IGVFDS4021XJLW

released
{
    "@context": "/terms/",
    "@id": "/analysis-sets/IGVFDS4021XJLW/",
    "@type": [
        "AnalysisSet",
        "FileSet",
        "Item"
    ],
    "accession": "IGVFDS4021XJLW",
    "aliases": [
        "jay-shendure:analysis_set_CRISPRa_ipscNeurons"
    ],
    "assay_titles": [
        "scCRISPR screen"
    ],
    "audit": {
        "NOT_COMPLIANT": [
            {
                "category": "missing reference files",
                "detail": "Analysis set [IGVFDS4021XJLW](/analysis-sets/IGVFDS4021XJLW/) has file(s) with no transcriptome `reference_files`: [IGVFFI8270PCLP](/matrix-files/IGVFFI8270PCLP/)  Analysis set files processed from transcript sequence data are expected to link to a transcriptome reference.",
                "level": 50,
                "level_name": "NOT_COMPLIANT",
                "name": "audit_missing_transcriptome",
                "path": "/analysis-sets/IGVFDS4021XJLW/"
            },
            {
                "category": "missing file format specifications",
                "detail": "Matrix file [IGVFFI8270PCLP](/matrix-files/IGVFFI8270PCLP/) has no `file_format_specifications`. Matrix files are expected to link to a file format specifications document describing the axes and layers of the file.",
                "level": 50,
                "level_name": "NOT_COMPLIANT",
                "name": "audit_file_no_file_format_specifications",
                "path": "/matrix-files/IGVFFI8270PCLP/"
            }
        ],
        "WARNING": [
            {
                "category": "missing nucleic acid delivery",
                "detail": "In vitro system [IGVFSM8317ZTFV](/in-vitro-systems/IGVFSM8317ZTFV/) has `construct_library_sets` but is missing `nucleic_acid_delivery`. Samples linked to construct library sets are expected to specify nucleic acid delivery method.",
                "level": 40,
                "level_name": "WARNING",
                "name": "audit_missing_nucleic_acid_delivery",
                "path": "/in-vitro-systems/IGVFSM8317ZTFV/"
            },
            {
                "category": "missing nucleic acid delivery",
                "detail": "In vitro system [IGVFSM7750SNNY](/in-vitro-systems/IGVFSM7750SNNY/) has `construct_library_sets` but is missing `nucleic_acid_delivery`. Samples linked to construct library sets are expected to specify nucleic acid delivery method.",
                "level": 40,
                "level_name": "WARNING",
                "name": "audit_missing_nucleic_acid_delivery",
                "path": "/in-vitro-systems/IGVFSM7750SNNY/"
            },
            {
                "category": "unexpected workflows",
                "detail": "Analysis set [IGVFDS4021XJLW](/analysis-sets/IGVFDS4021XJLW/) has multiple `workflows` linked to its files: [IGVFFI8270PCLP](/matrix-files/IGVFFI8270PCLP/) link(s) to [IGVFWF7562QXLM](/workflows/IGVFWF7562QXLM/), [IGVFFI9048CVLI](/tabular-files/IGVFFI9048CVLI/), [IGVFFI4846IRZK](/tabular-files/IGVFFI4846IRZK/) link(s) to [IGVFWF1905PJEA](/workflows/IGVFWF1905PJEA/). Analysis sets are not expected to link to more than one workflow.",
                "level": 40,
                "level_name": "WARNING",
                "name": "audit_analysis_set_multiple_workflows",
                "path": "/analysis-sets/IGVFDS4021XJLW/"
            },
            {
                "category": "missing nucleic acid delivery",
                "detail": "In vitro system [IGVFSM9913PXTT](/in-vitro-systems/IGVFSM9913PXTT/) has `construct_library_sets` but is missing `nucleic_acid_delivery`. Samples linked to construct library sets are expected to specify nucleic acid delivery method.",
                "level": 40,
                "level_name": "WARNING",
                "name": "audit_missing_nucleic_acid_delivery",
                "path": "/in-vitro-systems/IGVFSM9913PXTT/"
            },
            {
                "category": "missing nucleic acid delivery",
                "detail": "In vitro system [IGVFSM8382KOXO](/in-vitro-systems/IGVFSM8382KOXO/) has `construct_library_sets` but is missing `nucleic_acid_delivery`. Samples linked to construct library sets are expected to specify nucleic acid delivery method.",
