IGVFDS2266YDVM

{
    "@context": "/terms/",
    "@id": "/analysis-sets/IGVFDS2266YDVM/",
    "@type": [
        "AnalysisSet",
        "FileSet",
        "Item"
    ],
    "accession": "IGVFDS2266YDVM",
    "aliases": [
        "gary-hon:H9_CM_Pilot2_Mini_PB9_PrimaryAnalysis"
    ],
    "assay_titles": [
        "Perturb-seq"
    ],
    "audit": {
        "ERROR": [
            {
                "category": "unexpected input file set",
                "detail": "Analysis set [IGVFDS2266YDVM](/analysis-sets/IGVFDS2266YDVM/) links to file set(s): [IGVFDS5403GYDH](/auxiliary-sets/IGVFDS5403GYDH/), [IGVFDS1340IBKW](/auxiliary-sets/IGVFDS1340IBKW/), [IGVFDS8183DTKY](/measurement-sets/IGVFDS8183DTKY/), [IGVFDS1182KBMU](/auxiliary-sets/IGVFDS1182KBMU/), [IGVFDS2275IPCJ](/auxiliary-sets/IGVFDS2275IPCJ/), [IGVFDS8751LXWJ](/measurement-sets/IGVFDS8751LXWJ/), [IGVFDS6475OLUM](/auxiliary-sets/IGVFDS6475OLUM/), [IGVFDS7288IQLC](/measurement-sets/IGVFDS7288IQLC/), [IGVFDS3919NBFE](/auxiliary-sets/IGVFDS3919NBFE/), [IGVFDS5502LTCL](/measurement-sets/IGVFDS5502LTCL/), [IGVFDS0785CQUX](/auxiliary-sets/IGVFDS0785CQUX/), [IGVFDS3774FYIW](/auxiliary-sets/IGVFDS3774FYIW/) 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/IGVFDS2266YDVM/"
            },
            {
                "category": "upload status not validated",
                "detail": "Tabular file [IGVFFI1867ROFS](/tabular-files/IGVFFI1867ROFS/) has `upload_status` invalidated. Validation error detail: {\"md5sum\": \"original md5sum 808b1e9a7f146376437acda477b4431d does not match newly calculated md5sum 8000063afa1312cd17c3cb3db550b32f.\"}. Files are expected to be validated or validation exempted.",
                "level": 60,
                "level_name": "ERROR",
                "name": "audit_upload_status",
                "path": "/tabular-files/IGVFFI1867ROFS/"
            },
            {
                "category": "upload status not validated",
                "detail": "Tabular file [IGVFFI8753JHNH](/tabular-files/IGVFFI8753JHNH/) has `upload_status` invalidated. Validation error detail: {\"md5sum\": \"original md5sum 5c4b4d4cc503658025fcd6ca2cb8fba6 does not match newly calculated md5sum a19b65f2011b45b4d15bbc54de2b6a70.\"}. Files are expected to be validated or validation exempted.",
                "level": 60,
                "level_name": "ERROR",
                "name": "audit_upload_status",
                "path": "/tabular-files/IGVFFI8753JHNH/"
            }
        ],
        "INTERNAL_ACTION": [
            {
                "category": "mismatched status",
                "detail": "Preview matrix file [IGVFFI6483VROG](/matrix-files/IGVFFI6483VROG/) 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/IGVFFI6483VROG/"
            },
            {
                "category": "mismatched status",
                "detail": "Preview matrix file [IGVFFI5815NBHE](/matrix-files/IGVFFI5815NBHE/) 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/IGVFFI5815NBHE/"
            },
            {
                "category": "mismatched status",
                "detail": "Preview matrix file [IGVFFI1539OEIK](/matrix-files/IGVFFI1539OEIK/) 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/IGVFFI1539OEIK/"
            }
        ],
        "NOT_COMPLIANT": [
            {
                "category": "missing analysis step version",
                "detail": "Analysis set [IGVFDS2266YDVM](/analysis-sets/IGVFDS2266YDVM/) links to file(s) [IGVFFI8753JHNH](/tabular-files/IGVFFI8753JHNH/), [IGVFFI1867ROFS](/tabular-files/IGVFFI1867ROFS/) 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/IGVFDS2266YDVM/"
            },
            {
                "category": "missing derived from",
                "detail": "Analysis set [IGVFDS2266YDVM](/analysis-sets/IGVFDS2266YDVM/) links to file(s) [IGVFFI6483VROG](/matrix-files/IGVFFI6483VROG/), [IGVFFI1539OEIK](/matrix-files/IGVFFI1539OEIK/), [IGVFFI5815NBHE](/matrix-files/IGVFFI5815NBHE/), [IGVFFI8753JHNH](/tabular-files/IGVFFI8753JHNH/), [IGVFFI1867ROFS](/tabular-files/IGVFFI1867ROFS/) 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/IGVFDS2266YDVM/"
            },
            {
                "category": "missing file format specifications",
                "detail": "Tabular file [IGVFFI1867ROFS](/tabular-files/IGVFFI1867ROFS/) 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/IGVFFI1867ROFS/"
            },
            {
                "category": "missing file format specifications",
