": [
                "jay-shendure:CRISPRa_singlecell_K562_VP64_10Xlane1_exprs"
            ],
            "file_set_type": "experimental data"
        },
        {
            "@id": "/measurement-sets/IGVFDS8535CXVX/",
            "accession": "IGVFDS8535CXVX",
            "aliases": [
                "jay-shendure:CRISPRa_singlecell_K562_VP64_10Xlane2_exprs"
            ],
            "file_set_type": "experimental data"
        },
        {
            "@id": "/measurement-sets/IGVFDS7395DPAD/",
            "accession": "IGVFDS7395DPAD",
            "aliases": [
                "jay-shendure:CRISPRa_singlecell_K562_VPR_10Xlane1_exprs"
            ],
            "file_set_type": "experimental data"
        },
        {
            "@id": "/measurement-sets/IGVFDS0508ERUQ/",
            "accession": "IGVFDS0508ERUQ",
            "aliases": [
                "jay-shendure:CRISPRa_singlecell_K562_VPR_10Xlane2_exprs"
            ],
            "file_set_type": "experimental data"
        },
        {
            "@id": "/auxiliary-sets/IGVFDS4502LQQH/",
            "accession": "IGVFDS4502LQQH",
            "aliases": [
                "jay-shendure:CRISPRa_singlecell_K562_VP64_10Xlane1_CS1"
            ],
            "file_set_type": "gRNA sequencing"
        },
        {
            "@id": "/auxiliary-sets/IGVFDS8929VNCP/",
            "accession": "IGVFDS8929VNCP",
            "aliases": [
                "jay-shendure:CRISPRa_singlecell_K562_VP64_10Xlane2_CS1"
            ],
            "file_set_type": "gRNA sequencing"
        },
        {
            "@id": "/auxiliary-sets/IGVFDS4621HUKP/",
            "accession": "IGVFDS4621HUKP",
            "aliases": [
                "jay-shendure:CRISPRa_singlecell_K562_VPR_10Xlane1_CS1"
            ],
            "file_set_type": "gRNA sequencing"
        },
        {
            "@id": "/auxiliary-sets/IGVFDS4834SKZS/",
            "accession": "IGVFDS4834SKZS",
            "aliases": [
                "jay-shendure:CRISPRa_singlecell_K562_VPR_10Xlane2_CS1"
            ],
            "file_set_type": "gRNA sequencing"
        }
    ],
    "input_for": [],
    "lab": {
        "@id": "/labs/jay-shendure/",
        "title": "Jay Shendure, UW"
    },
    "notes": "This object's file_set_type was primary analysis and has been updated to be principal analysis.",
    "protocols": [
        "https://www.protocols.io/view/methods-from-multiplex-single-cell-crispra-screeni-c5zvy766"
    ],
    "publications": [
        {
            "@id": "/publications/20fcbdbb-5a47-41c6-b80b-e6dd0e8a8d3e/",
            "publication_identifiers": [
                "doi:10.1101/2023.03.28.534017"
            ]
        }
    ],
    "release_timestamp": "2024-08-13T20:47:06.196314+00:00",
    "sample_summary": "K562 cell line, modified with CRISPR modifications, transfected with a guide library",
    "samples": [
        {
            "@id": "/in-vitro-systems/IGVFSM1594ZOQH/",
            "@type": [
                "InVitroSystem",
                "Biosample",
                "Sample",
                "Item"
            ],
            "accession": "IGVFSM1594ZOQH",
            "aliases": [
                "jay-shendure:CRISPRa_VPR_K562_10Xlane1"
            ],
            "classifications": [
                "cell line"
            ],
            "construct_library_sets": [
                "/construct-library-sets/IGVFDS7581DNXF/"
            ],
            "modifications": [
                {
                    "@id": "/crispr-modifications/8b61bce4-105c-435e-9b32-1c8903566a9b/",
                    "modality": "activation"
                }
            ],
            "sample_terms": [
                {
                    "@id": "/sample-terms/EFO_0002067/",
                    "@type": [
                        "SampleTerm",
                        "OntologyTerm",
                        "Item"
                    ],
                    "aliases": [
                        "igvf:K562"
                    ],
                    "status": "released",
                    "summary": "K562",
                    "term_name": "K562"
                }
            ],
            "status": "released",
            "summary": "K562 cell line (cellular sub pool: 10Xlane1), female, Homo sapiens modified with CRISPRa Sp-dCas9-VP64-p65-Rta (VPR), transfected with a guide library",
            "taxa": "Homo sapiens"
        },
        {
            "@id": "/in-vitro-systems/IGVFSM9390JSDH/",
            "@type": [
                "InVitroSystem",
                "Biosample",
                "Sample",
                "Item"
            ],
            "accession": "IGVFSM9390JSDH",
            "aliases": [
                "jay-shendure:CRISPRa_VP64_K562_10Xlane2"
            ],
            "classifications": [