                "level": 40,
                "level_name": "WARNING",
                "name": "audit_missing_nucleic_acid_delivery",
                "path": "/in-vitro-systems/IGVFSM8382KOXO/"
            }
        ]
    },
    "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"
    },
    "construct_library_sets": [
        {
            "@id": "/construct-library-sets/IGVFDS7581DNXF/",
            "accession": "IGVFDS7581DNXF",
            "file_set_type": "guide library",
            "integrated_content_files": [
                {
                    "@id": "/tabular-files/IGVFFI2463QNJD/",
                    "accession": "IGVFFI2463QNJD",
                    "content_type": "guide RNA sequences",
                    "status": "released",
                    "summary": "GRCh38 guide RNA sequences"
                }
            ],
            "status": "released",
            "summary": "guide (sgRNA) library targeting TF binding sites, candidate cis-regulatory elements in many genomic loci"
        }
    ],
    "control_for": [],
    "creation_timestamp": "2023-12-12T23:07:35.141749+00:00",
    "donors": [
        {
            "@id": "/human-donors/IGVFDO1756PPKO/",
            "accession": "IGVFDO1756PPKO",
            "aliases": [
                "igvf:donor_of_WTC11"
            ],
            "sex": "male",
            "status": "released",
            "taxa": "Homo sapiens"
        }
    ],
    "file_set_type": "principal analysis",
    "files": [
        {
            "@id": "/matrix-files/IGVFFI8270PCLP/",
            "accession": "IGVFFI8270PCLP",
            "aliases": [
                "jay-shendure:analysis_set_CRISPRa_ipscNeurons_matrix"
            ],
            "content_type": "filtered feature barcode matrix",
            "creation_timestamp": "2023-12-13T00:09:58.340992+00:00",
            "file_format": "tar",
            "file_size": 441930008,
            "href": "/matrix-files/IGVFFI8270PCLP/@@download/IGVFFI8270PCLP.tar.gz",
            "s3_uri": "s3://igvf-files/2023/12/13/543c9f4e-1511-4167-8a5b-843c99af20b3/IGVFFI8270PCLP.tar.gz",
            "status": "released",
            "submitted_file_name": "/net/shendure/vol10/projects/IGVFtemp/Shendure_IpscNeurons_CRISPRa_matrix.tar.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/tabular-files/IGVFFI9048CVLI/",
            "accession": "IGVFFI9048CVLI",
            "aliases": [
                "jay-shendure:tabularfile_S7_Chardon-McDiarmid"
            ],
            "content_type": "differential gene expression quantifications",
            "controlled_access": false,
            "creation_timestamp": "2024-10-14T18:39:01.617294+00:00",
            "file_format": "csv",
            "file_size": 2012,
            "href": "/tabular-files/IGVFFI9048CVLI/@@download/IGVFFI9048CVLI.csv.gz",
            "s3_uri": "s3://igvf-files/2024/10/14/8d65544d-405c-4fa3-91f8-2fcaa3be20e1/IGVFFI9048CVLI.csv.gz",
            "status": "released",
            "submitted_file_name": "/net/shendure/vol1/home/martin91/IGVF/forupload/CRISPRa/41467_2024_52490_MOESM10_ESM.csv.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/tabular-files/IGVFFI4846IRZK/",
            "accession": "IGVFFI4846IRZK",
            "aliases": [
                "jay-shendure:tabularfile_S14_Chardon-McDiarmid"
            ],
            "content_type": "differential gene expression quantifications",
            "controlled_access": false,
            "creation_timestamp": "2024-10-14T18:39:05.424482+00:00",
            "file_format": "csv",
            "file_size": 1732,
            "href": "/tabular-files/IGVFFI4846IRZK/@@download/IGVFFI4846IRZK.csv.gz",
            "s3_uri": "s3://igvf-files/2024/10/14/b3b5abba-927b-4a72-aa4a-a827d2ddff32/IGVFFI4846IRZK.csv.gz",
            "status": "released",
            "submitted_file_name": "/net/shendure/vol1/home/martin91/IGVF/forupload/CRISPRa/41467_2024_52490_MOESM17_ESM.csv.gz",
            "upload_status": "validated"
        }
    ],
    "functional_assay_mechanisms": [],
    "input_file_sets": [
        {
            "@id": "/measurement-sets/IGVFDS9384BVGM/",
            "accession": "IGVFDS9384BVGM",
            "aliases": [
                "jay-shendure:CRISPRa_singlecell_iPSC-derived-neurons_VPH_10Xlane1_exprs"
