IGVFDS4252LFRU

{
    "@context": "/terms/",
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    "@type": [
        "AnalysisSet",
        "FileSet",
        "Item"
    ],
    "accession": "IGVFDS4252LFRU",
    "aliases": [
        "gary-hon:WTC11_CM_Pilot2_Mini_PB9_PrimaryAnalysis"
    ],
    "assay_titles": [
        "Perturb-seq"
    ],
    "audit": {
        "ERROR": [
            {
                "category": "upload status not validated",
                "detail": "Tabular file [IGVFFI4410YZQZ](/tabular-files/IGVFFI4410YZQZ/) has `upload_status` invalidated. Validation error detail: {\"md5sum\": \"original md5sum 521928c40e2bdf2234d01082cf035998 does not match newly calculated md5sum 5529ced80d67d34b604a49a2e7a0404a.\"}. Files are expected to be validated or validation exempted.",
                "level": 60,
                "level_name": "ERROR",
                "name": "audit_upload_status",
                "path": "/tabular-files/IGVFFI4410YZQZ/"
            },
            {
                "category": "upload status not validated",
                "detail": "Tabular file [IGVFFI8786YBUA](/tabular-files/IGVFFI8786YBUA/) has `upload_status` invalidated. Validation error detail: {\"md5sum\": \"original md5sum 8475fc7d510636e9ce69059573955f41 does not match newly calculated md5sum a6f6f1723cf01626f1f1df693dc3208f.\"}. Files are expected to be validated or validation exempted.",
                "level": 60,
                "level_name": "ERROR",
                "name": "audit_upload_status",
                "path": "/tabular-files/IGVFFI8786YBUA/"
            },
            {
                "category": "unexpected input file set",
                "detail": "Analysis set [IGVFDS4252LFRU](/analysis-sets/IGVFDS4252LFRU/) links to file set(s): [IGVFDS8878JVPZ](/auxiliary-sets/IGVFDS8878JVPZ/), [IGVFDS3881UZJT](/auxiliary-sets/IGVFDS3881UZJT/), [IGVFDS5210TKRS](/auxiliary-sets/IGVFDS5210TKRS/), [IGVFDS9289FWZN](/auxiliary-sets/IGVFDS9289FWZN/), [IGVFDS9781HZZV](/auxiliary-sets/IGVFDS9781HZZV/), [IGVFDS7818HFMO](/measurement-sets/IGVFDS7818HFMO/), [IGVFDS0373CFJS](/auxiliary-sets/IGVFDS0373CFJS/), [IGVFDS3701EFIG](/auxiliary-sets/IGVFDS3701EFIG/), [IGVFDS1417TPKZ](/auxiliary-sets/IGVFDS1417TPKZ/), [IGVFDS9614JGLX](/measurement-sets/IGVFDS9614JGLX/), [IGVFDS0961NLGM](/measurement-sets/IGVFDS0961NLGM/), [IGVFDS4615AXMO](/measurement-sets/IGVFDS4615AXMO/) in `input_file_sets` that are not represented in the `derived_from` of the file sets of the files in this analysis. The analysis set input files are expected to belong to the input file sets.",
                "level": 60,
                "level_name": "ERROR",
                "name": "audit_input_file_sets_derived_from",
                "path": "/analysis-sets/IGVFDS4252LFRU/"
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        ],
        "INTERNAL_ACTION": [
            {
                "category": "mismatched status",
                "detail": "Preview matrix file [IGVFFI3141VIGP](/matrix-files/IGVFFI3141VIGP/) has in progress subobject analysis step version [4cfc022a-ff63-4d13-99f7-257a6bfe4bd7](/analysis-step-versions/4cfc022a-ff63-4d13-99f7-257a6bfe4bd7/).",
                "level": 30,
                "level_name": "INTERNAL_ACTION",
                "name": "audit_item_status",
                "path": "/matrix-files/IGVFFI3141VIGP/"
            },
            {
                "category": "mismatched status",
                "detail": "Preview matrix file [IGVFFI8929UOQW](/matrix-files/IGVFFI8929UOQW/) has in progress subobject analysis step version [65c095ee-8330-48d0-bc03-d930326fe393](/analysis-step-versions/65c095ee-8330-48d0-bc03-d930326fe393/).",
                "level": 30,
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                "name": "audit_item_status",
                "path": "/matrix-files/IGVFFI8929UOQW/"
            },
            {
                "category": "mismatched status",