                "cell line"
            ],
            "construct_library_sets": [
                "/construct-library-sets/IGVFDS7581DNXF/"
            ],
            "modifications": [
                {
                    "@id": "/crispr-modifications/ee99bf66-2a5a-4ec6-8380-9434b259afd1/",
                    "modality": "activation"
                }
            ],
            "sample_terms": [
                {
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                    "@type": [
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                        "OntologyTerm",
                        "Item"
                    ],
                    "aliases": [
                        "igvf:K562"
                    ],
                    "status": "released",
                    "summary": "K562",
                    "term_name": "K562"
                }
            ],
            "status": "released",
            "summary": "K562 cell line (cellular sub pool: 10Xlane2), female, Homo sapiens modified with CRISPRa Sp-dCas9-VP64, transfected with a guide library",
            "taxa": "Homo sapiens"
        },
        {
            "@id": "/in-vitro-systems/IGVFSM9542NUGS/",
            "@type": [
                "InVitroSystem",
                "Biosample",
                "Sample",
                "Item"
            ],
            "accession": "IGVFSM9542NUGS",
            "aliases": [
                "jay-shendure:CRISPRa_VPR_K562_10Xlane2"
            ],
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                "cell line"
            ],
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            ],
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                    "@id": "/crispr-modifications/8b61bce4-105c-435e-9b32-1c8903566a9b/",
                    "modality": "activation"
                }
            ],
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                    "@type": [
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                        "OntologyTerm",
                        "Item"
                    ],
                    "aliases": [
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                    ],
                    "status": "released",
                    "summary": "K562",
                    "term_name": "K562"
                }
            ],
            "status": "released",
            "summary": "K562 cell line (cellular sub pool: 10Xlane2), female, Homo sapiens modified with CRISPRa Sp-dCas9-VP64-p65-Rta (VPR), transfected with a guide library",
            "taxa": "Homo sapiens"
        },
        {
            "@id": "/in-vitro-systems/IGVFSM4521QSSO/",
            "@type": [
                "InVitroSystem",
                "Biosample",
                "Sample",
                "Item"
            ],
            "accession": "IGVFSM4521QSSO",
            "aliases": [
                "jay-shendure:CRISPRa_VP64_K562_10Xlane1"
            ],
            "classifications": [
                "cell line"
            ],
            "construct_library_sets": [
                "/construct-library-sets/IGVFDS7581DNXF/"
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                {
                    "@id": "/crispr-modifications/ee99bf66-2a5a-4ec6-8380-9434b259afd1/",
                    "modality": "activation"
                }
            ],
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                {
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                    "@type": [
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                        "OntologyTerm",
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                    ],
                    "aliases": [
                        "igvf:K562"
                    ],
                    "status": "released",
                    "summary": "K562",
                    "term_name": "K562"
                }
            ],
            "status": "released",
            "summary": "K562 cell line (cellular sub pool: 10Xlane1), female, Homo sapiens modified with CRISPRa Sp-dCas9-VP64, transfected with a guide library",
            "taxa": "Homo sapiens"
        }
    ],
    "schema_version": "9",
    "status": "released",
    "submitted_by": {
        "@id": "/users/73f58e9f-8f5d-4fee-a7cd-dd63c0167e4b/",
        "title": "Beth Martin"
    },
    "submitted_files_timestamp": "2023-12-13T00:09:56.255569+00:00",
    "summary": "scCRISPR activation screen: differential gene expression quantifications, sparse gene count matrix",
    "uuid": "5257dd49-492f-49b1-88fd-8b812ae8c188",
    "workflows": [
        {
            "@id": "/workflows/IGVFWF7562QXLM/",
            "accession": "IGVFWF7562QXLM",
            "name": "Cell Ranger Gene Count Pipeline"
        }
    ]
}