            ],
            "file_set_type": "experimental data",
            "status": "released"
        },
        {
            "@id": "/measurement-sets/IGVFDS0272VVTX/",
            "accession": "IGVFDS0272VVTX",
            "aliases": [
                "jay-shendure:CRISPRa_singlecell_iPSC-derived-neurons_VPH_10Xlane2_exprs"
            ],
            "file_set_type": "experimental data",
            "status": "released"
        },
        {
            "@id": "/measurement-sets/IGVFDS2385QENN/",
            "accession": "IGVFDS2385QENN",
            "aliases": [
                "jay-shendure:CRISPRa_singlecell_iPSC-derived-neurons_VPH_10Xlane3_exprs"
            ],
            "file_set_type": "experimental data",
            "status": "released"
        },
        {
            "@id": "/measurement-sets/IGVFDS2133JAFB/",
            "accession": "IGVFDS2133JAFB",
            "aliases": [
                "jay-shendure:CRISPRa_singlecell_iPSC-derived-neurons_VPH_10Xlane4_exprs"
            ],
            "file_set_type": "experimental data",
            "status": "released"
        },
        {
            "@id": "/auxiliary-sets/IGVFDS8386FNRJ/",
            "accession": "IGVFDS8386FNRJ",
            "aliases": [
                "jay-shendure:CRISPRa_singlecell_iPSC-derived-neurons_VPH_10Xlane1_CS1"
            ],
            "file_set_type": "gRNA sequencing",
            "status": "released"
        },
        {
            "@id": "/auxiliary-sets/IGVFDS2220HHTN/",
            "accession": "IGVFDS2220HHTN",
            "aliases": [
                "jay-shendure:CRISPRa_singlecell_iPSC-derived-neurons_VPH_10Xlane2_CS1"
            ],
            "file_set_type": "gRNA sequencing",
            "status": "released"
        },
        {
            "@id": "/auxiliary-sets/IGVFDS2532AVSC/",
            "accession": "IGVFDS2532AVSC",
            "aliases": [
                "jay-shendure:CRISPRa_singlecell_iPSC-derived-neurons_VPH_10Xlane3_CS1"
            ],
            "file_set_type": "gRNA sequencing",
            "status": "released"
        },
        {
            "@id": "/auxiliary-sets/IGVFDS7598WPXV/",
            "accession": "IGVFDS7598WPXV",
            "aliases": [
                "jay-shendure:CRISPRa_singlecell_iPSC-derived-neurons_VPH_10Xlane4_CS1"
            ],
            "file_set_type": "gRNA sequencing",
            "status": "released"
        }
    ],
    "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:10.1038/s41467-024-52490-4"
            ],
            "status": "released"
        }
    ],
    "release_timestamp": "2024-08-13T20:47:19.906363+00:00",
    "sample_summary": "GM25256 (WTC-11) differentiated cell specimen induced to neuron, at 1 time point(s) post change, modified with CRISPR modifications, transfected with a guide library",
    "samples": [
        {
            "@id": "/in-vitro-systems/IGVFSM8317ZTFV/",
            "@type": [
                "InVitroSystem",
                "Biosample",
                "Sample",
                "Item"
            ],
            "accession": "IGVFSM8317ZTFV",
            "aliases": [
                "jay-shendure:CRISPRa_VPH_NGN2_WTC11_neurons_10Xlane3"
            ],
            "cellular_sub_pool": "10Xlane3",
            "classifications": [
                "differentiated cell specimen"
            ],
            "institutional_certificates": [],
            "modifications": [
                {
                    "@id": "/crispr-modifications/426a4099-35d9-4c65-8851-5e788a3d4e70/",
                    "modality": "activation",
                    "status": "released"
                }
            ],
            "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 CRISPRa Sp-dCas9-VPH, transfected with a guide library",
            "targeted_sample_term": {
                "@id": "/sample-terms/CL_0000540/",
                "status": "released",
                "term_name": "neuron"
            },
            "taxa": "Homo sapiens"
        },
        {
            "@id": "/in-vitro-systems/IGVFSM7750SNNY/",
            "@type": [
                "InVitroSystem",
                "Biosample",
                "Sample",
                "Item"
            ],