                "detail": "Tabular file [IGVFFI8753JHNH](/tabular-files/IGVFFI8753JHNH/) 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/IGVFFI8753JHNH/"
            }
        ]
    },
    "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": "2024-12-04T20:07:34.656354+00:00",
    "donors": [
        {
            "@id": "/human-donors/IGVFDO2718IDDQ/",
            "accession": "IGVFDO2718IDDQ",
            "aliases": [
                "igvf:donor_of_H9"
            ],
            "sex": "female",
            "status": "released",
            "taxa": "Homo sapiens"
        }
    ],
    "file_set_type": "principal analysis",
    "files": [
        {
            "@id": "/matrix-files/IGVFFI6483VROG/",
            "accession": "IGVFFI6483VROG",
            "aliases": [
                "gary-hon:H9_CM_Pilot2_Mini_PB9_PrimaryAnalysis_h5ad"
            ],
            "content_type": "sparse gene count matrix",
            "creation_timestamp": "2024-12-17T22:47:39.541942+00:00",
            "file_format": "h5ad",
            "file_size": 18825207540,
            "href": "/matrix-files/IGVFFI6483VROG/@@download/IGVFFI6483VROG.h5ad",
            "s3_uri": "s3://igvf-files/2024/12/17/98195f6d-bb09-4ade-bf51-43aec1ee6ced/IGVFFI6483VROG.h5ad",
            "status": "preview",
            "submitted_file_name": "/project/shared/gcrb_igvf/data/shared/mini_cm_pilot02_PB9/H5AD/V0._mini_cm02_H9_PB9_sgRNACells_filtered_w_embedding.h5ad",
            "upload_status": "validated"
        },
        {
            "@id": "/matrix-files/IGVFFI1539OEIK/",
            "accession": "IGVFFI1539OEIK",
            "aliases": [
                "gary-hon:H9_CM_Pilot2_Mini_PB9_PrimaryAnalysis_h5"
            ],
            "content_type": "filtered feature barcode matrix",
            "creation_timestamp": "2024-12-17T23:43:18.772479+00:00",
            "file_format": "hdf5",
            "file_size": 667371297,
            "href": "/matrix-files/IGVFFI1539OEIK/@@download/IGVFFI1539OEIK.h5",
            "s3_uri": "s3://igvf-files/2024/12/17/0325499e-338d-4d5d-8564-ef943a4e44fe/IGVFFI1539OEIK.h5",
            "status": "preview",
            "submitted_file_name": "/project/GCRB/Hon_lab/s215194/Single_Cell/mini_cm_pilot_02_inducible/_431_434_H9_PB9/_aggr_transcriptome/cm_pilot_mini_02_no_normalization_H9_PB9/outs/count/filtered_feature_bc_matrix.h5",
            "upload_status": "validated"
        },
        {
            "@id": "/matrix-files/IGVFFI5815NBHE/",
            "accession": "IGVFFI5815NBHE",
            "aliases": [
                "gary-hon:H9_CM_Pilot2_Mini_PB9_PrimaryAnalysis_pkl"
            ],
            "content_type": "raw feature barcode matrix",
            "creation_timestamp": "2024-12-17T23:43:38.946141+00:00",
            "file_format": "pkl",
            "file_size": 2159941743,
            "href": "/matrix-files/IGVFFI5815NBHE/@@download/IGVFFI5815NBHEpkl",
            "s3_uri": "s3://igvf-files/2024/12/17/7005f296-49b6-4585-a872-1a33551558eb/IGVFFI5815NBHEpkl",
            "status": "preview",
            "submitted_file_name": "/project/GCRB/Hon_lab/s215194/Single_Cell/mini_cm_pilot_02_inducible/_431_434_H9_PB9/aggr_dataframe/aggr_combined_df_full.pkl",
            "upload_status": "validated"
        },
        {
            "@id": "/tabular-files/IGVFFI8753JHNH/",
            "accession": "IGVFFI8753JHNH",
            "aliases": [
                "gary-hon:H9_CM_Pilot2_Mini_PB9_PrimaryAnalysis_DE_local"
            ],
            "content_type": "unfiltered local differential expression",
            "controlled_access": false,
            "creation_timestamp": "2024-12-18T20:48:04.760181+00:00",
            "file_format": "csv",
            "file_size": 6817,
            "href": "/tabular-files/IGVFFI8753JHNH/@@download/IGVFFI8753JHNH.csv.gz",
            "s3_uri": "s3://igvf-files/2024/12/18/dea5b153-2f6d-46ec-97b9-c7497be75c63/IGVFFI8753JHNH.csv.gz",
            "status": "preview",
            "submitted_file_name": "/project/GCRB/Hon_lab/s215194/IGVF/data_submission/reference_files/H9_CM_Pilot2_Mini_PB9_PrimaryAnalysis_DE_local.csv.gz",
            "upload_status": "invalidated"
        },
        {
            "@id": "/tabular-files/IGVFFI1867ROFS/",
            "accession": "IGVFFI1867ROFS",
            "aliases": [
                "gary-hon:H9_CM_Pilot2_Mini_PB9_PrimaryAnalysis_DE_global"
            ],
            "content_type": "unfiltered global differential expression",
            "controlled_access": false,