                "detail": "Preview matrix file [IGVFFI8767IWEB](/matrix-files/IGVFFI8767IWEB/) has in progress subobject analysis step version [65c095ee-8330-48d0-bc03-d930326fe393](/analysis-step-versions/65c095ee-8330-48d0-bc03-d930326fe393/).",
                "level": 30,
                "level_name": "INTERNAL_ACTION",
                "name": "audit_item_status",
                "path": "/matrix-files/IGVFFI8767IWEB/"
            }
        ],
        "NOT_COMPLIANT": [
            {
                "category": "missing file format specifications",
                "detail": "Tabular file [IGVFFI4410YZQZ](/tabular-files/IGVFFI4410YZQZ/) has no `file_format_specifications`. Tabular files are expected to link to a file format specifications document describing the headers of the file.",
                "level": 50,
                "level_name": "NOT_COMPLIANT",
                "name": "audit_tabular_file_no_file_format_specifications",
                "path": "/tabular-files/IGVFFI4410YZQZ/"
            },
            {
                "category": "missing file format specifications",
                "detail": "Tabular file [IGVFFI8786YBUA](/tabular-files/IGVFFI8786YBUA/) has no `file_format_specifications`. Tabular files are expected to link to a file format specifications document describing the headers of the file.",
                "level": 50,
                "level_name": "NOT_COMPLIANT",
                "name": "audit_tabular_file_no_file_format_specifications",
                "path": "/tabular-files/IGVFFI8786YBUA/"
            },
            {
                "category": "missing analysis step version",
                "detail": "Analysis set [IGVFDS4252LFRU](/analysis-sets/IGVFDS4252LFRU/) links to file(s) [IGVFFI4410YZQZ](/tabular-files/IGVFFI4410YZQZ/), [IGVFFI8786YBUA](/tabular-files/IGVFFI8786YBUA/) that are missing `analysis_step_version`. Analysis set files are expected to specify analysis step version.",
                "level": 50,
                "level_name": "NOT_COMPLIANT",
                "name": "audit_analysis_set_files_missing_analysis_step_version",
                "path": "/analysis-sets/IGVFDS4252LFRU/"
            },
            {
                "category": "missing derived from",
                "detail": "Analysis set [IGVFDS4252LFRU](/analysis-sets/IGVFDS4252LFRU/) links to file(s) [IGVFFI3141VIGP](/matrix-files/IGVFFI3141VIGP/), [IGVFFI8767IWEB](/matrix-files/IGVFFI8767IWEB/), [IGVFFI8929UOQW](/matrix-files/IGVFFI8929UOQW/), [IGVFFI4410YZQZ](/tabular-files/IGVFFI4410YZQZ/), [IGVFFI8786YBUA](/tabular-files/IGVFFI8786YBUA/) that have no `derived_from`. Files in an analysis set are expected to be derived from other files.",
                "level": 50,
                "level_name": "NOT_COMPLIANT",
                "name": "audit_input_file_sets_derived_from",
                "path": "/analysis-sets/IGVFDS4252LFRU/"
            }
        ]
    },
    "award": {
        "@id": "/awards/HG011996/",
        "component": "functional characterization",
        "contact_pi": {
            "@id": "/users/95d84f03-8ce0-489c-a755-f33ced139c5d/",
            "title": "Gary Hon"
        },
        "title": "Multiscale functional characterization of genomic variation in human developmental disorders"
    },
    "control_for": [],
    "creation_timestamp": "2024-12-04T20:07:37.878701+00:00",
    "donors": [
        {
            "@id": "/human-donors/IGVFDO1756PPKO/",
            "accession": "IGVFDO1756PPKO",
            "aliases": [
                "igvf:donor_of_WTC11"
            ],
            "sex": "male",
            "status": "released",
            "taxa": "Homo sapiens"
        }
    ],
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            "aliases": [
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            ],
            "content_type": "sparse gene count matrix",
            "creation_timestamp": "2024-12-17T22:50:36.376287+00:00",
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            "submitted_file_name": "/project/shared/gcrb_igvf/data/shared/mini_cm_pilot02_PB9/H5AD/V0._mini_cm02_WTC11_PB9_sgRNACells_filtered_w_embedding.h5ad",