            "accession": "IGVFSM7750SNNY",
            "aliases": [
                "jay-shendure:CRISPRa_VPH_NGN2_WTC11_neurons_10Xlane1"
            ],
            "cellular_sub_pool": "10Xlane1",
            "classifications": [
                "differentiated cell specimen"
            ],
            "institutional_certificates": [],
            "modifications": [
                {
                    "@id": "/crispr-modifications/426a4099-35d9-4c65-8851-5e788a3d4e70/",
                    "modality": "activation",
                    "status": "released"
                }
            ],
            "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 CRISPRa Sp-dCas9-VPH, transfected with a guide library",
            "targeted_sample_term": {
                "@id": "/sample-terms/CL_0000540/",
                "status": "released",
                "term_name": "neuron"
            },
            "taxa": "Homo sapiens"
        },
        {
            "@id": "/in-vitro-systems/IGVFSM9913PXTT/",
            "@type": [
                "InVitroSystem",
                "Biosample",
                "Sample",
                "Item"
            ],
            "accession": "IGVFSM9913PXTT",
            "aliases": [
                "jay-shendure:CRISPRa_VPH_NGN2_WTC11_neurons_10Xlane2"
            ],
            "cellular_sub_pool": "10Xlane2",
            "classifications": [
                "differentiated cell specimen"
            ],
            "institutional_certificates": [],
            "modifications": [
                {
                    "@id": "/crispr-modifications/426a4099-35d9-4c65-8851-5e788a3d4e70/",
                    "modality": "activation",
                    "status": "released"
                }
            ],
            "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: 10Xlane2), male, Homo sapiens modified with CRISPRa Sp-dCas9-VPH, transfected with a guide library",
            "targeted_sample_term": {
                "@id": "/sample-terms/CL_0000540/",
                "status": "released",
                "term_name": "neuron"
            },
            "taxa": "Homo sapiens"
        },
        {
            "@id": "/in-vitro-systems/IGVFSM8382KOXO/",
            "@type": [
                "InVitroSystem",
                "Biosample",
                "Sample",
                "Item"
            ],
            "accession": "IGVFSM8382KOXO",
            "aliases": [
                "jay-shendure:CRISPRa_VPH_NGN2_WTC11_neurons_10Xlane4"
            ],
            "cellular_sub_pool": "10Xlane4",
            "classifications": [
                "differentiated cell specimen"
            ],
            "institutional_certificates": [],
            "modifications": [
                {
                    "@id": "/crispr-modifications/426a4099-35d9-4c65-8851-5e788a3d4e70/",
                    "modality": "activation",
                    "status": "released"
                }
            ],
            "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: 10Xlane4), male, Homo sapiens modified with CRISPRa Sp-dCas9-VPH, transfected with a guide library",
            "targeted_sample_term": {
                "@id": "/sample-terms/CL_0000540/",
                "status": "released",
                "term_name": "neuron"
            },
            "taxa": "Homo sapiens"
        }
    ],
    "schema_version": "9",
    "status": "released",
    "submitted_by": {
        "@id": "/users/73f58e9f-8f5d-4fee-a7cd-dd63c0167e4b/",
        "title": "Beth Martin"
    },
    "submitted_files_timestamp": "2023-12-13T00:09:58.340992+00:00",
    "summary": "scCRISPR activation screen: differential gene expression quantifications, filtered feature barcode matrix",
    "uuid": "c54949f6-6673-4a8e-a213-5cb972f23dea",
    "workflows": [
        {
            "@id": "/workflows/IGVFWF7562QXLM/",
            "accession": "IGVFWF7562QXLM",
            "name": "Cell Ranger Gene Count Pipeline",
            "status": "released"
        },
        {
            "@id": "/workflows/IGVFWF1905PJEA/",
            "accession": "IGVFWF1905PJEA",
            "name": "Shendure scCRISPRa Pipeline",
            "status": "released",
            "uniform_pipeline": false
        }
    ]
}