            "creation_timestamp": "2024-12-18T20:48:20.349603+00:00",
            "file_format": "csv",
            "file_size": 1545525,
            "href": "/tabular-files/IGVFFI1867ROFS/@@download/IGVFFI1867ROFS.csv.gz",
            "s3_uri": "s3://igvf-files/2024/12/18/9dfb6e0f-fd12-4f55-9f9c-5edce46702eb/IGVFFI1867ROFS.csv.gz",
            "status": "preview",
            "submitted_file_name": "/project/GCRB/Hon_lab/s215194/IGVF/data_submission/reference_files/H9_CM_Pilot2_Mini_PB9_PrimaryAnalysis_DE_global.csv.gz",
            "upload_status": "invalidated"
        }
    ],
    "functional_assay_mechanisms": [],
    "input_file_sets": [
        {
            "@id": "/measurement-sets/IGVFDS5502LTCL/",
            "accession": "IGVFDS5502LTCL",
            "aliases": [
                "gary-hon:differentited_H9_CM_Pilot2_Mini_PB9_LW431"
            ],
            "file_set_type": "experimental data",
            "status": "preview"
        },
        {
            "@id": "/auxiliary-sets/IGVFDS1182KBMU/",
            "accession": "IGVFDS1182KBMU",
            "aliases": [
                "gary-hon:differentited_H9_CM_Pilot2_Mini_PB9_sgRNA_LW431"
            ],
            "file_set_type": "gRNA sequencing",
            "status": "preview"
        },
        {
            "@id": "/auxiliary-sets/IGVFDS2275IPCJ/",
            "accession": "IGVFDS2275IPCJ",
            "aliases": [
                "gary-hon:differentited_H9_CM_Pilot2_Mini_PB9_HTO_LW431"
            ],
            "file_set_type": "cell hashing barcode sequencing",
            "status": "preview"
        },
        {
            "@id": "/measurement-sets/IGVFDS8183DTKY/",
            "accession": "IGVFDS8183DTKY",
            "aliases": [
                "gary-hon:differentited_H9_CM_Pilot2_Mini_PB9_LW432"
            ],
            "file_set_type": "experimental data",
            "status": "preview"
        },
        {
            "@id": "/auxiliary-sets/IGVFDS5403GYDH/",
            "accession": "IGVFDS5403GYDH",
            "aliases": [
                "gary-hon:differentited_H9_CM_Pilot2_Mini_PB9_sgRNA_LW432"
            ],
            "file_set_type": "gRNA sequencing",
            "status": "preview"
        },
        {
            "@id": "/auxiliary-sets/IGVFDS6475OLUM/",
            "accession": "IGVFDS6475OLUM",
            "aliases": [
                "gary-hon:differentited_H9_CM_Pilot2_Mini_PB9_HTO_LW432"
            ],
            "file_set_type": "cell hashing barcode sequencing",
            "status": "preview"
        },
        {
            "@id": "/measurement-sets/IGVFDS8751LXWJ/",
            "accession": "IGVFDS8751LXWJ",
            "aliases": [
                "gary-hon:differentited_H9_CM_Pilot2_Mini_PB9_LW433"
            ],
            "file_set_type": "experimental data",
            "status": "preview"
        },
        {
            "@id": "/auxiliary-sets/IGVFDS3919NBFE/",
            "accession": "IGVFDS3919NBFE",
            "aliases": [
                "gary-hon:differentited_H9_CM_Pilot2_Mini_PB9_sgRNA_LW433"
            ],
            "file_set_type": "gRNA sequencing",
            "status": "preview"
        },
        {
            "@id": "/auxiliary-sets/IGVFDS3774FYIW/",
            "accession": "IGVFDS3774FYIW",
            "aliases": [
                "gary-hon:differentited_H9_CM_Pilot2_Mini_PB9_HTO_LW433"
            ],
            "file_set_type": "cell hashing barcode sequencing",
            "status": "preview"
        },
        {
            "@id": "/measurement-sets/IGVFDS7288IQLC/",
            "accession": "IGVFDS7288IQLC",
            "aliases": [
                "gary-hon:differentited_H9_CM_Pilot2_Mini_PB9_LW434"
            ],
            "file_set_type": "experimental data",
            "status": "preview"
        },
        {
            "@id": "/auxiliary-sets/IGVFDS0785CQUX/",
            "accession": "IGVFDS0785CQUX",
            "aliases": [
                "gary-hon:differentited_H9_CM_Pilot2_Mini_PB9_sgRNA_LW434"
            ],
            "file_set_type": "gRNA sequencing",
            "status": "preview"
        },
        {
            "@id": "/auxiliary-sets/IGVFDS1340IBKW/",
            "accession": "IGVFDS1340IBKW",
            "aliases": [
                "gary-hon:differentited_H9_CM_Pilot2_Mini_PB9_HTO_LW434"
            ],
            "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": "H9 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/IGVFSM8133YEXK/",