            "upload_status": "validated"
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            "creation_timestamp": "2024-12-17T23:44:11.744242+00:00",
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            "accession": "IGVFFI8929UOQW",
            "aliases": [
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            "upload_status": "validated"
        },
        {
            "@id": "/tabular-files/IGVFFI4410YZQZ/",
            "accession": "IGVFFI4410YZQZ",
            "aliases": [
                "gary-hon:WTC11_CM_Pilot2_Mini_PB9_PrimaryAnalysis_DE_local"
            ],
            "content_type": "unfiltered local differential expression",
            "controlled_access": false,
            "creation_timestamp": "2024-12-18T20:48:34.756501+00:00",
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            "@id": "/tabular-files/IGVFFI8786YBUA/",
            "accession": "IGVFFI8786YBUA",
            "aliases": [
                "gary-hon:WTC11_CM_Pilot2_Mini_PB9_PrimaryAnalysis_DE_global"
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            "upload_status": "invalidated"
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    ],
    "functional_assay_mechanisms": [],
    "input_file_sets": [
        {
            "@id": "/measurement-sets/IGVFDS7818HFMO/",
            "accession": "IGVFDS7818HFMO",
            "aliases": [
                "gary-hon:differentited_WTC11_CM_Pilot2_Mini_PB9_LW435"
            ],
            "file_set_type": "experimental data",
            "status": "preview"
        },
        {
            "@id": "/auxiliary-sets/IGVFDS3881UZJT/",
            "accession": "IGVFDS3881UZJT",
            "aliases": [
                "gary-hon:differentited_WTC11_CM_Pilot2_Mini_PB9_sgRNA_LW435"
            ],
            "file_set_type": "gRNA sequencing",
            "status": "preview"
        },
        {
            "@id": "/auxiliary-sets/IGVFDS9289FWZN/",
            "accession": "IGVFDS9289FWZN",
            "aliases": [
                "gary-hon:differentited_WTC11_CM_Pilot2_Mini_PB9_HTO_LW435"
            ],
            "file_set_type": "cell hashing barcode sequencing",
            "status": "preview"
        },
        {
            "@id": "/measurement-sets/IGVFDS4615AXMO/",
            "accession": "IGVFDS4615AXMO",
            "aliases": [
                "gary-hon:differentited_WTC11_CM_Pilot2_Mini_PB9_LW436"
            ],
            "file_set_type": "experimental data",
            "status": "preview"
        },
        {
            "@id": "/auxiliary-sets/IGVFDS9781HZZV/",
            "accession": "IGVFDS9781HZZV",
            "aliases": [
                "gary-hon:differentited_WTC11_CM_Pilot2_Mini_PB9_sgRNA_LW436"
            ],
            "file_set_type": "gRNA sequencing",
            "status": "preview"
        },
        {
            "@id": "/auxiliary-sets/IGVFDS5210TKRS/",
            "accession": "IGVFDS5210TKRS",
            "aliases": [
                "gary-hon:differentited_WTC11_CM_Pilot2_Mini_PB9_HTO_LW436"
            ],
            "file_set_type": "cell hashing barcode sequencing",
            "status": "preview"
        },
        {
            "@id": "/measurement-sets/IGVFDS9614JGLX/",
            "accession": "IGVFDS9614JGLX",
            "aliases": [
                "gary-hon:differentited_WTC11_CM_Pilot2_Mini_PB9_LW437"
            ],
            "file_set_type": "experimental data",
            "status": "preview"
        },
        {
            "@id": "/auxiliary-sets/IGVFDS1417TPKZ/",
            "accession": "IGVFDS1417TPKZ",
            "aliases": [
                "gary-hon:differentited_WTC11_CM_Pilot2_Mini_PB9_sgRNA_LW437"
            ],
            "file_set_type": "gRNA sequencing",
            "status": "preview"
        },
        {
            "@id": "/auxiliary-sets/IGVFDS8878JVPZ/",
            "accession": "IGVFDS8878JVPZ",
            "aliases": [
                "gary-hon:differentited_WTC11_CM_Pilot2_Mini_PB9_HTO_LW437"
            ],
            "file_set_type": "cell hashing barcode sequencing",
            "status": "preview"
        },
        {
            "@id": "/measurement-sets/IGVFDS0961NLGM/",
            "accession": "IGVFDS0961NLGM",
            "aliases": [
                "gary-hon:differentited_WTC11_CM_Pilot2_Mini_PB9_LW438"
            ],
            "file_set_type": "experimental data",
            "status": "preview"
        },
        {
            "@id": "/auxiliary-sets/IGVFDS0373CFJS/",
            "accession": "IGVFDS0373CFJS",
            "aliases": [
                "gary-hon:differentited_WTC11_CM_Pilot2_Mini_PB9_sgRNA_LW438"
            ],
            "file_set_type": "gRNA sequencing",
            "status": "preview"
        },
        {
            "@id": "/auxiliary-sets/IGVFDS3701EFIG/",
            "accession": "IGVFDS3701EFIG",
            "aliases": [
                "gary-hon:differentited_WTC11_CM_Pilot2_Mini_PB9_HTO_LW438"
            ],
            "file_set_type": "cell hashing barcode sequencing",
            "status": "preview"
        }
    ],
    "input_for": [],
    "lab": {
        "@id": "/labs/gary-hon/",
        "title": "Gary Hon, UT"
    },
    "protocols": [
        "https://www.protocols.io/view/experimental-procedures-for-tf-perturb-seq-ut-sout-denf3dbn"
    ],
    "sample_summary": "GM25256 (WTC-11) differentiated cell specimen induced to cardiac muscle cell, at 1 time point(s) post change, modified with CRISPR modifications, transfected with a guide library",
    "samples": [
        {
            "@id": "/in-vitro-systems/IGVFSM2176YXFG/",
            "@type": [
                "InVitroSystem",
                "Biosample",
                "Sample",
                "Item"
            ],
            "accession": "IGVFSM2176YXFG",
            "aliases": [
                "nikhil-munshi:differentited_WTC11_CM_Pilot2_Mini_PB9_LW438"
            ],
            "classifications": [
                "differentiated cell specimen"
            ],
            "construct_library_sets": [
                "/construct-library-sets/IGVFDS0346MQBH/"
            ],
            "modifications": [
                {
                    "@id": "/crispr-modifications/0a63b754-eca4-44aa-bbc2-fccdc6c44fb5/",
                    "modality": "interference",
                    "status": "preview"
                }
            ],
            "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": "preview",
            "summary": "GM25256 (WTC-11) differentiated cell specimen induced to cardiac muscle cell for 12 days (cellular sub pool: subpool_LW438), male, Homo sapiens modified with CRISPRi Sp-dCas9, transfected with a guide library",
            "targeted_sample_term": {
                "@id": "/sample-terms/CL_0000746/",
                "status": "released",
                "term_name": "cardiac muscle cell"
            },
            "taxa": "Homo sapiens"
        },
        {
            "@id": "/in-vitro-systems/IGVFSM8072YOLO/",
            "@type": [
                "InVitroSystem",
                "Biosample",
                "Sample",
                "Item"
            ],
            "accession": "IGVFSM8072YOLO",
            "aliases": [
                "nikhil-munshi:differentited_WTC11_CM_Pilot2_Mini_PB9_LW437"
            ],
            "classifications": [
                "differentiated cell specimen"
            ],
            "construct_library_sets": [
                "/construct-library-sets/IGVFDS0346MQBH/"
            ],
            "modifications": [
                {
                    "@id": "/crispr-modifications/0a63b754-eca4-44aa-bbc2-fccdc6c44fb5/",
                    "modality": "interference",
                    "status": "preview"
                }
            ],
            "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": "preview",