            "@type": [
                "InVitroSystem",
                "Biosample",
                "Sample",
                "Item"
            ],
            "accession": "IGVFSM8133YEXK",
            "aliases": [
                "nikhil-munshi:differentited_H9_CM_Pilot2_Mini_PB9_LW434"
            ],
            "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_0003045/",
                    "@type": [
                        "SampleTerm",
                        "OntologyTerm",
                        "Item"
                    ],
                    "aliases": [
                        "igvf:H9"
                    ],
                    "status": "released",
                    "summary": "H9",
                    "term_name": "H9"
                }
            ],
            "status": "preview",
            "summary": "H9 differentiated cell specimen induced to cardiac muscle cell for 12 days (cellular sub pool: subpool_LW434), female, 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/IGVFSM5829AVCL/",
            "@type": [
                "InVitroSystem",
                "Biosample",
                "Sample",
                "Item"
            ],
            "accession": "IGVFSM5829AVCL",
            "aliases": [
                "nikhil-munshi:differentited_H9_CM_Pilot2_Mini_PB9_LW431"
            ],
            "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_0003045/",
                    "@type": [
                        "SampleTerm",
                        "OntologyTerm",
                        "Item"
                    ],
                    "aliases": [
                        "igvf:H9"
                    ],
                    "status": "released",
                    "summary": "H9",
                    "term_name": "H9"
                }
            ],
            "status": "preview",
            "summary": "H9 differentiated cell specimen induced to cardiac muscle cell for 12 days (cellular sub pool: subpool_LW431), female, 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/IGVFSM3839SOTK/",
            "@type": [
                "InVitroSystem",
                "Biosample",
                "Sample",
                "Item"
            ],
            "accession": "IGVFSM3839SOTK",
            "aliases": [
                "nikhil-munshi:differentited_H9_CM_Pilot2_Mini_PB9_LW432"
            ],
            "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_0003045/",
                    "@type": [
                        "SampleTerm",
                        "OntologyTerm",
                        "Item"
                    ],
                    "aliases": [
                        "igvf:H9"
                    ],
                    "status": "released",
                    "summary": "H9",
                    "term_name": "H9"
                }
            ],
            "status": "preview",
            "summary": "H9 differentiated cell specimen induced to cardiac muscle cell for 12 days (cellular sub pool: subpool_LW432), female, 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/IGVFSM1513DHGW/",
            "@type": [
                "InVitroSystem",
                "Biosample",
                "Sample",
                "Item"
            ],
            "accession": "IGVFSM1513DHGW",
            "aliases": [
                "nikhil-munshi:differentited_H9_CM_Pilot2_Mini_PB9_LW433"
            ],
            "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_0003045/",
                    "@type": [
                        "SampleTerm",
                        "OntologyTerm",
                        "Item"
                    ],
                    "aliases": [
                        "igvf:H9"
                    ],
                    "status": "released",
                    "summary": "H9",
                    "term_name": "H9"
                }
            ],
            "status": "preview",
            "summary": "H9 differentiated cell specimen induced to cardiac muscle cell for 12 days (cellular sub pool: subpool_LW433), female, 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": "2024-12-17T22:47:39.541942+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": "9459771b-9580-4cf8-9ca5-757bc9a1f303",
    "workflows": [
        {
            "@id": "/workflows/IGVFWF0190YALU/",
            "accession": "IGVFWF0190YALU",
            "name": "Hon Perturb-seq Workflow",
            "status": "in progress",
            "uniform_pipeline": false
        }
    ]
}