            "summary": "GM25256 (WTC-11) differentiated cell specimen induced to cardiac muscle cell for 12 days (cellular sub pool: subpool_LW437), male, Homo sapiens modified with CRISPRi Sp-dCas9, transfected with a guide library",
            "targeted_sample_term": {
                "@id": "/sample-terms/CL_0000746/",
                "status": "released",
                "term_name": "cardiac muscle cell"
            },
            "taxa": "Homo sapiens"
        },
        {
            "@id": "/in-vitro-systems/IGVFSM8889XSOR/",
            "@type": [
                "InVitroSystem",
                "Biosample",
                "Sample",
                "Item"
            ],
            "accession": "IGVFSM8889XSOR",
            "aliases": [
                "nikhil-munshi:differentited_WTC11_CM_Pilot2_Mini_PB9_LW436"
            ],
            "classifications": [
                "differentiated cell specimen"
            ],
            "construct_library_sets": [
                "/construct-library-sets/IGVFDS0346MQBH/"
            ],
            "modifications": [
                {
                    "@id": "/crispr-modifications/0a63b754-eca4-44aa-bbc2-fccdc6c44fb5/",
                    "modality": "interference",
                    "status": "preview"
                }
            ],
            "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": "preview",
            "summary": "GM25256 (WTC-11) differentiated cell specimen induced to cardiac muscle cell for 12 days (cellular sub pool: subpool_LW436), male, Homo sapiens modified with CRISPRi Sp-dCas9, transfected with a guide library",
            "targeted_sample_term": {
                "@id": "/sample-terms/CL_0000746/",
                "status": "released",
                "term_name": "cardiac muscle cell"
            },
            "taxa": "Homo sapiens"
        },
        {
            "@id": "/in-vitro-systems/IGVFSM4418NJET/",
            "@type": [
                "InVitroSystem",
                "Biosample",
                "Sample",
                "Item"
            ],
            "accession": "IGVFSM4418NJET",
            "aliases": [
                "nikhil-munshi:differentited_WTC11_CM_Pilot2_Mini_PB9_LW435"
            ],
            "classifications": [
                "differentiated cell specimen"
            ],
            "construct_library_sets": [
                "/construct-library-sets/IGVFDS0346MQBH/"
            ],
            "modifications": [
                {
                    "@id": "/crispr-modifications/0a63b754-eca4-44aa-bbc2-fccdc6c44fb5/",
                    "modality": "interference",
                    "status": "preview"
                }
            ],
            "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": "preview",
            "summary": "GM25256 (WTC-11) differentiated cell specimen induced to cardiac muscle cell for 12 days (cellular sub pool: subpool_LW435), male, Homo sapiens modified with CRISPRi Sp-dCas9, transfected with a guide library",
            "targeted_sample_term": {
                "@id": "/sample-terms/CL_0000746/",
                "status": "released",
                "term_name": "cardiac muscle cell"
            },
            "taxa": "Homo sapiens"
        }
    ],
    "schema_version": "9",
    "status": "preview",
    "submitted_by": {
        "@id": "/users/b05645f1-2d56-4a5e-b272-4601e555a3fa/",
        "title": "Mpathi Nzima"
    },
    "submitted_files_timestamp": "2024-12-17T22:50:36.376287+00:00",
    "summary": "interference Perturb-seq: filtered feature barcode matrix, raw feature barcode matrix, sparse gene count matrix, unfiltered global differential expression, unfiltered local differential expression",
    "uuid": "51e138b8-6ad6-4bee-a743-3f3da05d4073",
    "workflows": [
        {
            "@id": "/workflows/IGVFWF0190YALU/",
            "accession": "IGVFWF0190YALU",
            "name": "Hon Perturb-seq Workflow",
            "status": "in progress",
            "uniform_pipeline": false
        }
    ]
}